Subcellular Location2GO

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 UniProt-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 UniProt curators. Subcellular location comments in TrEMBL come from automatic annotation, either from manually created or the automatically created rules.

The UniProtKB-SL2GO mapping file is available at:
ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/uniprotkb_sl2go

Example. The UniProtKB-Subcellular Location (UniProtKB-SL) identifier for ‘nucleus’ is SL-0191. The definitions of ‘nucleus’ in both UniProtKB-SL 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.

The annotations created by Subcellular Location2GO mapping are displayed in the UniProt-GOA gene association files (Fig. 1), the UniProtKB-Subcellular Location identifier will be indicated in column 8 ('With') and column 6 (DB:Reference) will indicate that this method has either GO reference: GO_REF:0000039 or GO_REF:0000040 depending on whether the subcellular location is applied to a curator reviewed (UniProtKB/Swiss-Prot) or unreviewed (UniProtKB/TrEMBL) entry. Subcellular Location2GO annotations can also be viewed in QuickGO .

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

Database Object ID Object Symbol Qualifier GO ID Reference Evidence 'With' Column
UniProt Q96EB1 ELP4_HUMAN   GO:0005634 GO_REF:0000039 IEA UniProtKB-SL:SL-0191

 

Aspect Object Name Object Synonym Object Type Taxon ID Date Source DB
C

ELP4, C11orf19, PAXNEB: Elongator complex protein 4

IPI00061376 protein taxon:9606 20080521 UniProtKB

spacer