[Bioperl-l] Conversion of Wormbase Gene ID into Ensembl Gene ID with BioPerl

[William Spooner]

On 10 Dec 2008, at 06:40, Gundala Viswanath wrote:

> Dear all,
>
> I want to convert Wormbase Gene Id such as these:
>
WBGene00004094
WBGene00018862
WBGene00011061
>
> into Ensemblized ID.
>
> I can't seem to find such a method in Ensembl API.
>
> At the end of the day, I just want to extract the position
> of these genes from Ensembl database via the API.
>
> - Gundala Viswanath
> Jakarta - Indonesia
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> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l


Hi Gundala,

The Ensembl C. elegans database is a mirror of wormbase's, so a good  
place to look is WormMart. See, for example, this query;

http://biomart.wormbase.org/biomart/martview?VIRTUALSCHEMANAME=WS190&ATTRIBUTES=wormbase_gene.default.attributes.gene 
|wormbase_gene.default.attributes.public_name| 
wormbase_gene 
.default 
.attributes 
.sequence_name 
&FILTERS 
=wormbase_gene.default.filters.species_selection."Caenorhabditis  
elegans"| 
wormbase_gene 
.default.filters.gene."WBGene00004094,WBGene00018862,WBGene00011061"| 
wormbase_gene 
.default.filters.identity_status."Live"&VISIBLEPANEL=resultspanel
For details on how to do this programatically, see the 'Perl' button  
on the mart interface.
All the best,
Will




---
William Spooner
Visiting Scientist
whs at ebi.ac.uk