[BioC] org.Dm.egACCNUM2EG

[Marc Carlson]

Tiandao Li wrote:
> Hello,
>
> Recently I installed org.Dm.eg.db for GO analysis. My sequences were 
> blasted against siwssprot, using the following format in the annotation 
> part of genepix files
>
> ID	Name
> 16A-A02.g	P80096
> 16A-A03.g	Q9U572
> ...
>
> I tried org.Dm.egACCUM2EG$"P80096" to get Entrez gene id. and it came with 
> NULL. How can I get EG from swissprot acc?
>
> Thanks,
>
> Tiandao
>
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>   
I am afraid that the answer is that the ACCNUM maps are for genbank IDs
only.  Because of the way that NCBI handles genebank and its affiliated
nucleotide sequences, genebank accessions are sometimes connected to
TrEMBL (translated sequences), but never to Swissprot IDs.  Swissprot
IDs have not been included in our annotation packages before.  In the
past, the focus of the annotation packages has been to make them
gene-centric and so to date no protein-centric IDs have been included in
these packages.

However, the data packages are a work in progress and we are always
interested in user feedback to make them better.  Do you feel that there
is a wide reaching need for the associated protein IDs to be mapped in
to these annotation packages?  If you feel this is so, please let us
know what you think. 

In the meantime I believe that the biomart package can be used for
mapping your swissprot IDs.

    Marc