[ensembl-dev] Retrieving gene coordinates

[Kieron Taylor]

Hi Christina,

What you can do depends on what you have to begin with. If you know an Ensembl stable ID [1], if you know a HGNC or other popular name for a gene [2], or if you have to do something more complex [3], we have a number of endpoints to suit. Using multiple queries to get a result can take an awful lot longer if you're working with many variants for example. If time is an issue we can make some further suggestions to speed things along with batches via POST requests.

As far as Ensembl Genomes is concerned, their server is less fully featured due to lack of data, but supports many of the main functions. We continue to expand the capabilities of our REST server, so please do inform us of your needs on the understanding that it may be many months before any functionality appears.

We don't have any other mechanisms for on-the-fly data retrieval that don't require Perl, so at that point you'd best go to our FTP site.

I hope that helps,

Kieron


[1] http://rest.ensembl.org/lookup/id/ENSG00000157764?content-type=application/json
[2] http://rest.ensembl.org/lookup/symbol/homo_sapiens/BRCA2?content-type=application/json
[3] http://rest.ensembl.org/variation/human/rs56116432?content-type=application/json
  -  http://rest.ensembl.org/overlap/region/human/9:133256042-133256042?feature=gene;content-type=application/json

Kieron Taylor PhD.
Ensembl Developer

EMBL, European Bioinformatics Institute






> On 25 Jul 2016, at 18:38, Cristina Yenyxe Gonzalez Garcia <cyenyxe at ebi.ac.uk> wrote:
> 
> Hello,
> 
> We are exploring possible ways to retrieve gene coordinates to optimize certain queries at the European Variation Archive (EVA). We haven't managed to find an Ensembl REST endpoint to get this information, is there one available? Would it work for any species, including those in Ensembl Genomes (e.g. sorghum bicolor or strongyloides ratti)?
> 
> Otherwise, what would be the best option? Parsing the GFF files for each species?
> 
> The last idea we can come up with is extracting this information from the VEP cache, is that even possible? That would help to reduce the number of our data dependencies, since we will always have one for the species supported in our variant browser.
> 
> Thanks,
> Cristina
> 
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