Cross-references of external classification systems to GO
Many Gene Ontology terms are cross-referenced to corresponding concepts from a number of external vocabularies, including Enzyme Commission numbers, KEGG, Reactome Pathways, and Wikipedia. The cross-references (mappings) are typically made manually. Please report any errors or suggest alternatives to the GO helpdesk.
Using and citing cross-references and mappings
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.
Cross-references format
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Cross-references files are simple text files that start with a comment line describing the date generated and the GO release used, for example:
! Generated on 2018-10-05T08:40Z from the ontology 'go' with data version: 'releases/2017-03-31' -
Each cross-reference is on a different line, in the format:
database:term identifier (id/name) > GO:GO term name ; GO:idFor example:
EC:1.1.1.1 > GO:alcohol dehydrogenase (NAD) activity ; GO:0004022 -
Cross-references to GO mappings can be many-to-many. Each cross-reference is on a separate line of the file.
Mappings file directory
Direct access to the mappings file directory is available here: http://current.geneontology.org/ontology/external2go/
Links to cross-references files derived the Gene Ontology
| Mapping | Last update | Download |
|---|---|---|
| Enzyme Commission (EC) enzyme numbers Enzyme Commission; contact: 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 ] |
Continuous | txt |
| KEGG pathways and reactions Kyoto Encyclopaedia of Genes and Genomes Constructed and maintained by Amelia Ireland and a script |
Continuous | txt |
| MetaCyc pathways and reactions MetaCyc; contact: GO Ontology editors Constructed and maintained in the GO ontology file by GO editorial staff |
Continuous | txt |
| MIPS FunCat MIPS Functional Catalogue (FunCat) Constructed by Michael Ashburner and Midori Harris |
Continuous | no link |
| Reactome events and catalyst activities Reactome Constructed by Reactome curators and maintained in the GO ontology file by GO editorial staff |
Continuous | txt |
| Rhea Annotated Reactions Database Rhea Constructed and maintained by Amelia Ireland and a script |
Continuous | txt |
| EAWAG-BBD enzyme IDs Swiss Federal Institute of Aquatic Science and Technology Biocatalysis/Biodegradation Database (EAWAG-BBD); contact: GO Ontology editors Maintained in the GO ontology file by GO editorial staff |
Continuous | txt |
| EAWAG-BBD pathway IDs Swiss Federal Institute of Aquatic Science and Technology Biocatalysis/Biodegradation Database (EAWAG-BBD); contact: GO Ontology editors Maintained in the GO ontology file by GO editorial staff |
Continuous | txt |
| EAWAG-BBD reaction IDs Swiss Federal Institute of Aquatic Science and Technology Biocatalysis/Biodegradation Database (EAWAG-BBD); contact: GO Ontology editors Maintained in the GO ontology file by GO editorial staff |
Continuous | no link |
Mappings files provided by external groups
| Mapping | Last update | Download |
|---|---|---|
| COG functional categories Clusters of Orthologous Groups (COG) Constructed by Michael Ashburner and Jane Lomax |
June 2004 | no link |
| Expressed Gene Anatomy Database (EGAD) Constructed by Michael Ashburner |
Oct 2000 | no link |
| E. coli Genome and Proteome functional categories (GenProtEC) Constructed by Heather Butler and Michael Ashburner |
Dec 2000 | no link |
| HAMAP families High-Quality Automated and Manual Annotation of Microbial Proteomes (HAMAP); contact: 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: 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 |
| MultiFun cell function assignment schema classifications Constructed by Michael Ashburner, Jane Lomax and Margrethe Hauge Serres |
Dec 2005 | no link |
| Pfam domains Pfam; contact: 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: 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: 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: 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: 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 |
| Rfam RNA families Rfam Constructed and maintained by Sam Griffiths-Jones and Jennifer Daub |
May 2006 | txt |
| SMART domains SMART; contact: InterPro team This mapping is generated from data supplied by InterPro for the InterPro2GO mapping Citation:Letunic I, Bork P; 20 years of the SMART protein domain annotation resource. Nucleic Acids Res.. Jan 2018;46(D1):D493–D496. [ PMID:29040681 | doi.org/10.1093/nar/gkx922 ] |
Monthly | txt |
| JCVI (TIGRFAM) protein families JCVI (TIGRFAM) protein families Constructed by Michelle Gwinn and other TIGR staff |
Monthly | no link |
| JCVI roles JCVI roles Constructed by Michael Ashburner |
Jan 2004 | no link |
| 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: UniProtKB-GOA team Citation: Huntley RP, Sawford T, Mutowo-Meullenet P, Shypitsyna A, Bonilla C, Martin MJ, O’Donovan C. The GOA database: gene Ontology annotation updates for 2015. Nucleic Acids Res.. Jan 2015;43(Database issue):D1057–1063. [ PMID:25378336 | doi:10.1093/nar/gku1113 ] |
Monthly | txt |
| UniProt subcellular location UniProt; contact: UniProtKB-GOA team Citation: Huntley RP, Sawford T, Mutowo-Meullenet P, Shypitsyna A, Bonilla C, Martin MJ, O’Donovan C. The GOA database: gene Ontology annotation updates for 2015. Nucleic Acids Res.. Jan 2015;43(Database issue):D1057–1063. [ PMID:25378336 | doi:10.1093/nar/gku1113 ] |
Monthly | txt |
Nota Bene. 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.