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

Tue May 20 12:02:32 BST 2014

Yes I am making pauses inbetween queries. I am also thinking to switch 
from xml to json, as it seems to be more resource "efficient".

Am 19.05.2014 19:35, schrieb Cook, Malcolm:
>
> 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
>     <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
>         <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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-- 
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
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