[ensembl-dev] Gene Ontology attributes in biomart

Sébastien Moretti sebastien.moretti at unil.ch
Thu Jun 23 15:35:55 BST 2011

> 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

Thanks for these info. We will modify our scripts accordingly.
And yes, a more sensible name would be better to guess the meaning of 
the attribute.


>> 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 Now, it seems they have been replaced by: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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