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Expand Up @@ -5,13 +5,30 @@ redirect_from: /page/download-mappings
---

# Cross-references to external classification systems
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. Please report any errors or suggest alternatives to the [GO helpdesk](https://help.geneontology.org/).
The Gene Ontology (GO) project maps its terms to commonly used bioinformatics resources. These mappings (or "cross-references") help integrate GO annotations with other biological databases and resources, creating a network of information that helps researchers to navigate across data types.

External classification systems mapped to GO terms:

|**Database resource** |**Scope**|**Relevant GO aspect(s)**|**Direct access to mapping file(s)**|
|--------|---------|---------|---------|
|[Enzyme Commission (EC)](https://enzyme.expasy.org/){:target="blank"}| Reactions| Molecular Function |[ec2go](https://geneontology.org/external2go/ec2go)|
|[KEGG: Kyoto Encyclopaedia of Genes and Genomes ](http://www.genome.jp/kegg/){:target="blank"} | Reactions |Molecular Function|[kegg_reaction2go](https://geneontology.org/external2go/kegg_reaction2go)|
|[HAMAP](http://www.expasy.org/sprot/hamap/){:target="blank"} | High-Quality Automated and Manual Annotation of Microbial Proteomes |All aspects | [hamap2go](https://geneontology.org/external2go/hamap2go) |
|[InterPro](http://www.ebi.ac.uk/interpro/){:target="blank"} | Protein families, domains and functional sites. Ecnompasses contributing databases: [PantherDB](https://www.pantherdb.org/), [PFAM](http://pfam.xfam.org/), [PIRSF](https://proteininformationresource.org/pirsf/), [PRINTS], [PROSITE](https://prosite.expasy.org/) and [SMART](https://smart.embl-heidelberg.de/) |All aspects | [interpro2go](https://geneontology.org/external2go/interpro2go)|
|[MetaCyc](http://metacyc.org/){:target="blank"} | Pathways and reactions |Molecular Function & Biological Process | [metacyc2go](https://geneontology.org/external2go/metacyc2go)|
|[Reactome](http://www.reactome.org/){:target="blank"} | Events and catalyst activities|Molecular Function |[reactome2go](https://geneontology.org/external2go/reactome2go)|
|[Rfam - RNA families](http://rfam.xfam.org/){:target="blank"}<br>| RNA entities| All aspects| [rfam2go](https://geneontology.org/external2go/rfam2go)|
|[Rhea](https://www.rhea-db.org/){:target="blank"}| Reactions | Molecular Function|[rhea2go](https://geneontology.org/external2go/rhea2go)|
|[UM-BBD](http://eawag-bbd.ethz.ch/aboutBBD.html){:target="blank"} | Biocatalysis/Biodegradation Database: enzymes, reactions and pathways |Molecular Function & Biological Process|[um-bbd_enzymeid2go](https://geneontology.org/external2go/um-bbd_enzymeid2go)<br>[um-bbd_reactionid2go](https://geneontology.org/external2go/um-bbd_reactionid2go)<br>[um-bbd_pathwayid2go](https://geneontology.org/external2go/um-bbd_pathwayid2go) |
|[UniProt Keywords](https://www.uniprot.org/keywords/){:target="blank"}| Mapping of GO terms to UniProt Knowledgebase keywords. | All aspects| [uniprotkb_kw2go](https://geneontology.org/external2go/uniprotkb_kw2go)|
|[UniProt Subcellular location](https://www.uniprot.org/locations/){:target="blank"}| Mapping of GO terms to UniProt Subcellular location terms | Cellular Component| [uniprotkb_sl2go](https://geneontology.org/external2go/uniprotkb_sl2go)|
|[UniRules](https://www.uniprot.org/help/unirule){:target="blank"}|UniProt Automatic Annotation pipeline| All aspects| [unirule2go](https://geneontology.org/external2go/unirule2go)|
[Wikipedia](https://www.wikipedia.org/){:target="blank"} | General | All aspects | [wikipedia2go](https://current.geneontology.org/ontology/external2go/wikipedia2go)

## Using and citing cross-references and mappings
Direct access to the mappings file directory is available here: [https://current.geneontology.org/ontology/external2go/](https://current.geneontology.org/ontology/external2go/).

If you have used a mapping in a publication or presentation, please ensure that you cite both the GO knowledgebase and the source of the mapping (detailed below). See the [GO citation guide](/docs/go-citation-policy/) for citing the GO knowledgebase.

## Cross-references format
## Cross-references files format

+ Header describing the date generated and the GO release used, for example:

Expand All @@ -21,61 +38,23 @@ If you have used a mapping in a publication or presentation, please ensure that

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

For example:

`EC:1.1.1.1 > GO:alcohol dehydrogenase (NAD) activity ; GO:0004022`
For example: `EC:1.1.1.1 > GO:alcohol dehydrogenase (NAD+) activity ; GO:0004022`

## Mapping types & cardinality
+ Certain types of cross-references to GO mappings can be many-to-many.
+ Cross-references can be one of 4 types: exact, broad, narrow general database cross references
+ **Exact database cross references**: GO and cross reference object have the same meaning.
+ Cardinality: 1:1
+ **Narrow database cross references**: The concept represented by the cross-reference represents a *narrower* or more specific concept than the GO term.
+ Cardinality: 1 GO:n narrow cross-references
+ **Broad database cross references**: The concept represented by the cross-reference represents a *broader* or more general concept than the GO term.
+ Cardinality: n:n
+ **Related database cross references**: The concept represented by the cross-reference is broad in some aspect, narrow in another.
+ Cardinality: n:n
+ Cross references deprecated in the source database should not be included in GO.

+ Note that cross-references to GO mappings can be many-to-many.
## Using and citing cross-references and mappings

## Mappings file directory
If you have used a mapping in a publication or presentation, please ensure that you cite both the GO knowledgebase and the source of the mapping (detailed below). See the [GO citation guide](/docs/go-citation-policy/) for citing the GO knowledgebase.

Direct access to the mappings file directory is available here: [https://current.geneontology.org/ontology/external2go/](https://current.geneontology.org/ontology/external2go/).

## Cross-references maintained by the GO Consortium

Those cross-references are maintained by GO editors. Please report issues in the [GO GitHub tracker](https://github.com/geneontology/go-ontology/issues/new){:target="blank"}.

|**Mapping** |**Entities mapped**|**Direct access to mapping file**|
|--------|---------|---------|
|[EC: Enzyme Commission](https://www.qmul.ac.uk/sbcs/iubmb/){:target="blank"}| EC numbers |[ec2go](https://geneontology.org/external2go/ec2go)|
|[EAWAG-BBD](http://eawag-bbd.ethz.ch/aboutBBD.html){:target="blank"} | Enzymes |[um-bbd_enzymeid2go](https://geneontology.org/external2go/um-bbd_enzymeid2go)|
|[EAWAG-BBD](http://eawag-bbd.ethz.ch/aboutBBD.html){:target="blank"} | Pathways |[um-bbd_pathwayid2go](https://geneontology.org/external2go/um-bbd_pathwayid2go)|
|[EAWAG-BBD](http://eawag-bbd.ethz.ch/aboutBBD.html){:target="blank"} | Reactions |[um-bbd_reactionid2go](https://geneontology.org/external2go/um-bbd_reactionid2go)|
|[KEGG: Kyoto Encyclopaedia of Genes and Genomes ](http://www.genome.jp/kegg/){:target="blank"} | Pathways and reactions  |[kegg_reaction2go](https://geneontology.org/external2go/kegg_reaction2go)|
|[MetaCyc](http://metacyc.org/){:target="blank"} | Pathways and reactions |[metacyc2go](https://geneontology.org/external2go/metacyc2go)|
|[Reactome](http://www.reactome.org/){:target="blank"} | Events and catalyst activities |[reactome2go](https://geneontology.org/external2go/reactome2go)|
|[Rhea](https://www.rhea-db.org/){:target="blank"}|Biochemical reactions |[rhea2go](https://geneontology.org/external2go/rhea2go)|


## Cross-references maintained by external groups

Note: Those files are regenerated during the bi-monthly [UniProtKB-GOA release](https://www.ebi.ac.uk/GOA/){:target="blank"}. Please report issues in the [GO GitHub tracker](https://github.com/geneontology/go-annotation/issues/new).


|**Mapping** |**Direct access to mapping file**|
|--------|---------|
|[HAMAP: High-Quality Automated and Manual Annotation of Microbial Proteomes - Families](http://www.expasy.org/sprot/hamap/){:target="blank"} <br> *Maintainted by the [UniProtKB](https://www.uniprot.org/){:target="blank"} team* <br> [PMID:18849571](http://www.ncbi.nlm.nih.gov/pubmed/18849571){:target="blank"} |[hamap2go](https://geneontology.org/external2go/hamap2go) |
|[InterPro - Protein families, domains and functional sites](http://www.ebi.ac.uk/interpro/){:target="blank"} <br>*Maintainted by the [InterPro](http://www.ebi.ac.uk/interpro/) team* <br>[PMID:18940856](http://www.ncbi.nlm.nih.gov/pubmed/18940856){:target="blank"} |[interpro2go](https://geneontology.org/external2go/interpro2go)|
|[Pfam domains](http://pfam.xfam.org/){:target="blank"} <br>*Maintainted by the [InterPro](http://www.ebi.ac.uk/interpro/) team* <br>[PMID:18940856](http://www.ncbi.nlm.nih.gov/pubmed/18940856){:target="blank"}|[pfam2go](https://geneontology.org/external2go/pfam2go)|
|[PIRSF - Protein superfamilies](http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml){:target="blank"} <br>*Maintainted by the [InterPro](http://www.ebi.ac.uk/interpro/) team* <br>[PMID:18940856](http://www.ncbi.nlm.nih.gov/pubmed/18940856){:target="blank"}|[pirsf2go](https://geneontology.org/external2go/pirsf2go)|
|[PRINTS - Domains](http://www.bioinf.manchester.ac.uk/dbbrowser/PRINTS/){:target="blank"}<br>*Maintainted by the [InterPro](http://www.ebi.ac.uk/interpro/) team* <br>[PMID:18940856](http://www.ncbi.nlm.nih.gov/pubmed/18940856){:target="blank"} |[pirsf2go](https://geneontology.org/external2go/pirsf2go)|
|[ProDom - Domains](http://prodom.prabi.fr/prodom/current/html/home.php){:target="blank"} <br>*Maintainted by the [InterPro](http://www.ebi.ac.uk/interpro/) team* <br>[PMID:18940856](http://www.ncbi.nlm.nih.gov/pubmed/18940856){:target="blank"} |[prodom2go](https://geneontology.org/external2go/prodom2go)|
|[ProSite - Domains](http://www.expasy.ch/prosite/){:target="blank"}<br>*Maintainted by the [InterPro](http://www.ebi.ac.uk/interpro/) team* <br>[PMID:18940856](http://www.ncbi.nlm.nih.gov/pubmed/18940856){:target="blank"} |[prosite2go](https://geneontology.org/external2go/prosite2go)|
|[Rfam - RNA families](http://rfam.xfam.org/){:target="blank"}<br>|[rfam2go](http://geneontology.org/external2go/rfam2go)|
|[SMART - Domains](http://smart.embl-heidelberg.de/){:target="blank"}<br> *Maintainted by the [InterPro](http://www.ebi.ac.uk/interpro/) team* <br>[PMID:29040681](http://www.ncbi.nlm.nih.gov/pubmed/29040681){:target="blank"} |[smart2go](https://geneontology.org/external2go/smart2go)|
|[UniProt Keywords](https://www.uniprot.org/keywords/)<br>Mapping of GO terms to UniProt Knowledgebase keywords. <br>*Maintainted by the [UniProt](http://www.uniprot.org/){:target="blank"} and [UniProtKB-GOA](https://www.ebi.ac.uk/GOA/){:target="blank"}* <br> [PMID:25378336](https://www.ncbi.nlm.nih.gov/pubmed/25378336){:target="blank"} |[uniprotkb_kw2go](https://geneontology.org/external2go/uniprotkb_kw2go)|
|[UniProt Subcellular location](https://www.uniprot.org/locations/)<br> Mapping of GO terms to UniProt Subcellular location terms. <br>*Maintainted by the [UniProt](http://www.uniprot.org/){:target="blank"} and [UniProtKB-GOA](https://www.ebi.ac.uk/GOA/)*{:target="blank"}<br>[PMID:25378336](https://www.ncbi.nlm.nih.gov/pubmed/25378336){:target="blank"} |[uniprotkb_sl2go](https://geneontology.org/external2go/uniprotkb_sl2go)|
|[UniRules](https://www.uniprot.org/unirule/)<br> Mapping of GO terms to UniProt Subcellular location terms. <br>*Maintainted by the [UniProt](http://www.uniprot.org/){:target="blank"} team* |[unirule2go](https://geneontology.org/external2go/unirule2go)|


## Archived cross-references

|**Mapping** |**Last update** |**Direct access to mapping file**|
|--------|------------|---------|
|**COG - Functional categories** <br>[Clusters of Orthologous Groups (COG)](https://www.ncbi.nlm.nih.gov/COG/index.html){:target="blank"}<br> *Constructed by Michael Ashburner and Jane Lomax* |June 2004 | cog2go|
|**EGAD: Expressed Gene Anatomy Database** <br> *Constructed by Michael Ashburner* | Oct 2000 | egad2go|
|**GenProtEC: E. coli Genome and Proteome functional categories** <br>*Constructed by Heather Butler and Michael Ashburner*|Dec 2000 |genprotec2go|
|**TIGRFAM: JCVI protein families**<br>[JCVI (TIGRFAM) protein families](https://www.jcvi.org/publications/tigrfams-protein-family-resource-functional-identification-proteins){:target="blank"}<br>*Constructed by Michelle Gwinn and other TIGR staff*| NA | tigrfams2go|
|**JCVI roles**<br>[JCVI roles](https://www.jcvi.org/){:target="blank"}<br> *Constructed by Michael Ashburner*|Jan 2004 | tigr2go|
|**MIPS FunCat**<br>[MIPS Functional Catalogue (FunCat)](http://mips.gsf.de/funcatDB/){:target="blank"}<br> *Constructed by Michael Ashburner and Midori Harris*|NA| mips2go|
|**MultiFun cell function assignment schema classifications**<br> *Constructed by Michael Ashburner, Jane Lomax and Margrethe Hauge Serres*|Dec 2005 | multifun2go|