[BioC] ENSEMBL-centered annotations, how to?

[Marc Carlson]

Hi Guido,

It is true that the libraries built by AnnotationDbi will be 
NCBI-centric, but I have also recently improved them by also including 
Ensembl gene IDs.  If you need more information, the organism based 
packages have maps for even more Ensembl information in them (transcript 
and protein IDs) that you can use in a platform agnostic fashion. 

Hope this helps,


    Marc




Hooiveld, Guido wrote:
>  
> Dear list,
> Has anyone a pointer on a library that can be used to create annotation
> packages based on ENSEMBL IDs? Like the tools embedded in
> 'AnnotationDbi' / 'AnnBuilder', but using info directly available from
> ENSEMBL instead of NCBI?
>  
> I do know that biomaRt can be used to query ENSEMBL, but AFAIK this can
> not be used to build annotation libraries.
>  
> Thanks,
> Guido
>
> ------------------------------------------------ 
> Guido Hooiveld, PhD 
> Nutrition, Metabolism & Genomics Group 
> Division of Human Nutrition 
> Wageningen University 
> Biotechnion, Bomenweg 2 
> NL-6703 HD Wageningen 
> the Netherlands 
> tel: (+)31 317 485788 
> fax: (+)31 317 483342 
> internet:   http://nutrigene.4t.com <http://nutrigene.4t.com/>  
> email:      guido.hooiveld at wur.nl 
>
>
>
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