[BioMart Users] Gene Ontology attributes in biomart

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[BioMart Users] Gene Ontology attributes in biomart

Moretti 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Now, it seems they have been replaced by: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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Re: [BioMart Users] Gene Ontology attributes in biomart

Junjun Zhang
Cc'ing to Ensembl helpdesk. They should be able to answer this question.

Junjun


On 11-06-23 9:03 AM, "Sébastien Moretti" <[hidden email]> 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Now, it seems they have been replaced by: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/
>_______________________________________________
>Users mailing list
>[hidden email]
>https://lists.biomart.org/mailman/listinfo/users

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Re: [BioMart Users] [ensembl-dev] Gene Ontology attributes in biomart

Rhoda Kinsella
In reply to this post by Moretti Sébastien
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/
>
> _______________________________________________
> Dev mailing list    [hidden email]
> List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.

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Re: [BioMart Users] [ensembl-dev] Gene Ontology attributes in biomart

Moretti Sébastien
> 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/
_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users