[ensembl-dev] Retrieving gene coordinates

Cristina Yenyxe Gonzalez Garcia cyenyxe at ebi.ac.uk
Mon Jul 25 18:38:02 BST 2016


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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