[ensembl-dev] Rest API lookup

[Kieron Taylor]

Hi David,

The lookup/id endpoint has no species argument to know in which database to look. Our REST servers have access to a database called ensembl_stable_ids which contains all the gene, transcript etc. ids and what species they belong to, which the lookup endpoint searches. Your ID is probably not in this "lookup" database.

The script we use to populate that database is found here: https://github.com/Ensembl/ensembl/tree/master/misc-scripts/stable_id_lookup
I don't know how well it will work outside of our production environment, but we can try to help.

The lookup mechanism can be made to search all tables of all databases to find your ID, but this can be terribly slow. If you try the overlap endpoint and specify the coordinates of stable_id 123456, you should be able to see your feature as normal, because you will have had to specify the feature in the URL.



Regards,

Kieron


> On 23 Nov 2016, at 12:38, Herzig, David <david.herzig at roche.com> wrote:
> 
> Hi Ensembl Team
> 
> I set up the ensembl database with several species. I also set up the REST API. Everything works fine.
> 
> Now I have loaded custom species files into a new database (created the schema, loaded sequences, loaded GFF, ...)
> 
> If I now go the the REST API on the address: GET info/species I can see my new specie. Also if I connect to the database and check the tables gene, transcript and exon, everything looks fine.
> 
> Now my issue: I have an entry in the gene table of my custom specie. The gene has the stable_id :123456 (just some ID). If I go now to the REST API and lookup for this id:
> 
> GET lookup/id/123456
> 
> I do not retrieve the gene. It seems like I have missed something.
> 
> Any ideas?
> 
> regads,
> David
> 
> -- 
> David Herzig
> Scientific Application Developer
> SIAD Solution Delivery & Architecture, pRED Informatics
> Roche Pharma Research and Early Development
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> 
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