[ensembl-dev] REST Service and Ontology

[Saren Tasciyan]

Hi Andy,

Thanks a lot for this fast answer. This helps a lot and also makes me 
understand the logic of REST Service better. I have expected there to be 
a separate method and did not think GO terms as an external DB.

Cheers,
Saren

Am 30.07.2013 16:30, schrieb Andy Yates:
> Hi Sarah,
>
> The ontology endpoint helps you retrieve terms from our parsed OBO ontology database. You can think of it as a publicly accessible record of our view on an ontology for a given release. GO terms are linked to translations as refs. They can be accessed via the /xrefs/id/:id endpoint e.g.
>
> http://beta.rest.ensembl.org/xrefs/id/ENST00000288602.json?external_db=GO;all_levels=1
>
> The external_db param is set to GO meaning we just want GO xrefs. all_levels means we will query both the transcript & linked translations for this type of xref. Once you have a GO term you can use the ontology endpoint to get more information such as description, parents & children e.g.
>
> http://beta.rest.ensembl.org/ontology/id/GO:0000186.json
>
> Hope this helps & thanks for the kind words :)
>
> Andy
>
> Andrew Yates                   Ensembl Core Software Project Leader
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensembl.org/
>
> On 30 Jul 2013, at 14:57, Saren Tasciyan <saren.tasciyan at univie.ac.at> wrote:
>
>> Hi,
>>
>> This is the first time I post here. First of all, thanks for the REST service, it makes life less complicated. However, I was trying to find (Gene) Ontology queries but I am unsuccessful so far. Are there any way to retrieve GO Terms? There are methods, such as:
>> GET ontology/id/:id
>> GET ontology/name/:name
>> etc...
>> But I could not find any, where I can get GO Terms for a particular transcript/gene. Excuse me if I am too blind to see.
>>
>> Regards,
>> Saren
>> -- 
>> Saren Tasciyan
>>
>> Master Student & IT Technician at Karl Kuchler Group
>> Room: 2.107
>>
>> Max F. Perutz Laboratories GmbH
>> Dr. Bohr-Gasse 9
>> A-1030 Wien
>>
>> T: +43-1-4277- 61812
>> E:
>> saren.tasciyan at univie.ac.at
>>
>> E:
>> saren.tasciyan at meduniwien.ac.at
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-- 
Saren Tasciyan

Master Student & IT Technician at Karl Kuchler Group
Room: 2.107

Max F. Perutz Laboratories GmbH
Dr. Bohr-Gasse 9
A-1030 Wien

T: +43-1-4277- 61812
E: saren.tasciyan at univie.ac.at
E: saren.tasciyan at meduniwien.ac.at