[Feedback] Site Feedback: GO annotations

[feedback at gramene.org]

URL         : http://www.gramene.org/

Subject     : Site Feedback: GO annotations

Name        : Terence Murphy

Email       : murphyte at ncbi.nlm.nih.gov

Organization: NCBI

Comments    : 

Hi Gramene -- I head the Gene project at NCBI, and I'm trying to connect your GO annotations (downloaded from geneontology.org) to our current annotation. For Oryza sativa Japonica Group (txid39947), the current genome annotation available in INSDC (via DDBJ) I believe is from RAP-DB, submitted on the IRGSP-1.0 assembly which was submitted about a year ago. That annotation includes /gene identifiers like  Os06g0275000, and /locus_tag identifiers like  OSNPB_060275000 (the two can be inter-converted with a few string manipulations).

For the current GO data downloaded from:
http://geneontology.org/gene-associations/gene_association.gramene_oryza.gz

And restricting to annotations for taxon:39947, I see a Os##g####### type identifier in column 3 or 11 for about half of the genes. Would you be able to include the Os##g####### type identifiers for the rest of the genes? Some of those include identifiers like "LOC_Os03g54960" in column 11, or "OSJNBa0050N08.1" in column 3, which I think are from an older assembly and annotation. Would you be able to connect your old GO annotations to the latest genome annotation, at least as synonyms (column 11) if not as the primary identifiers in column 3?

Thanks for your help

http://www.warelab.org/bugs/view.php?id=5514