[ensembl-dev] REST API: Feature ID returns multiple results

[mag]

Hi Saren,

The feature look up will return all features of the given object type 
that overlap your queried region.

In your example, the region is the input gene and two transcripts 
overlap this region.

To retrieve the gene linked to a transcript, I would recommend using 
'feature=transcript' instead
Among the fields returned, there is a 'Parent' field that will specify 
which gene the transcript belongs to.

http://beta.rest.ensembl.org/feature/id/ENSMUST00000163188?feature=transcript;content-type=text/xml
<dataID="ENSMUST00000163188"Parent="ENSMUSG00000057729"biotype="processed_transcript"description=""end="79883041"external_name="Prtn3-004"feature_type="transcript"logic_name="havana"seq_region_name="10"source="ensembl_havana"start="79874476"strand="1"/>

This will still return more transcripts than your input, but you will be 
able to uniquely associate each transcript to its gene.


Hope that helps,
Magali

On 19/05/2014 10:00, Saren Tasciyan wrote:
> Hi,
>
> I am using REST API for my Java application, however I am stuck with a 
> problem:
> I have a list of transcript IDs (ENSMUST....) from which, I want to 
> gather gene IDs. So I have decided to use following endpoint:
> http://beta.rest.ensembl.org*/feature/id/ENSMUST00000163188**?feature=gene*;content-type=text/xml
> as you can see that this returns 2 IDs:
>
> <opt>
> <dataID="ENSMUSG00000035835"biotype="protein_coding"description="cDNA 
> sequence BC005764 [Source:MGI 
> Symbol;Acc:MGI:2388640]"end="79874634"external_name="BC005764"feature_type="gene"logic_name="ensembl_havana_gene"seq_region_name="10"source="ensembl_havana"start="79860475"strand="-1"/>
> <dataID="ENSMUSG00000057729"biotype="protein_coding"description="proteinase 
> 3 [Source:MGI 
> Symbol;Acc:MGI:893580]"end="79883174"external_name="Prtn3"feature_type="gene"logic_name="ensembl_havana_gene"seq_region_name="10"source="ensembl_havana"start="79874476"strand="1"/>
> </opt>
>
> When queried from Ensembl website I "only" get one result:
> http://www.ensembl.org/Mus_musculus/Transcript/Summary?db=core;g=ENSMUSG00000057729;r=10:79874476-79883041;t=ENSMUST00000163188
>
> My idea, when I first ran into this problem was to use logic_name as 
> an indicator, as this problem is even more frequent with ncrna, etc. 
> However both results here have same logic_name.
> Correct results would be "according to my dataset" the second one. Am 
> I using a wrong approach here or should I include more parameters in 
> my query?
>
> As an example here are more queries with multiple results:
> http://beta.rest.ensembl.org/feature/id/ENSMUST00000040746?feature=gene;content-type=text/xml
> http://beta.rest.ensembl.org/feature/id/ENSMUST00000075162?feature=gene;content-type=text/xml
> http://beta.rest.ensembl.org/feature/id/ENSMUST00000080673?feature=gene;content-type=text/xml
> http://beta.rest.ensembl.org/feature/id/ENSMUST00000118639?feature=gene;content-type=text/xml
>
> Cheers,
> 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
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140519/fd24c2b7/attachment.html>