[ensembl-dev] Finding RefSeq transcripts from gene symbol

[Andrew Yates]

Hi Erik,

This depends on what you are trying to get a hold of since we do not hold the link from symbol to RefSeq in our databases. We do store the link between symbol and ENST as you have noted below. Perhaps the best workflow I can suggest is the one you have outlined below to identify the Ensembl transcript that is linked to the RefSeq. Also are you aiming to get the RefSeq transcripts back or the linked ENST?

As for the attributes I do not believe these are currently available via the REST API. We will look into making them available since they would be useful to have access to.

Andy

> On 13 Oct 2015, at 14:50, Erik Severinsen <erik.severinsen at medisin.uio.no> wrote:
> 
> What is the best strategy to get RefSeq transcripts given a gene symbol using the Rest API?
> 
> Currently I use a combination of these endpoints:
> - xrefs/symbol
> - lookup/id
> - and xrefs/id
> 
> Example:
> http://grch37.rest.ensembl.org/xrefs/symbol/homo_sapiens/BRCA2?content-type=application/json&object_type=gene
> 
> http://grch37.rest.ensembl.org/lookup/id/ENSG00000139618?content-type=application/json;expand=1
> 
> http://grch37.rest.ensembl.org/xrefs/id/ENST00000288602?content-type=application/json&external_db=RefSeq_mRNA
> 
> 
> Also how do I find the flags associated with a transcript, like the ones mentioned here: http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000139618;r=13:32315474-32400266
> 
> I'm specifically interested in the GENCODE basic flag.
> 
> Using Rest api: 4.3, Data release 82 if that is relevant info.
> 
> 
> Thanks
> 
> Erik Severinsen
> Oslo University Hospital
> Norway
> 
> 
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