The mapping of UniPathway pathway terms to GO terms started in 2009, in collaboration with the Swiss Institute of Bioinformatics, INRIA (Rhone-Alpes) and Laboratoire d'Ecologie Alpine (Grenoble),
UniPathway is a manually curated resource of enzyme-catalyzed and spontaneous chemical reactions that provides a hierarchical representation of metabolic pathways and a controlled vocabulary for pathway annotation in UniProtKB.(http://www.grenoble.prabi.fr/obiwarehouse/unipathway).
UniPathway data are cross-linked to existing metabolic resources such as ChEBI/Rhea, KEGG and MetaCyc.
UniPathway pathway terms from the ‘Pathway’ Comment 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).
The UniPathway2GO mapping file is available at: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/external2go/unipathway2go
Example. The UniPathway identifier for ‘glycogen biosynthesis’ is UPA00164. The definition of ‘glycogen biosynthesis’ in UniPathway was manually compared to the definition of ‘glycogen biosynthetic process’ in the GO and found to be equivalent, therefore the GO term ‘glycogen biosynthetic process’ (GO: 0005978) was manually mapped to UPA00164. For UniPathway pathway terms that could not be mapped to an existing term, a new GO term was created. Any protein in UniProtKB, such as glgC (see Fig. 1), which contains ‘glycogen biosynthesis’ in its CC lines will automatically be assigned the GO term ‘glycogen biosynthetic process’.
Exceptions : Currently annotations from UniPathway to isoforms are only mapped up to the main UniProtKB entry not to the specific isoform identifier.
The annotations created by UniPathway2GO mapping are displayed in the UniProt-GOA gene association files (Fig. 1), the UniPathway identifier will be indicated in column 8 ('With') and column 6 (DB:Reference) will indicate this method by the GO reference GO_REF:0000041.
UniPathway2GO annotations can also be viewed in QuickGO .
Figure 1. Representation of a UniPathway2GO annotation in the gene association file.
|Database||Gene Product ID||Symbol||Qualifier||GO Identifier||Reference||Evidence||'With' Column|
|Aspect||Object Name||Object Synonym||Object Type||Taxon ID||Date||Source DB|
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