[ensembl-dev] Fwd: Queries regarding API

[Magali]

Hi Taruna,

With the rest API, you are retrieving all the exons for a gene, in this
case ENSG00000146648.

That gene has in turn 11 transcripts, ENST00000275493 is one of them.

So with the rest API, you will get all exons for all 11 transcripts.
But you can see that, from the 154 lines the rest API returns, 28 are
for transcript ENST00000275493, the others are for the other transcripts.


Hope that helps,
Magali

On 27/06/13 08:35, Taruna Kewalya wrote:
> Hello
> I am Taruna Kewalya student of B.Tech. Bioinformatics doing a research
> work over gene-transcript-protein relations, I am referring rest API
> 1.3.2 and with your help I retrieved many valuable data. While
> studying about exons I understood the chromosomes coordinate concept
> which you have send me in the last reply. Now I am facing a problem of
> getting accurate length of
> exons. http://beta.rest.ensembl.org/feature/id/ENSG00000146648?feature=exon;content-type=text/xml in
> this we are given start and end coordinates of genomic DNA referring
> exons, but in online result we are shown that for a particular
> transcript just like ENST00000275493
> has 28 exons whereas the chromosome coordinates say that there are 264
> positions for exons. So please let me know how to relate both the
> number of exons with each other as they shown a big variation.
> Thanking you
>
>
> On Thu, Jun 27, 2013 at 7:32 AM, Taruna Kewalya
> <kewalyataruna at gmail.com <mailto:kewalyataruna at gmail.com>> wrote:
>
>
>
>     ---------- Forwarded message ----------
>     From: *Emily Pritchard* <emily at ebi.ac.uk <mailto:emily at ebi.ac.uk>>
>     Date: Mon, Jun 24, 2013 at 6:43 PM
>     Subject: Re: [ensembl-dev] Fwd: Queries regarding API
>     To: dev at ensembl.org <mailto:dev at ensembl.org>
>
>
>     Hi Taruna
>
>     The REST link you've used asks for all the exons in a gene. The
>     script returns these in a per-transcript manner, which means that
>     some exons will appear more than once as they appear in more than
>     one transcript.
>
>     Let's take a look at the first line of the output:
>     {"ID":"ENSE00001633131","feature_type":"exon","Parent":"ENST00000455089","ensembl_phase":"-1","end":55087058,"seq_region_name":"7","ensembl_end_phase":"1","strand":1,"constitutive":"0","rank":"1","start":55086714},
>
>     This firstly gives me the exon ID, then tells me that it is an
>     exon. The parent is the ID of the transcript that this exon is
>     found in. The start and end coordinates refer to the genomic
>     position of the exon, with the seq_region_name referring to the
>     chromosome number, and strand indicating if it's on the positive
>     (1) or negative (-1) strand. The phases refer to the position of
>     the start and end of the exon in the codons. The rank is the
>     position of the exon in the transcript.
>
>     These are complete exons of the cDNA. Some of the them will
>     include the UTRs of the transcripts and some will be of non-coding
>     transcripts.
>
>     Hope this helps
>
>     Emily
>     Ensembl helpdesk
>
>
>     On 24/06/2013 13:20, Taruna Kewalya wrote:
>>
>>
>>     ---------- Forwarded message ----------
>>     From: *Taruna Kewalya* <kewalyataruna at gmail.com
>>     <mailto:kewalyataruna at gmail.com>>
>>     Date: Thu, Jun 20, 2013 at 11:33 AM
>>     Subject: Queries regarding API
>>     To: dev at ensembl.org <mailto:dev at ensembl.org>, ktaylor at ebi.ac.uk
>>     <mailto:ktaylor at ebi.ac.uk>
>>
>>
>>     Hello
>>     I am Taruna Kewalya, student of Bioinformatics doing a research
>>     work on gene and transcript. Thank you for your reply it helped
>>     me in finding the details properly but now I am stuck with a new
>>     problem. I have downloaded the Rest API 1.3.2
>>     link http://beta.rest.ensembl.org/feature/id/ENSG00000146648?feature=exon;content-type=application/json 
>>     this shares a common parent id. So please let me know what is it
>>     relating to? The transcript belongs to cdna or cds or genomic and
>>     please let me know what this parent id refers to? And please also
>>     let me know how to understand the starting and ending position of
>>     exons in a Fasta sequence.
>>     Thanking you
>>
>>
>>
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>
>     -- 
>     Dr Emily Pritchard
>     Ensembl Outreach Officer
>
>     EMBL - European Bioinformatics Institute
>     Wellcome Trust Genome Campus
>     Hinxton
>     Cambridge
>     CB10 1SD
>     UK 
>
>
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>
>
>
>
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