[ensembl-dev] Fwd: Queries regarding API

[Emily Pritchard]

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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