[ensembl-dev] REST Service and Ontology

[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
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> saren.tasciyan at univie.ac.at
> 
> E: 
> saren.tasciyan at meduniwien.ac.at
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