Importing GO terms from UniProt to a PGDB Markus Krummenacker Bioinformatics Research Group SRI International kr@ai.sri.com

GO in EcoCyc Introduction GO (http://geneontology.org) is used widely to annotate gene products with functions, processes, and cellular locations Manual curation of GO annotations in EcoCyc:

UniProtKB GO annotations GO consortium hosts UniProtKB annotations file Big, several GB. grep file for E. coli taxon ID Import code maps UniProtKB IDs to EcoCyc gene products, via DBLINKs of the products Most imported GO annots have comp. evidence Comp. ev. annots get timestamps bumped up (because they expire after 1 yr.) Suppress comp. ev. annots if redundant with an existing exp. ev. annot Prune comp. ev. annots if a more specific annot of the same kind exists (several dozens)

EcoliWiki – EcoCyc collaboration Collaboration with Jim Hu / EcoliWiki Workflow: GO UniProtKB  EcoCyc EcoCyc exports GO annots file EcoCyc GO annots  EcoliWiki Merging of EcoCyc and additional EcoliWiki annots EcoliWiki  GO consortium, deposit file for E. coli Annots are absorbed into UniProtKB Repeat in half a year

Open Issues Round-trip problem of deleted annots EcoCyc curator deletes an annot, because wrong EcoliWiki should detect this. Protocol not clear yet. For now: UniProtKB import into EcoCyc checks history logs, to prevent annot addition if that annot was deleted in the past No EcoCyc support yet for some qualifiers: NOT Contributes_to No easy user interface yet for annot import

Do it Yourself Disclaimer: Has never been tried outside of EcoCyc Prepare input file (using grep). DBLINKS need to exist on gene products. (add-go-terms-to-monomers (incorporate-ecocyc-go-terms-from-GOAFF-file :filename “…../gene_association.goa” :db-type ‘UNIPROT) ) (save-kb) (loop for p in (all-frames-that-could-contain-go-annots) do (prune-unnecessary-go-terms p :destructively-prune! t))