1. Bioinformatics Research Group
GO Annot Import
Markus Krummenacker
Bioinformatics Research Group
SRI, International
Q3 2014 1 1

2. Preparation The PGDB has to have UniProt dblinks on the proteins
mkdir ~/go-import/
Download the UniProt GO file (in GAF format)
curl 'ftp://ftp.geneontology.org/pub/go/gene-associations/submission/gene_association.goa_uniprot.gz' -o gene_association.goa_uniprot.gz
Find the NCBI Taxonomy ID of your PGDB
Filter out the GO annot by the NCBI ID:
zgrep taxon:85962 gene_association.goa_uniprot.gz |cat > gene_association.goa_uniprot_85962
(The UNIX command above should be all on 1 line.)
The NCBI ID in the example was (HPY) 2 2

3. Running the GO Annot Import
Start pathway-tools –lisp
Open the target PGDB
At the LISP prompt, run the following command:
(update-uniprot-go-annots “~/go-import/”)
Expects the GAF input file to have the specific name:
gene_association.goa_uniprot_ (ends in NCBI ID) 3 3

4. Workflow Write gene_association.ecocyc-before file
Read input GAF and map UniProt IDs to PGDB protein monomer frames
Write raw-go-terms lisp file
Run GO-stats
Add GO annots to the protein frames
Prune redundant EV-COMP annots (less specific parent GO terms) 4 4

5. Workflow (cont’d) Remove annots that are no longer in UniProt
Run GO-stats
Import or download citations (PMID etc.) 5 5