[BioC] Gene ID of yeast in GOSemSim and other GO related package may need update

Gang Chen chen.gang1983 at gmail.com
Tue Sep 8 14:17:48 CEST 2009

Hi All,

I met a problem when I try to use GOSemSim and GOSim to calculate the
GO semantic similarities between yeast proteins. Both of the two
packages work well on other organisms.

I use biomaRt package to map the Swiss Acc name to NCBI gene ID.
Unfortunately, when I use GOSemSim and GOSim package to calculate the
semantic similarity between genes, both of the two packages told me
that none of these genes has GO annotation. I check this manually and
found that nearly all yeast genes in NCBI database have been updated
at 6th, September. Therefore, I think related annotation packages in
Bioconductor need update to solve this problem.

I wonder if there is any other way to solve this problem? Any comments
or advice are welcome.

Thanks the developers of these packages.

Gang Chen
Gang Chen
Computer Science Ph.D Candidate
Central South University, Changsha, China
E-mail: chen.gang1983 at gmail.com
Cell Phone:13574886823

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