Subcellular locations SPSL2GO

Method

The mapping of UniProt subcellular location terms to GO terms started in November 2007, in collaboration with the Swiss Institute of Bioinformatics. Subcellular location terms from the Comment (CC) lines of UniProtKB entries are manually mapped to GO terms. The mapping is then applied electronically to enhance the electronic GO annotation in our UniProtKB-GOA releases. GO annotations using this technique will receive the evidence code Inferred from Electronic Annotation (IEA).

UniProt Subcellular Location comments are applied to the Swiss-Prot section of the UniProt KnowledgeBase manually by Swiss-Prot curators. Subcellular location comments in TrEMBL come from automatic annotation, either from manually created or the automatically created rules.

GO Reference

The GO reference for this method is GO_REF:0000023. Abstracts for all GO references can be seen here.

Mapping file

The spsl2go mapping file is available from the UniProtKB-GOA ftp site: ftp://ftp.ebi.ac.uk/pub/databases/GO/GOA/external2go/spsl2go

Example

The Swiss-Prot Subcellular Location (SPSL) identifier for ‘nucleus’ is SL-0191. The definitions of ‘nucleus’ in both SPSL and GO were compared by a curator and found to be equivalent, therefore the GO term ‘nucleus’ (GO:0005634) was manually mapped to SL-0191. Any protein in UniProtKB, such as ELP4 (see Fig. 1), which contains ‘nucleus’ in its CC lines will automatically be assigned the GO term ‘nucleus’.

Exceptions

Currently annotations from Subcellular Location to isoforms are only mapped up to the main UniProtKB entry not to the specific isoform identifier.

Annotations

The annotations created by Subcellular Location2GO mapping are displayed in the UniProtKB-GOA gene association files (Fig. 1), the Swiss-Prot Subcellular Location identifier will be indicated in column 8 ('With') and column 6 (DB:Reference) will indicate that this method has the GO reference: GO_REF:0000023. Subcellular Location2GO annotations can also be viewed in QuickGO.

Figure 1. Representation of an Subcellular Location2GO annotation in the gene association file.