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

Cook, Malcolm MEC at stowers.org
Mon May 19 18:35:44 BST 2014


Careful there, since, you might not get the response your application needs if you have "too many" queries, due to throttling at, if memory serves, three queries per second.



From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Saren Tasciyan
Sent: Monday, May 19, 2014 8:02 AM
To: dev at ensembl.org
Subject: Re: [ensembl-dev] REST API: Feature ID returns multiple results

This allows me to filter unwanted results out. I can ignore entries with different IDs.
This approach seems to be working perfectly. Also my understanding for the usage of feature=... was a bit wrong.

Thanks a lot Magali!

Saren
Am 19.05.2014 12:29, schrieb 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
<data ID="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>
<data ID="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"/>
<data ID="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<mailto:saren.tasciyan at univie.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<mailto:saren.tasciyan at univie.ac.at>
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