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Mappings of External Classification Systems to GO

The Gene Ontology is not the only attempt to build structured controlled vocabularies for genome annotation. To aid users, the GO Consortium provides mappings of its terms to those in a number of external vocabularies.

What is a mapping?

These files contain classes or entities from external database systems, such as Enzyme Commission numbers, UniProt keywords, or ProSite domains, indexed to identical, similar or related GO terms. The mappings are typically made manually; details can be found in the file headers.

Mappings should be used as a guide only.

Although we endeavour to make mappings as accurate as possible, we cannot guarantee that the mappings provided by the GO project are either complete or exact. This may be due to the absence of definitions from GO terms or from terms in some external systems; the GO ontologies and the external database may also have changed since the mapping was made. Please report any errors or suggest alternatives to the GO helpdesk.

Using and citing a mapping

If you have used a mapping in a publication or presentation, please ensure that you cite both the GO project and the source of the mapping (detailed below). See the GO citation guide for citing the GO project.

Mapping Format

Mapping files are in the format:

external database:term identifier (id/name) > GO:GO term name ; GO:id

More details can be found in the external mapping file format guide.

Mappings File Directory

Direct access to the mappings file directory is available via the following routes:

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The Mappings

Mappings of external databases to GO
Mapping Last update Download
COG functional categories
Clusters of Orthologous Groups (COG)
Constructed by Michael Ashburner and Jane Lomax
June 2004 txt
Enzyme Commission (EC) enzyme numbers
Enzyme Commission; contact: go-ontology@lists.stanford.edu (GO ontology editors)
Constructed and maintained in the GO ontology file by GO editorial staff
Citation: Hill DP, Davis AP, Richardson JE, Corradi JP, Ringwald M, Eppig JT, Blake JA. Program description: Strategies for biological annotation of mammalian systems: implementing gene ontologies in mouse genome informatics. Genomics. May 2001;74(1):121–8. [ PMID:11374909 | doi:10.1006/geno.2001.6513 ]
Monthly txt
Expressed Gene Anatomy Database
Expressed Gene Anatomy Database (EGAD)
Constructed by Michael Ashburner
Oct 2000 txt
E. coli Genome and Proteome functional categories
E. coli Genome and Proteome (GenProtEC)
Constructed by Heather Butler and Michael Ashburner
Dec 2000 txt
HAMAP families
High-Quality Automated and Manual Annotation of Microbial Proteomes (HAMAP); contact: goa@ebi.ac.uk (UniProtKB-GOA team)
Mapping generated by the HAMAP and UniProtKB UniProtKB-GOA teams
Citation: Lima T, Auchincloss AH, Coudert E, Keller G, Michoud K, Rivoire C, Bulliard V, de Castro E, Lachaize C, Baratin D, Phan I, Bougueleret L, Bairoch A. HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic Acids Res.. Jan 2009;37(Database issue):D471–8. [ PMID:18849571 | doi:10.1093/nar/gkn661 ]
Monthly txt
InterPro protein families, domains and functional sites
InterPro; contact: interhelp@ebi.ac.uk (InterPro team)
Citation: Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. InterPro: the integrative protein signature database. Nucleic Acids Res.. Jan 2009;37(Database issue):D211–5. [ PMID:18940856 | doi:10.1093/nar/gkn785 ]
Monthly txt
KEGG pathways and reactions
Kyoto Encyclopaedia of Genes and Genomes
Constructed and maintained by Amelia Ireland and a script.
Daily txt
MetaCyc pathways and reactions
MetaCyc; contact: go-ontology@lists.stanford.edu (GO ontology editors)
Constructed and maintained in the GO ontology file by GO editorial staff
Daily txt
MIPS FunCat
MIPS Functional Catalogue (FunCat)
Constructed by Michael Ashburner and Midori Harris
Jan 2006 txt
MultiFun cell function assignment schema classifications
MultiFun
Constructed by Michael Ashburner, Jane Lomax and Margrethe Hauge Serres.
Dec 2005 txt
Pfam domains
Pfam; contact: interhelp@ebi.ac.uk (InterPro team)
This mapping is generated from data supplied by InterPro for the InterPro2GO mapping.
Citation: Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. InterPro: the integrative protein signature database. Nucleic Acids Res.. Jan 2009;37(Database issue):D211–5. [ PMID:18940856 | doi:10.1093/nar/gkn785 ]
Monthly txt
PIRSF protein superfamilies
PIRSF; contact: interhelp@ebi.ac.uk (InterPro team)
This mapping is generated from data supplied by InterPro for the InterPro2GO mapping.
Citation: Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. InterPro: the integrative protein signature database. Nucleic Acids Res.. Jan 2009;37(Database issue):D211–5. [ PMID:18940856 | doi:10.1093/nar/gkn785 ]
Monthly txt
PRINTS domains
PRINTS; contact: interhelp@ebi.ac.uk (InterPro team)
This mapping is generated from data supplied by InterPro for the InterPro2GO mapping.
Citation: Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. InterPro: the integrative protein signature database. Nucleic Acids Res.. Jan 2009;37(Database issue):D211–5. [ PMID:18940856 | doi:10.1093/nar/gkn785 ]
 
Monthly txt
ProDom domains
ProDom; contact: interhelp@ebi.ac.uk (InterPro team)
This mapping is generated from data supplied by InterPro for the InterPro2GO mapping.
Citation: Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. InterPro: the integrative protein signature database. Nucleic Acids Res.. Jan 2009;37(Database issue):D211–5. [ PMID:18940856 | doi:10.1093/nar/gkn785 ]
 
Monthly txt
ProSite domains
ProSite; contact: interhelp@ebi.ac.uk (InterPro team)
This mapping is generated from data supplied by InterPro for the InterPro2GO mapping.
Citation: Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. InterPro: the integrative protein signature database. Nucleic Acids Res.. Jan 2009;37(Database issue):D211–5. [ PMID:18940856 | doi:10.1093/nar/gkn785 ]
 
Monthly txt
Reactome events and catalyst activities
Reactome
Constructed by Reactome curators and maintained in the GO ontology file by GO editorial staff
Daily txt
Rfam RNA families
Rfam
Constructed and maintained by Sam Griffiths-Jones and Jennifer Daub.
May 2006 txt
Rhea Annotated Reactions Database
Rhea
Constructed and maintained by Amelia Ireland and a script.
Daily txt
SMART domains
SMART; contact: interhelp@ebi.ac.uk (InterPro team)
This mapping is generated from data supplied by InterPro for the InterPro2GO mapping.
Citation: Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. InterPro: the integrative protein signature database. Nucleic Acids Res.. Jan 2009;37(Database issue):D211–5. [ PMID:18940856 | doi:10.1093/nar/gkn785 ]
 
Monthly txt
JCVI (TIGRFAM) protein families
JCVI (TIGRFAM) protein families
Constructed by Michelle Gwinn and other TIGR staff.
Monthly txt
JCVI roles
JCVI roles
Constructed by Michael Ashburner
Jan 2004 txt
UniProt Knowledgebase
Mapping of GO terms to UniProt Knowledgebase keywords. This mapping is generated by the UniProtKB and UniProtKB-GOA teams. [was SwissProt keyword]
UniProt; contact: goa@ebi.ac.uk (UniProtKB-GOA team)
Citation: Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R. The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Res.. Jan 2009;37(Database issue):D396–403. [ PMID:18957448 | doi:10.1093/nar/gkn803 ]
 
Monthly txt
UM-BBD enzyme IDs
University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD); contact: ontology@lists.stanford.edu (GO ontology editors)
Maintained in the GO ontology file by GO editorial staff
 
Daily txt
UM-BBD pathway IDs
University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD); contact: go-ontology@lists.stanford.edu (GO ontology editors)
Maintained in the GO ontology file by GO editorial staff
Daily txt
UM-BBD reaction IDs
University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD); contact: go-ontology@lists.stanford.edu (GO ontology editors)
Maintained in the GO ontology file by GO editorial staff
Daily txt
UniProt subcellular location
UniProt; contact goa@ebi.ac.uk (UniProtKB-GOA team)
Citation: Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R. The GOA database in 2009--an integrated Gene Ontology Annotation resource. Nucleic Acids Res.. Jan 2009;37(Database issue):D396–403. [ PMID:18957448 | doi:10.1093/nar/gkn803 ]
Monthly txt

N.B. Files listed as being updated monthly are completely regenerated during the monthly UniProtKB-GOA release. Minor corrections to files are not mentioned here, and only comprehensive updates are listed.

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