[Bioc-devel] About annotation package mapping different types of gene identifiers

Nianhua Li nli at fhcrc.org
Fri Mar 30 01:42:25 CEST 2007

Pan Du wrote:
> Hi Seth,
> Is there any annotation packages mapping different types of gene
> identifiers, for example from gene symbol to Refseq, unigene to refseq, or
> other combination? I think they are really useful in the practice.
> Currently, we have to use some websites to do batch retrieve, which is not
> convenient. Actually, when using AnnBuilder to build annotation packages,
> all of these information has been retrieved. So why not build a package for
> each common organism?
> Thanks!
> Pan
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> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

Hi, Pan,

We already have some in the LLMappings packages (e.g.
humanLLMappings). But they only provide GenBank accessions, go,
UniGene and PubMed mappings to Entrez Gene. We will provide three new
SQLite-based annotation packages in the next release (in a month), for
human, mouse and rat, respectively. Their structure will be similar to
affymetrix gene chip annotation packages such as hgu95av2, but the
index will be Entrez Gene ID instead of probeset ID. Stay tuned...



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