[ensembl-dev] Rest API lookup

[Herzig, David]

Hi Kieron

Thx for your feedback.

As I have only downloaded the mysql dumps for several species, where is the
lookup db in my case?

Is there a easy way to change the lookup in a way that all db's/tables will
be searched?

regards,
David

On Wed, Nov 23, 2016 at 3:00 PM, Kieron Taylor <ktaylor at ebi.ac.uk> wrote:

> 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
> > Roche Innovation Center Basel
> >
> > F. Hoffmann-La Roche Ltd
> > Grenzacherstrasse 124
> > 4070 Basel
> > Switzerland
> > Phone +41 61 687 31 70
> > Learn more about pRED Informatics at http://go.roche.com/pREDi
> >
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-- 
David Herzig
Scientific Application Developer
SIAD Solution Delivery & Architecture, pRED Informatics
Roche Pharma Research and Early Development
Roche Innovation Center Basel

F. Hoffmann-La Roche Ltd
Grenzacherstrasse 124
4070 Basel
Switzerland
Phone +41 61 687 31 70

Learn more about pRED Informatics at http://go.roche.com/*pREDi*
<http://go.roche.com/pREDi>
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