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Now, it seems they have been replaced by: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.
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