[BioC] Genbank accessions for GOstuff

[Nianhua Li]

adlai burman <fsajb4 at ...> writes:

> 
> The GO packages seem to rely solely on LocusLink ids but there are a 
> host of onboard affy translators. Now LL seems to be deprecated and I 
> don't use affymetrix. I have thousands of genes which I would love to 
> continue using with BioC. Does anyone know of a mapping somewhere where 
> I can batch convert gb nums or gene symbols in a way that R's GO 
> packages will accept. Thanks in advance.
> 
> AB
> 
Hi, adlai,

ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2accession.gz gives GenBank to Entrez
Gene mapping

ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz gives gene symbol to Entrez
Gene mapping

GO package gives the GO to Entrez Gene mapping even though the environment name
is GOLOCUSID. It will be fixed in next release.

However, I think biomaRt is much more handy for your case.

HTH

nianhua