[ensembl-dev] Gene Ontology attributes in biomart

[Rhoda Kinsella]

Hi Sébastien
We noticed that there was a bug in the previous set up and after some  
consultation with individuals from the GO team, we decided to merge  
the three domains into one. We have introduced the GO domain (i.e.  
namespace_1003) so that users know what domain the information comes  
from. The namespace is the name of the column from the ontology table  
in the ensembl_ontology database from which we get the domain name.  
The martbuilder software adds a number suffix onto all columns, I  
guess to make each column unique. Hence the ( _1003) attached to the  
namespace. I can change this to a more sensible name for release 64 as  
it is too late to make changes for release 63. I hope that answers  
your questions but please feel  free to contact me should you require  
more information.
Regards
Rhoda

On 23 Jun 2011, at 14:03, Sébastien Moretti wrote:

> Hi
>
> I have noticed some changes in biomart regarding Gene Ontology  
> filters.
> Previously, these attributes were available:
> go_biological_process_id
> go_cellular_component_id
> go_molecular_function_id
>
>
> Now, it seems they have been replaced by:
> go_id
> namespace_1003
>
>
> Do you plan to change them again (come back to previous attributes) ?
> What does 1003 mean ?
>
> Best regards
>
> -- 
> Sébastien Moretti
> SIB Vital-IT EMBnet, Quartier Sorge - Genopode
> CH-1015 Lausanne, Switzerland
> Tel.: +41 (21) 692 4079/4221
> http://www.vital-it.ch/ http://ch.embnet.org/ http://myhits.vital-it.ch/
>
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.