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 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 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 .