[ensembl-dev] REST Service and Ontology

[Andy Yates]

Hi Saren,

It's obvious if you've come from the Perl API since GO terms are linked to objects via the xref schema. Coming fresh into Ensembl the link isn't anywhere near as obvious. Also apologies I mis-read your name. Sorry if this caused any offence

All the best,

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 16:32, Saren Tasciyan <saren.tasciyan at univie.ac.at> wrote:

> 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
> 
> 
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