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.
Regards
Sébastien
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Now, it seems they have been replaced by: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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