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Importing GO terms from UniProt to a PGDB. Markus Krummenacker Bioinformatics Research Group SRI International [email protected]. GO in EcoCyc Introduction. GO ( http://geneontology.org ) is used widely to annotate gene products with functions, processes, and cellular locations - PowerPoint PPT Presentation
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SRI International Bioinformatics1
Importing GO terms from UniProt to a PGDB
Markus Krummenacker
Bioinformatics Research Group
SRI International
SRI International Bioinformatics2
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:
SRI International Bioinformatics3
UniProtKB GO annotations
GO consortium hosts UniProtKB annotations fileBig, several GB. grep file for E. coli taxon IDImport code maps UniProtKB IDs to EcoCyc gene
products, via DBLINKs of the productsMost imported GO annots have comp. evidenceComp. ev. annots get timestamps bumped up
(because they expire after 1 yr.)Suppress comp. ev. annots if redundant with an
existing exp. ev. annotPrune comp. ev. annots if a more specific annot
of the same kind exists (several dozens)
SRI International Bioinformatics4
EcoliWiki – EcoCyc collaboration
Collaboration with Jim Hu / EcoliWikiWorkflow:
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
SRI International Bioinformatics5
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
SRI International Bioinformatics6
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))
