1. Importing GO terms from UniProt to a PGDB
Markus Krummenacker
Bioinformatics Research Group
SRI International

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

3. 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)

4. 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

5. 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

6. 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))