GO Database Abbreviations

COG_Cluster

NCBI COG cluster

object: Identifier
example ID: COG_Cluster:COG0001
URL syntax: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog=COG0001

COG_Function

NCBI COG function

object: Identifier
example ID: COG_Function:H
URL syntax: http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi?fun=H

COG_Pathway

NCBI COG pathway

http://mips.gsf.de/genre/proj/corum/

object: Identifier
example ID: COG_Pathway:14
URL syntax: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw=14

CORUM

CORUM - the Comprehensive Resource of Mammalian protein complexes

object: Identifier
example ID: CORUM:837
URL syntax: http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=[example_id]
URL example: http://mips.gsf.de/genre/proj/corum/complexdetails.html?id=837

dbSNP

NCBI dbSNP

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

object: Identifier
example ID: dbSNP:rs3131969
URL syntax: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=rs3131969

DDBJ

DNA Databank of Japan

http://www.ddbj.nig.ac.jp/

object: Sequence accession
example ID: DDBJ:AA816246
URL syntax: http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=[example_id]
URL example: http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord=AA816246

DFLAT

Developmental FunctionaL Annotation at Tufts

http://bcb.cs.tufts.edu/dflat/

dictyBase

http://dictybase.org

object: Identifier
synonym: DDB, DictyBase
example ID: dictyBase:DDB_G0277859
URL syntax: http://dictybase.org/gene/[example_id]
URL example: http://dictybase.org/gene/DDB_G0277859

dictyBase_gene_name

dictyBase

http://dictybase.org

object: Gene name
example ID: dictyBase_gene_name:mlcE
URL syntax: http://dictybase.org/gene/[example_id]
URL example: http://dictybase.org/gene/mlcE

dictyBase_REF

dictyBase literature references

http://dictybase.org

object: Literature Reference Identifier
synonym: DDB_REF
example ID: dictyBase_REF:10157
URL syntax: http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=[example_id]
URL example: http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo=10157

DOI

Digital Object Identifier

http://dx.doi.org/

object: Identifier
example ID: DOI:10.1016/S0963-9969(99)00021-6
URL syntax: http://dx.doi.org/DOI:[example_id]
URL example: http://dx.doi.org/DOI:10.1016/S0963-9969(99)00021-6

EC

Enzyme Commission

http://ww.expasy.org/enzyme/
http://www.chem.qmul.ac.uk/iubmb/enzyme/

example ID: EC:1.4.3.6
URL syntax: http://www.expasy.org/enzyme/[example_id]
URL example: http://www.expasy.org/enzyme/1.4.3.6

EchoBASE

EchoBASE post-genomic database for Escherichia coli

http://www.ecoli-york.org/

object: Identifier
example ID: EchoBASE:EB0231
URL syntax: http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=[example_id]
URL example: http://www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=EB0231

ECK

EcoGene Database of Escherichia coli Sequence and Function

http://www.ecogene.org/

object: ECK accession (E. coli K-12 gene identifier)
example ID: ECK:ECK3746
URL syntax: http://www.ecogene.org/geneInfo.php?eck_id=[example_id]
URL example: http://www.ecogene.org/geneInfo.php?eck_id=ECK3746

ECO

Evidence Code ontology

http://www.geneontology.org/

object: Identifier
example ID: ECO:0000002

EcoCyc

Encyclopedia of E. coli metabolism

http://ecocyc.org/

object: Pathway identifier
example ID: EcoCyc:P2-PWY
URL syntax: http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=[example_id]
URL example: http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=P2-PWY

EcoCyc_REF

Encyclopedia of E. coli metabolism

http://ecocyc.org/

object: Reference identifier
synonym: ECOCYC_REF
example ID: EcoCyc_REF:COLISALII
URL syntax: http://biocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=[example_id]
URL example: http://biocyc.org/ECOLI/reference.html?type=CITATION-FRAME&object=COLISALII

ECOGENE

EcoGene Database of Escherichia coli Sequence and Function

http://www.ecogene.org/

object: EcoGene accession
example ID: ECOGENE:EG10818
URL syntax: http://www.ecogene.org/geneInfo.php?eg_id=[example_id]
URL example: http://www.ecogene.org/geneInfo.php?eg_id=EG10818

ECOGENE_G

EcoGene Database of Escherichia coli Sequence and Function

http://www.ecogene.org/

object: EcoGene Primary Gene Name
example ID: ECOGENE_G:deoC

EcoliWiki

EcoliWiki from EcoliHub

EcoliHub's subsystem for community annotation of E. coli K-12

http://ecoliwiki.net/

EMBL

EMBL Nucleotide Sequence Database

International nucleotide sequence database collaboration, comprising EMBL-EBI nucleotide sequence data library (EMBL-Bank), DNA DataBank of Japan (DDBJ), and NCBI GenBank

http://www.ebi.ac.uk/embl/

object: Sequence accession
example ID: EMBL:AA816246
URL syntax: http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=[example_id]
URL example: http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id=AA816246

ENA

European Nucleotide Archive

ENA is made up of a number of distinct databases that includes EMBL-Bank, the newly established Sequence Read Archive (SRA) and the Trace Archive. International nucleotide sequence database collaboration, comprising ENA-EBI nucleotide sequence data library (EMBL-Bank), DNA DataBank of Japan (DDBJ), and NCBI GenBank

http://www.ebi.ac.uk/ena/

object: Sequence accession
example ID: ENA:AA816246
URL syntax: http://www.ebi.ac.uk/ena/data/view/[example_id]
URL example: http://www.ebi.ac.uk/ena/data/view/AA816246

ENSEMBL

Ensembl database of automatically annotated genomic data

object: Identifier (unspecified)
example ID: ENSEMBL:ENSP00000265949
URL syntax: http://www.ensembl.org/id/[example_id]
URL example: http://www.ensembl.org/id/ENSP00000265949

ENSEMBL_GeneID

Ensembl database of automatically annotated genomic data

object: Gene identifier
example ID: ENSEMBL_GeneID:ENSG00000126016
URL syntax: http://www.ensembl.org/id/[example_id]
URL example: http://www.ensembl.org/id/ENSG00000126016

ENSEMBL_ProteinID

Ensembl database of automatically annotated genomic data

object: Protein identifier
example ID: ENSEMBL_ProteinID:ENSP00000361027
URL syntax: http://www.ensembl.org/id/[example_id]
URL example: http://www.ensembl.org/id/ENSP00000361027

ENSEMBL_TranscriptID

Ensembl database of automatically annotated genomic data

http://plants.ensembl.org/

object: Transcript identifier
example ID: ENSEMBL_TranscriptID:ENST00000371959
URL syntax: http://www.ensembl.org/id/[example_id]
URL example: http://www.ensembl.org/id/ENST00000371959

EnsemblPlants/Gramene

Ensembl Plants, the Ensembl Genomes database for accessing plant genome data

object: Identifier
synonym: EnsemblPlants
example ID: EnsemblPlants:LOC_Os01g22954
URL syntax: http://www.ensemblgenomes.org/id/[example_ID]
URL example: http://www.ensemblgenomes.org/id/LOC_Os01g22954

ENZYME

Swiss Institute of Bioinformatics enzyme database

http://www.expasy.ch/

object: Identifier
example ID: ENZYME:EC 1.1.1.1
URL syntax: http://www.expasy.ch/cgi-bin/nicezyme.pl?[example_id]
URL example: http://www.expasy.ch/cgi-bin/nicezyme.pl?1.1.1.1

Eurofung

Eurofungbase community annotation

http://www.eurofung.net/option=com_content&task=section&id=3&Itemid=4

FB

FlyBase

http://flybase.org/

object: Identifier
synonym: FlyBase, FLYBASE
example ID: FB:FBgn0000024
URL syntax: http://flybase.org/reports/[example_id].html
URL example: http://flybase.org/reports/FBgn0000024.html

FBbt

Drosophila gross anatomy

http://flybase.org/

object: Identifier
example ID: FBbt:00005177
URL syntax: http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:[example_id]
URL example: http://flybase.org/cgi-bin/fbcvq.html?query=FBbt:00005177

FMA

Foundational Model of Anatomy

http://sig.biostr.washington.edu/projects/fm/index.html

object: Identifier
example ID: FMA:61905

FYPO

Fission Yeast Phenotype Ontology

http://www.pombase.org/

object: Identifier
example ID: FYPO:0000001

GDB

Human Genome Database

http://www.gdb.org/

object: Accession
example ID: GDB:306600
URL syntax: http://www.gdb.org/gdb-bin/genera/accno?accessionNum=GDB:[example_id]
URL example: http://www.gdb.org/gdb-bin/genera/accno?accessionNum=GDB:306600

GenBank

The NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.

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

object: Sequence accession
synonym: GB
example ID: GB:AA816246
URL syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=AA816246

Gene3D

Domain Architecture Classification

http://gene3d.biochem.ucl.ac.uk/Gene3D/

GeneDB_Gmorsitans

Glossina morsitans GeneDB (Tsetse)

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

object: Gene identifier
example ID: GeneDB_Gmorsitans:Gmm-0142
URL syntax: http://www.genedb.org/genedb/Search?organism=glossina&name=[example_id]
URL example: http://www.genedb.org/genedb/Search?organism=glossina&name=Gmm-0142

GeneDB_Lmajor

Leishmania major GeneDB (Lmajor)

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

object: Gene identifier
example ID: GeneDB_Lmajor:LM5.32
URL syntax: http://www.genedb.org/genedb/Search?organism=leish&name=[example_id]
URL example: http://www.genedb.org/genedb/Search?organism=leish&name=LM5.32

GeneDB_Pfalciparum

Plasmodium falciparum GeneDB (Pfalciparum)

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

object: Gene identifier
example ID: GeneDB_Pfalciparum:PFD0755c
URL syntax: http://www.genedb.org/genedb/Search?organism=malaria&name=[example_id]
URL example: http://www.genedb.org/genedb/Search?organism=malaria&name=PFD0755c

GeneDB_Spombe

Schizosaccharomyces pombe GeneDB (Spombe)

http://old.genedb.org/genedb/pombe/index.jsp

object: Gene identifier
example ID: GeneDB_Spombe:SPAC890.04C
URL syntax: http://old.genedb.org/genedb/Search?organism=pombe&name=[example_id]
URL example: http://old.genedb.org/genedb/Search?organism=pombe&name=SPAC890.04C

GeneDB_Tbrucei

Trypanosoma brucei GeneDB (Tbrucei)

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

object: Gene identifier
example ID: GeneDB_Tbrucei:Tb927.1.5250
URL syntax: http://www.genedb.org/genedb/Search?organism=tryp&name=[example_id]
URL example: http://www.genedb.org/genedb/Search?organism=tryp&name=Tb927.1.5250

GenProtEC

GenProtEC E. coli genome and proteome database

http://genprotec.mbl.edu/

GermOnline

http://www.germonline.org/

GO

Gene Ontology Database

http://amigo.geneontology.org/

object: Identifier
example ID: GO:0004352
URL syntax: http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:[example_id]
URL example: http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0004352

GO_REF

Gene Ontology Database references

http://www.geneontology.org/

object: Accession (for reference)
example ID: GO_REF:0000001
URL syntax: http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:[example_id]
URL example: http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000001

GOC

Gene Ontology Consortium

http://www.geneontology.org/

GONUTS

Gene Ontology Normal Usage Tracking System (GONUTS)

Third party documentation for GO and community annotation system.

http://gowiki.tamu.edu

object: Identifier (for gene or gene product)
example ID: GONUTS:MOUSE:CD28
URL syntax: http://gowiki.tamu.edu/wiki/index.php/[example_id]
URL example: http://gowiki.tamu.edu/wiki/index.php/MOUSE:CD28

GR

Gramene: A Comparative Mapping Resource for Grains

object: Identifier (any)
example ID: GR:sd1
URL syntax: http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=[example_id]
URL example: http://www.gramene.org/db/searches/browser?search_type=All&RGN=on&query=sd1

GR_GENE

Gramene: A Comparative Mapping Resource for Grains

object: Gene identifier
synonym: GR_gene
example ID: GR_GENE:GR:0060198
URL syntax: http://www.gramene.org/db/genes/search_gene?acc=[example_id]
URL example: http://www.gramene.org/db/genes/search_gene?acc=GR:0060198

GR_PROTEIN

Gramene: A Comparative Mapping Resource for Grains

object: Protein identifier
synonym: GR_protein
example ID: GR_PROTEIN:Q6VSV0
URL syntax: http://www.gramene.org/db/protein/protein_search?acc=[example_id]
URL example: http://www.gramene.org/db/protein/protein_search?acc=Q6VSV0

GR_QTL

Gramene: A Comparative Mapping Resource for Grains

object: QTL identifier
example ID: GR_QTL:CQU7
URL syntax: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=[example_id]
URL example: http://www.gramene.org/db/qtl/qtl_display?qtl_accession_id=CQU7

GR_REF

Gramene: A Comparative Mapping Resource for Grains

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

object: Reference
example ID: GR_REF:659
URL syntax: http://www.gramene.org/db/literature/pub_search?ref_id=[example_id]
URL example: http://www.gramene.org/db/literature/pub_search?ref_id=659

H-invDB

H-invitational Database

H-invDB_cDNA

H-invitational Database

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

object: Accession
example ID: H-invDB_cDNA:AK093148
URL syntax: http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=[example_id]
URL example: http://www.h-invitational.jp/hinv/spsoup/transcript_view?acc_id=AK093149

H-invDB_locus

H-invitational Database

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

object: Cluster identifier
example ID: H-invDB_locus:HIX0014446
URL syntax: http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=[example_id]
URL example: http://www.h-invitational.jp/hinv/spsoup/locus_view?hix_id=HIX0014446

HAMAP

High-quality Automated and Manual Annotation of microbial Proteomes

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

object: Identifier
example ID: HAMAP:MF_00031
URL syntax: http://us.expasy.org/unirules/[example_id]
URL example: http://us.expasy.org/unirules/MF_00031

HGNC

HUGO Gene Nomenclature Committee

http://www.genenames.org/

object: Identifier
example ID: HGNC:29
URL syntax: http://www.genenames.org/data/hgnc_data.php?hgnc_id=HGNC:[example_id]
URL example: http://www.genenames.org/data/hgnc_data.php?hgnc_id=HGNC:29

HGNC_gene

HUGO Gene Nomenclature Committee

http://www.genenames.org/

object: Gene symbol
example ID: HGNC_gene:ABCA1
URL syntax: http://www.genenames.org/data/hgnc_data.php?app_sym=[example_id]
URL example: http://www.genenames.org/data/hgnc_data.php?app_sym=ABCA1

HPA

Human Protein Atlas tissue profile information

http://www.proteinatlas.org/

object: Identifier
example ID: HPA:HPA000237
URL syntax: http://www.proteinatlas.org/tissue_profile.php?antibody_id=[example_id]
URL example: http://www.proteinatlas.org/tissue_profile.php?antibody_id=HPA000237

HPA_antibody

Human Protein Atlas antibody information

http://www.proteinatlas.org/

object: Identifier
example ID: HPA_antibody:HPA000237
URL syntax: http://www.proteinatlas.org/antibody_info.php?antibody_id=[example_id]
URL example: http://www.proteinatlas.org/antibody_info.php?antibody_id=HPA000237

HUGO

Human Genome Organisation

http://www.hugo-international.org/

IMG

Integrated Microbial Genomes; JGI web site for genome annotation

http://img.jgi.doe.gov

object: Identifier
example ID: IMG:640008772
URL syntax: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=[example_id]
URL example: http://img.jgi.doe.gov/cgi-bin/pub/main.cgi?section=GeneDetail&page=geneDetail&gene_oid=640008772

IMGT_HLA

IMGT/HLA human major histocompatibility complex sequence database

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

example ID: IMGT_HLA:HLA00031

IMGT_LIGM

ImMunoGeneTics database covering immunoglobulins and T-cell receptors

Database of immunoglobulins and T cell receptors from human and other vertebrates, with translation for fully annotated sequences.

http://imgt.cines.fr

example ID: IMGT_LIGM:U03895

IntAct

IntAct protein interaction database

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

object: Accession
example ID: IntAct:EBI-17086
URL syntax: http://www.ebi.ac.uk/intact/search/do/search?searchString=[example_id]
URL example: http://www.ebi.ac.uk/intact/search/do/search?searchString=EBI-17086

InterPro

InterPro database of protein domains and motifs

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

object: Identifier
synonym: INTERPRO, IPR
example ID: InterPro:IPR000001
URL syntax: http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=[example_id]
URL example: http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR000001

IPI

International Protein Index

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

object: Identifier
example ID: IPI:IPI00000005.1

ISBN

International Standard Book Number

http://isbntools.com/

object: Identifier
example ID: ISBN:0781702534
URL syntax: http://my.linkbaton.com/get?lbCC=q&nC=q&genre=book&item=[example_id]
URL example: http://my.linkbaton.com/get?lbCC=q&nC=q&genre=book&item=0781702534

ISSN

International Standard Serial Number

http://www.issn.org/

object: Identifier
example ID: ISSN:1234-1231

IUPHAR

International Union of Pharmacology

http://www.iuphar.org/

IUPHAR_GPCR

International Union of Pharmacology

http://www.iuphar.org/

object: G-protein-coupled receptor family identifier
example ID: IUPHAR_GPCR:1279
URL syntax: http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=[example_id]
URL example: http://www.iuphar-db.org/DATABASE/FamilyMenuForward?familyId=13

IUPHAR_RECEPTOR

International Union of Pharmacology

http://www.iuphar.org/

object: Receptor identifier
example ID: IUPHAR_RECEPTOR:2205
URL syntax: http://www.iuphar-db.org/DATABASE/ObjectDisplayForward?objectId=[example_id]
URL example: http://www.iuphar-db.org/DATABASE/ObjectDisplayForward?objectId=56

JCVI

J. Craig Venter Institute

http://www.jcvi.org/

JCVI_Ath1

Arabidopsis thaliana database at the J. Craig Venter Institute

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

This abbreviation is obsolete.

object: Accession
synonym: TIGR_Ath1
example ID: JCVI_Ath1:At3g01440

JCVI_CMR

Comprehensive Microbial Resource at the J. Craig Venter Institute

object: Locus
synonym: TIGR_CMR
example ID: JCVI_CMR:VCA0557
URL syntax: http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=[example_id]
URL example: http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=VCA0557

JCVI_EGAD

EGAD database at the J. Craig Venter Institute

object: Accession
synonym: TIGR_EGAD
example ID: JCVI_EGAD:74462
URL syntax: http://cmr.jcvi.org/cgi-bin/CMR/EgadSearch.cgi?search_string=[example_id]
URL example: http://cmr.jcvi.org/cgi-bin/CMR/EgadSearch.cgi?search_string=74462

JCVI_GenProp

Genome Properties database at the J. Craig Venter Institute

http://medicago.jcvi.org/cgi-bin/medicago/overview.cgi

object: Accession
synonym: TIGR_GenProp
example ID: JCVI_GenProp:GenProp0120
URL syntax: http://cmr.jcvi.org/cgi-bin/CMR/shared/GenomePropDefinition.cgi?prop_acc=[example_id]
URL example: http://cmr.jcvi.org/cgi-bin/CMR/shared/GenomePropDefinition.cgi?prop_acc=GenProp0120

JCVI_Medtr

Medicago truncatula genome database at the J. Craig Venter Institute

object: Accession
example ID: JCVI_Medtr:Medtr5g024510
URL syntax: http://medicago.jcvi.org/cgi-bin/medicago/search/shared/ORF_infopage.cgi?orf=[example_id]
URL example: http://medicago.jcvi.org/cgi-bin/medicago/search/shared/ORF_infopage.cgi?orf=Medtr5g024510

JCVI_Pfa1

Plasmodium falciparum database at the J. Craig Venter Institute

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

This abbreviation is obsolete.

object: Accession
synonym: TIGR_Pfa1
example ID: JCVI_Pfa1:PFB0010w

JCVI_REF

J. Craig Venter Institute

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

object: Reference locator
synonym: TIGR_REF
example ID: JCVI_REF:GO_ref
URL example: http://cmr.jcvi.org/CMR/AnnotationSops.shtml

JCVI_Tba1

Trypanosoma brucei database at the J. Craig Venter Institute

This abbreviation is obsolete.

object: Accession
synonym: TIGR_Tba1
example ID: JCVI_Tba1:25N14.10

JCVI_TIGRFAMS

TIGRFAMs HMM collection at the J. Craig Venter Institute

http://search.jcvi.org/

object: Accession
synonym: TIGR_TIGRFAMS
example ID: JCVI_TIGRFAMS:TIGR00254
URL syntax: http://search.jcvi.org/search?p&q=[example_id]
URL example: http://search.jcvi.org/search?p&q=TIGR00254

JSTOR

Digital archive of scholarly articles

http://www.jstor.org/

object: journal article
example ID: JSTOR:3093870
URL syntax: http://www.jstor.org/stable/[example_id]
URL example: http://www.jstor.org/stable/3093870

KEGG

Kyoto Encyclopedia of Genes and Genomes

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

object: identifier

KEGG_ENZYME

KEGG Enzyme Database

http://www.genome.jp/dbget-bin/www_bfind?enzyme

object: Enzyme Commission ID, as stored in KEGG
example ID: KEGG_ENZYME:2.1.1.4
URL syntax: http://www.genome.jp/dbget-bin/www_bget?ec:[example_id]
URL example: http://www.genome.jp/dbget-bin/www_bget?ec:2.1.1.4

KEGG_LIGAND

KEGG LIGAND Database

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

object: Compound
example ID: KEGG_LIGAND:C00577
URL syntax: http://www.genome.jp/dbget-bin/www_bget?cpd:[example_id]
URL example: http://www.genome.jp/dbget-bin/www_bget?cpd:C00577

KEGG_PATHWAY

KEGG Pathways Database

http://www.genome.jp/kegg/pathway.html

object: Pathway
example ID: KEGG_PATHWAY:ot00020
URL syntax: http://www.genome.jp/dbget-bin/www_bget?path:[example_id]
URL example: http://www.genome.jp/dbget-bin/www_bget?path:ot00020

KEGG_REACTION

KEGG Reaction Database

http://www.genome.jp/kegg/reaction/

object: Reaction
example ID: KEGG:R02328
URL syntax: http://www.genome.jp/dbget-bin/www_bget?rn:[example_id]
URL example: http://www.genome.jp/dbget-bin/www_bget?rn:R02328

LIFEdb

LifeDB

LifeDB is a database for information on protein localization, interaction, functional assays and expression.

http://www.lifedb.de/

object: cDNA clone identifier
example ID: LIFEdb:DKFZp564O1716
URL syntax: http://www.dkfz.de/LIFEdb/LIFEdb.aspx?ID=[example_id]
URL example: http://www.dkfz.de/LIFEdb/LIFEdb.aspx?ID=DKFZp564O1716

LOCSVMpsi

LOCSVMPSI

Subcellular localization for eukayotic proteins based on SVM and PSI-BLAST

http://bioinformatics.ustc.edu.cn/locsvmpsi/locsvmpsi.php

MA

Adult Mouse Anatomical Dictionary

Adult Mouse Anatomical Dictionary; part of Gene Expression Database

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

object: Identifier
example ID: MA:0000003
URL syntax: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:[example_id]
URL example: http://www.informatics.jax.org/searches/AMA.cgi?id=MA:0000003

MaizeGDB

http://www.maizegdb.org

object: MaizeGDB Object ID Number
example ID: MaizeGDB:881225
URL syntax: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=[example_id]
URL example: http://www.maizegdb.org/cgi-bin/id_search.cgi?id=881225

MaizeGDB_Locus

MaizeGDB

http://www.maizegdb.org

object: Maize gene name
example ID: MaizeGDB_Locus:ZmPK1
URL syntax: http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=[example_id]
URL example: http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=ZmPK1

MEDLINE

Medline literature database

http://www.nlm.nih.gov/databases/databases_medline.html

object: Identifier
example ID: MEDLINE:20572430

MENGO

Microbial ENergy processes Gene Ontology Project

http://mengo.vbi.vt.edu/

MEROPS

MEROPS peptidase database

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

object: Identifier
example ID: MEROPS:A08.001
URL syntax: http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=[example_id]
URL example: http://merops.sanger.ac.uk/cgi-bin/pepsum?mid=A08.001

MEROPS_fam

MEROPS peptidase database

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

object: Peptidase family identifier
example ID: MEROPS_fam:M18
URL syntax: http://merops.sanger.ac.uk/cgi-bin/famsum?family=[example_id]
URL example: http://merops.sanger.ac.uk/cgi-bin/famsum?family=m18

MeSH

Medical Subject Headings

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

object: MeSH heading
example ID: MeSH:mitosis
URL syntax: http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=[example_id]
URL example: http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term=mitosis

MetaCyc

Metabolic Encyclopedia of metabolic and other pathways

http://metacyc.org/

object: Identifier (pathway or reaction)
example ID: MetaCyc:GLUTDEG-PWY
URL syntax: http://biocyc.org/META/NEW-IMAGE?type=NIL&object=[example_id]
URL example: http://biocyc.org/META/NEW-IMAGE?type=NIL&object=GLUTDEG-PWY

MGD

Mouse Genome Database

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

object: Gene symbol
example ID: MGD:Adcy9

MGI

Mouse Genome Informatics

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

object: Accession
example ID: MGI:MGI:80863
URL syntax: http://www.informatics.jax.org/accession/[example_id]
URL example: http://www.informatics.jax.org/accession/MGI:80863

MIPS_funcat

MIPS Functional Catalogue

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

object: Identifier
example ID: MIPS_funcat:11.02
URL syntax: http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=[example_id]
URL example: http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert=11.02

MITRE

The MITRE Corporation

http://www.mitre.org/

MO

MGED Ontology

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

object: ontology term
example ID: MO:Action
URL syntax: http://mged.sourceforge.net/ontologies/MGEDontology.php#[example_id]
URL example: http://mged.sourceforge.net/ontologies/MGEDontology.php#Action

ModBase

ModBase comprehensive Database of Comparative Protein Structure Models

http://modbase.compbio.ucsf.edu/

object: Accession
example ID: ModBase:P10815
URL syntax: http://salilab.org/modbase/searchbyid?databaseID=[example_id]
URL example: http://salilab.org/modbase/searchbyid?databaseID=P04848

MTBBASE

Collection and Refinement of Physiological Data on Mycobacterium

http://www.ark.in-berlin.de/Site/MTBbase.html

MultiFun

MultiFun cell function assignment schema

http://genprotec.mbl.edu/files/MultiFun.html

NASC_code

Nottingham Arabidopsis Stock Centre Seeds Database

http://arabidopsis.info

object: NASC code Identifier
example ID: NASC_code:N3371
URL syntax: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=[example_id]
URL example: http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code=N3371

NC-IUBMB

Nomenclature Committee of the International Union of Biochemistry and Molecular Biology

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

NCBI

National Center for Biotechnology Information

object: Prefix

NCBI_Gene

NCBI Gene

object: Identifier
synonym: GeneID, LocusID
example ID: NCBI_Gene:4771
URL syntax: http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=gene&list_uids=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=gene&list_uids=4771

NCBI_gi

NCBI databases

object: Identifier
example ID: NCBI_gi:113194944
URL syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=113194944

NCBI_GP

NCBI GenPept

object: Protein identifier
example ID: NCBI_GP:EAL72968
URL syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val=EAL72968

NCBI_locus_tag

NCBI locus tag

object: Identifier
example ID: NCBI_locus_tag:CTN_0547

NCBI_NM

NCBI RefSeq

This abbreviation is obsolete.
Replaced by: RefSeq

object: mRNA identifier
synonym: RefSeq
example ID: NCBI_NM:123456

NCBI_NP

NCBI RefSeq

http://www.neurolex.org/wiki

This abbreviation is obsolete.
Replaced by: RefSeq

object: Protein identifier
synonym: RefSeq
example ID: NCBI_NP:123456

NIF_Subcellular

Neuroscience Information Framework standard ontology, subcellular hierarchy

object: ontology term
example ID: NIF_Subcellular:sao1186862860
URL syntax: http://www.neurolex.org/wiki/[example_id]
URL example: http://www.neurolex.org/wiki/sao1770195789

NMPDR

National Microbial Pathogen Data Resource

http://www.nmpdr.org

object: Identifier
example ID: NMPDR:fig|306254.1.peg.183
URL syntax: http://www.nmpdr.org/linkin.cgi?id=[example_id]
URL example: http://www.nmpdr.org/linkin.cgi?id=fig|306254.1.peg.183

NTNU_SB

Norwegian University of Science and Technology, Systems Biology team

http://www.ntnu.edu/nt/systemsbiology

OBI

Ontology for Biomedical Investigations

http://obi-ontology.org/page/Main_Page

object: Identifier
example ID: OBI:0000038

OBO_REL

OBO relation ontology

http://www.obofoundry.org/ro/

object: Identifier
example ID: OBO_REL:part_of

OBO_SF_PO

Source Forge OBO Plant Ontology (PO) term request tracker

http://sourceforge.net/tracker/?func=browse&group_id=76834&atid=835555

object: Term request
example ID: OBO_SF_PO:3184921
URL syntax: https://sourceforge.net/tracker/index.php?func=detail&aid=[example_id]&group_id=76834&atid=835555
URL example: https://sourceforge.net/tracker/index.php?func=detail&aid=3184921&group_id=76834&atid=835555

OMIM

Mendelian Inheritance in Man

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

object: Identifier
synonym: MIM
example ID: OMIM:190198
URL syntax: http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/htbin-post/entrez/dispomim.cgi?id=190198

OMSSA

Open Mass Spectrometry Search Algorithm

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

PAINT_REF

Phylogenetic Annotation INference Tool References

http://www.pantherdb.org/

object: Reference locator
example ID: PAINT_REF:PTHR10046
URL syntax: http://www.geneontology.org/gene-associations/submission/paint/[example_id]/[example_id].txt
URL example: http://www.geneontology.org/gene-associations/submission/paint/PTHR10046/PTHR10046.txt

PAMGO

Plant-Associated Microbe Gene Ontology Interest Group

http://pamgo.vbi.vt.edu/

PAMGO_GAT

Genome Annotation Tool (Agrobacterium tumefaciens C58); PAMGO Interest Group

http://agro.vbi.vt.edu/public/

object: Gene
example ID: PAMGO_GAT:Atu0001
URL syntax: http://agro.vbi.vt.edu/public/servlet/GeneEdit?&Search=Search&level=2&genename=[example_id]
URL example: http://agro.vbi.vt.edu/public/servlet/GeneEdit?&Search=Search&level=2&genename=atu0001

PAMGO_MGG

Magnaporthe grisea database

Magnaporthe grisea database at North Carolina State University; member of PAMGO Interest Group

http://scotland.fgl.ncsu.edu/smeng/GoAnnotationMagnaporthegrisea.html

object: Locus
example ID: PAMGO_MGG:MGG_05132
URL syntax: http://scotland.fgl.ncsu.edu/cgi-bin/adHocQuery.cgi?adHocQuery_dbName=smeng_goannotation&Action=Data&QueryName=Functional+Categorization+of+MGG+GO+Annotation&P_KeyWord=[example_id]
URL example: http://scotland.fgl.ncsu.edu/cgi-bin/adHocQuery.cgi?adHocQuery_dbName=smeng_goannotation&Action=Data&QueryName=Functional+Categorization+of+MGG+GO+Annotation&P_KeyWord=MGG_05132

PAMGO_VMD

Virginia Bioinformatics Institute Microbial Database

Virginia Bioinformatics Institute Microbial Database; member of PAMGO Interest Group

http://phytophthora.vbi.vt.edu

object: Gene identifier
example ID: PAMGO_VMD:109198
URL syntax: http://vmd.vbi.vt.edu/cgi-bin/browse/go_detail.cgi?gene_id=[example_id]
URL example: http://vmd.vbi.vt.edu/cgi-bin/browse/go_detail.cgi?gene_id=109198

PANTHER

Protein ANalysis THrough Evolutionary Relationships

http://www.pantherdb.org/

object: Protein family tree identifier
example ID: PANTHER:PTHR22573
URL syntax: http://pantree.org/node/annotationNode.jsp?id=[example_id]
URL example: http://pantree.org/node/annotationNode.jsp?id=PTHR11361_AN26

PATO

Phenotypic quality ontology

http://www.bioontology.org/wiki/index.php/PATO:Main_Page

object: Identifier
example ID: PATO:0001420

PATRIC

PathoSystems Resource Integration Center

PathoSystems Resource Integration Center at the Virginia Bioinformatics Institute

http://patric.vbi.vt.edu

object: Feature identifieer
example ID: PATRIC:cds.000002.436951
URL syntax: http://patric.vbi.vt.edu/gene/overview.php?fid=[example_id]
URL example: http://patric.vbi.vt.edu/gene/overview.php?fid=cds.000002.436951

PDB

Protein Data Bank

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

object: Identifier
example ID: PDB:1A4U
URL syntax: http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=[example_id]
URL example: http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1A4U

Pfam

Pfam database of protein families

Pfam is a collection of protein families represented by sequence alignments and hidden Markov models (HMMs)

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

object: Accession
example ID: Pfam:PF00046
URL syntax: http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?[example_id]
URL example: http://www.sanger.ac.uk/cgi-bin/Pfam/getacc?PF00046

PfamB

Pfam-B supplement to Pfam

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

object: Accession
example ID: PfamB:PB014624

PharmGKB

Pharmacogenetics and Pharmacogenomics Knowledge Base

http://www.pharmgkb.org

example ID: PharmGKB:PA267
URL syntax: http://www.pharmgkb.org/do/serve?objId=[example_id]
URL example: http://www.pharmgkb.org/do/serve?objId=PA267

PhenoScape

PhenoScape Knowledgebase

http://phenoscape.org/

PINC

Proteome Inc.

represents GO annotations created in 2001 for NCBI and extracted into UniProtKB-GOA from EntrezGene

http://www.proteome.com/

PIR

Protein Information Resource

http://pir.georgetown.edu/

object: Accession
example ID: PIR:I49499
URL syntax: http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=[example_id]
URL example: http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid=I49499

PIRSF

PIR Superfamily Classification System

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

object: Identifier
example ID: PIRSF:SF002327
URL syntax: http://pir.georgetown.edu/cgi-bin/ipcSF?id=[example_id]
URL example: http://pir.georgetown.edu/cgi-bin/ipcSF?id=SF002327

PMCID

Pubmed Central

http://www.pubmedcentral.nih.gov/

object: Identifier
example ID: PMCID:PMC201377
URL syntax: http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/sites/entrez?db=pmc&cmd=search&term=PMC201377

PMID

PubMed

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

object: Identifier
synonym: PUBMED, PubMed
example ID: PMID:4208797
URL syntax: http://www.ncbi.nlm.nih.gov/pubmed/[example_id]
URL example: http://www.ncbi.nlm.nih.gov/pubmed/4208797

PO

Plant Ontology Consortium Database

http://www.plantontology.org/

object: Identifier
example ID: PO:0009004
URL syntax: http://www.plantontology.org/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=PO:[example_id]
URL example: http://www.plantontology.org/amigo/go.cgi?action=query&view=query&search_constraint=terms&query=PO:0009004

PO_REF

Plant Ontology custom references

http://wiki.plantontology.org:8080/index.php/PO_references

object: Reference identifier
example ID: PO_REF:00001
URL syntax: http://wiki.plantontology.org:8080/index.php/PO_REF:[example_id]
URL example: http://wiki.plantontology.org:8080/index.php/PO_REF:00001

POC

Plant Ontology Consortium

http://www.plantontology.org/

PomBase

http://www.pombase.org/

object: Identifier
example ID: PomBase:SPBC11B10.09
URL syntax: http://www.pombase.org/spombe/result/[example_id]
URL example: http://www.pombase.org/spombe/result/SPBC11B10.09

Pompep

Schizosaccharomyces pombe protein data

ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Protein_data/

object: Gene/protein identifier
example ID: Pompep:SPAC890.04C

PPI

Pseudomonas syringae community annotation project

http://genome.pseudomonas-syringae.org/

PR

Protein Ontology

http://www.proconsortium.org/pro/pro.shtml

object: Identifer
synonym: PRO
example ID: PR:000025380
URL syntax: http://www.proconsortium.org/cgi-bin/pro/entry_pro?id=PR:[example_id]
URL example: http://www.proconsortium.org/cgi-bin/pro/entry_pro?id=PR:000025380

PRINTS

PRINTS compendium of protein fingerprints

http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/

object: Accession
example ID: PRINTS:PR00025
URL syntax: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&regexpr=off&prints_accn=[example_id]
URL example: http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&regexpr=off&prints_accn=PR00025

ProDom

ProDom protein domain families

ProDom protein domain families automatically generated from UniProtKB

http://prodom.prabi.fr/prodom/current/html/home.php

object: Accession
example ID: ProDom:PD000001
URL syntax: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=[example_id]
URL example: http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=PD000001

Prosite

Prosite database of protein families and domains

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

object: Accession
example ID: Prosite:PS00365
URL syntax: http://www.expasy.ch/cgi-bin/prosite-search-ac?[example_id]
URL example: http://www.expasy.ch/cgi-bin/prosite-search-ac?PS00365

protein_id

DDBJ / EMBL-Bank / GenBank

protein identifier shared by DDBJ/EMBL-bank/GenBank nucleotide sequence databases

http://www.ddbj.nig.ac.jp/
http://www.ebi.ac.uk/embl/
http://www.ncbi.nlm.nih.gov/Genbank/

object: Identifier
example ID: protein_id:CAA71991

PROW

Protein Reviews on the Web

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

PseudoCAP

Pseudomonas Genome Project

http://v2.pseudomonas.com/

object: Identifier
example ID: PseudoCAP:PA4756
URL syntax: http://v2.pseudomonas.com/getAnnotation.do?locusID=[example_id]
URL example: http://v2.pseudomonas.com/getAnnotation.do?locusID=PA4756

PSI-MI

Proteomic Standard Initiative for Molecular Interaction

http://psidev.sourceforge.net/mi/xml/doc/user/index.html

object: Interaction identifier
synonym: MI
example ID: MI:0018

PSI-MOD

Proteomics Standards Initiative protein modification ontology

http://psidev.sourceforge.net/mod/

object: Protein modification identifier
synonym: MOD
example ID: MOD:00219
URL syntax: http://www.ebi.ac.uk/ontology-lookup/?termId=MOD:[example_id]
URL example: http://www.ebi.ac.uk/ontology-lookup/?termId=MOD:00219

PSORT

PSORT protein subcellular localization databases and prediction tools for bacteria

http://www.psort.org/

pTARGET

pTARGET Prediction server for protein subcellular localization

http://bioinformatics.albany.edu/~ptarget/

PubChem_BioAssay

NCBI PubChem database of bioassay records

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

object: Identifier
example ID: PubChem_BioAssay:177
URL syntax: http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=[example_id]
URL example: http://pubchem.ncbi.nlm.nih.gov/assay/assay.cgi?aid=177

PubChem_Compound

NCBI PubChem database of chemical structures

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

object: Identifier
example ID: PubChem_Compound:2244
URL syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term=2244

PubChem_Substance

NCBI PubChem database of chemical substances

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

object: Identifier
example ID: PubChem_Substance:4594
URL syntax: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term=4594

Reactome

Reactome - a curated knowledgebase of biological pathways

http://www.reactome.org/

object: Identifier
example ID: Reactome:REACT_604
URL syntax: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=[example_id]
URL example: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_604

REBASE

REBASE restriction enzyme database

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

object: Restriction enzyme name
example ID: REBASE:EcoRI
URL syntax: http://rebase.neb.com/rebase/enz/[example_id].html
URL example: http://rebase.neb.com/rebase/enz/EcoRI.html

RefGenome

GO Reference Genomes

http://www.geneontology.org/GO.refgenome.shtml

RefSeq

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

object: Identifier
example ID: RefSeq:XP_001068954
URL syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=XP_001068954

RefSeq_NA

RefSeq (Nucleic Acid)

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

This abbreviation is obsolete.
Replaced by: RefSeq

object: Identifier
example ID: RefSeq_NA:NC_000913
URL syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NC_000913

RefSeq_Prot

RefSeq (Protein)

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

This abbreviation is obsolete.
Replaced by: RefSeq

object: Identifier
example ID: RefSeq_Prot:YP_498627
URL syntax: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=YP_498627

RESID

RESID Database of Protein Modifications

ftp://ftp.ncifcrf.gov/pub/users/residues/

object: Identifier
example ID: RESID:AA0062

Rfam

Rfam database of RNA families

http://rfam.sanger.ac.uk/

object: accession
example ID: Rfam:RF00012
URL syntax: http://rfam.sanger.ac.uk/family/[example_id]
URL example: http://rfam.sanger.ac.uk/family/RF00012

RGD

Rat Genome Database

http://rgd.mcw.edu/

object: Accession
synonym: RGDID
example ID: RGD:2004
URL syntax: http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword=[example_id]
URL example: http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword=2004

RHEA

Rhea, the Annotated Reactions Database

Rhea is a freely available, manually annotated database of chemical reactions created in collaboration with the Swiss Institute of Bioinformatics (SIB).

http://www.ebi.ac.uk/rhea/

object: Accession
example ID: RHEA:25811
URL syntax: http://www.ebi.ac.uk/rhea/reaction.xhtml?id=[example_id]
URL example: http://www.ebi.ac.uk/rhea/reaction.xhtml?id=25811

RNAmods

RNA Modification Database

http://s59.cas.albany.edu/RNAmods/

object: Identifier
synonym: RNAMDB
example ID: RNAmods:037
URL syntax: http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?[example_id]
URL example: http://s59.cas.albany.edu/RNAmods/cgi-bin/rnashow.cgi?091

RO

OBO Relation Ontology Ontology

A collection of relations used across OBO ontologies

http://purl.obolibrary.org/obo/ro

example ID: RO:0002211
URL syntax: http://purl.obolibrary.org/obo/RO_[example_id]
URL example: http://purl.obolibrary.org/obo/RO_0002211

Roslin_Institute

Roslin Institute

http://www.roslin.ac.uk/

SABIO-RK

SABIO Reaction Kinetics

The SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.

http://sabio.villa-bosch.de/

object: reaction
example ID: SABIO-RK:1858
URL syntax: http://sabio.villa-bosch.de/reacdetails.jsp?reactid=[example_id]
URL example: http://sabio.villa-bosch.de/reacdetails.jsp?reactid=1858

Sanger

Wellcome Trust Sanger Institute

http://www.sanger.ac.uk/

SEED

The SEED;

Project to annotate the first 1000 sequenced genomes, develop detailed metabolic reconstructions, and construct the corresponding stoichiometric matrices

http://www.theseed.org

object: identifier
example ID: SEED:fig|83331.1.peg.1
URL syntax: http://www.theseed.org/linkin.cgi?id=[example_id]
URL example: http://www.theseed.org/linkin.cgi?id=fig|83331.1.peg.1

SGD

Saccharomyces Genome Database

http://www.yeastgenome.org/

object: Identifier for SGD Loci
synonym: SGDID
example ID: SGD:S000006169
URL syntax: http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=[example_id]
URL example: http://db.yeastgenome.org/cgi-bin/locus.pl?dbid=S000006169

SGD_LOCUS

Saccharomyces Genome Database

http://www.yeastgenome.org/

object: Gene name (gene symbol in mammalian nomenclature)
example ID: SGD_LOCUS:GAL4
URL syntax: http://db.yeastgenome.org/cgi-bin/locus.pl?locus=[example_id]
URL example: http://db.yeastgenome.org/cgi-bin/locus.pl?locus=GAL4

SGD_REF

Saccharomyces Genome Database

http://www.yeastgenome.org/

object: Literature Reference Identifier
example ID: SGD_REF:S000049602
URL syntax: http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=[example_id]
URL example: http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid=S000049602

SGN

Sol Genomics Network

http://www.sgn.cornell.edu/

object: Gene identifier
example ID: SGN:4476
URL syntax: http://www.sgn.cornell.edu/phenome/locus_display.pl?locus_id=[example_id]
URL example: http://www.sgn.cornell.edu/phenome/locus_display.pl?locus_id=4476

SGN_ref

Sol Genomics Network

http://www.sgn.cornell.edu/

object: Reference identifier
example ID: SGN_ref:861
URL syntax: http://www.sgn.cornell.edu/chado/publication.pl?pub_id=[example_id]
URL example: http://www.sgn.cornell.edu/chado/publication.pl?pub_id=861

SMART

Simple Modular Architecture Research Tool

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

object: Accession
example ID: SMART:SM00005
URL syntax: http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=[example_id]
URL example: http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=SM00005

SMD

Stanford Microarray Database

http://genome-www.stanford.edu/microarray

SO

Sequence Ontology

http://sequenceontology.org/

object: Identifier
example ID: SO:0000195
URL syntax: http://song.sourceforge.net/SOterm_tables.html#SO:[example_id]
URL example: http://song.sourceforge.net/SOterm_tables.html#SO:0000195

SPD

Schizosaccharomyces pombe Postgenome Database at RIKEN; includes Orfeome Localisation data

http://www.riken.jp/SPD/

object: Identifier
example ID: SPD:05/05F01
URL syntax: http://www.riken.jp/SPD/[example_id].html
URL example: http://www.riken.jp/SPD/05/05F01.html

SUBTILIST

Bacillus subtilis Genome Sequence Project

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

object: Accession
example ID: SUBTILISTG:BG11384

SUBTILISTG

Bacillus subtilis Genome Sequence Project

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

object: Gene symbol
example ID: SUBTILISTG:accC

SUPERFAMILY

SUPERFAMILY protein annotation database

A database of structural and functional protein annotations for completely sequenced genomes

http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/

Swiss-Prot

UniProtKB/Swiss-Prot

A curated protein sequence database which provides a high level of annotation and a minimal level of redundancy

http://www.uniprot.org

object: Accession
synonym: UniProtKB/Swiss-Prot
example ID: Swiss-Prot:P51587
URL syntax: http://www.uniprot.org/uniprot/[example_id]
URL example: http://www.uniprot.org/uniprot/P51587

TAIR

The Arabidopsis Information Resource

http://www.arabidopsis.org/

object: Accession
example ID: TAIR:gene:2062713; TAIR:locus:2146653
URL syntax: http://arabidopsis.org/servlets/TairObject?accession=[example_id]
URL example: http://arabidopsis.org/servlets/TairObject?accession=gene:2062713; http://arabidopsis.org/servlets/TairObject?accession=locus:2146653

taxon

NCBI Taxonomy

http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/

object: Identifier
synonym: NCBITaxon, ncbi_taxid
example ID: taxon:7227
URL syntax: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=[example_id]
URL example: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=3702

TC

Transport Protein Database

http://www.tcdb.org/

object: Identifier
example ID: TC:9.A.4.1.1
URL syntax: http://www.tcdb.org/tcdb/index.php?tc=[example_id]
URL example: http://www.tcdb.org/tcdb/index.php?tc=9.A.4.1.1

TGD

Tetrahymena Genome Database

http://www.ciliate.org/

TGD_LOCUS

Tetrahymena Genome Database

http://www.ciliate.org/

object: Gene name (gene symbol in mammalian nomenclature)
example ID: TGD_LOCUS:PDD1
URL syntax: http://db.ciliate.org/cgi-bin/locus.pl?locus=[example_id]
URL example: http://db.ciliate.org/cgi-bin/locus.pl?locus=PDD1

TGD_REF

Tetrahymena Genome Database

http://www.ciliate.org/

object: Literature Reference Identifier
example ID: TGD_REF:T000005818
URL syntax: http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=[example_id]
URL example: http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid=T000005818

TRAIT

TRAnscript Integrated Table

an integrated database of transcripts expressed in human skeletal muscle

http://muscle.cribi.unipd.it/

TRANSFAC

TRANSFAC database of eukaryotic transcription factors

http://www.gene-regulation.com/pub/databases.html#transfac

TrEMBL

UniProtKB-TrEMBL protein sequence 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

http://www.uniprot.org

object: Accession
synonym: UniProtKB/TrEMBL
example ID: TrEMBL:O31124
URL syntax: http://www.uniprot.org/uniprot/[example_id]
URL example: http://www.uniprot.org/uniprot/O31124

UBERON

Uber-anatomy ontology

A multi-species anatomy ontology

http://berkeleybop.org/obo/UBERON

object: Identifier
example ID: URBERON:0000970
URL syntax: http://berkeleybop.org/obo/UBERON:[example_id]
URL example: http://berkeleybop.org/obo/UBERON:0000970

UM-BBD

University of Minnesota Biocatalysis/Biodegradation Database

object: Prefix

UM-BBD_enzymeID

University of Minnesota Biocatalysis/Biodegradation Database

object: Enzyme identifier
example ID: UM-BBD_enzymeID:e0413
URL syntax: http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=ep&enzymeID=[example_id]
URL example: http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=ep&enzymeID=e0230

UM-BBD_pathwayID

University of Minnesota Biocatalysis/Biodegradation Database

object: Pathway identifier
example ID: UM-BBD_pathwayID:acr
URL syntax: http://umbbd.msi.umn.edu/[example_id]/[example_id]_map.html
URL example: http://umbbd.msi.umn.edu/acr/acr_map.html

UM-BBD_reactionID

University of Minnesota Biocatalysis/Biodegradation Database

object: Reaction identifier
example ID: UM-BBD_reactionID:r0129
URL syntax: http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=r&reacID=[example_id]
URL example: http://umbbd.msi.umn.edu/servlets/pageservlet?ptype=r&reacID=r0129

UM-BBD_ruleID

University of Minnesota Biocatalysis/Biodegradation Database