[ensembl-dev] Rest API lookup

Fri Nov 25 11:57:09 GMT 2016

Hi David,

The ensembl_stable_id database has to be populated with respect to your available databases. We do provide MySQL dumps of our stable ID database, but that includes all Ensembl species and would lead to errors if you searched for IDs from databases you do not have:

ftp://ftp.ensembl.org/pub/release-86/mysql/ensembl_stable_ids_86/

The database is a multi-species one and thus is not part of the species you have already downloaded. The ensembl-core API bundle contains the ability to create one for yourself, see again the misc-scripts/stable_id_lookup/ I mentioned previously. That should be able to create and populate it for you.

If you want to only have the slow exhaustive search, you could try to force the issue with a patch. It might help us diagnose what is going on.

 diff --git a/lib/EnsEMBL/REST/Model/Lookup.pm b/lib/EnsEMBL/REST/Model/Lookup.pm
  index 94e8266..ead0440 100755

--- a/lib/EnsEMBL/REST/Model/Lookup.pm
+++ b/lib/EnsEMBL/REST/Model/Lookup.pm

  @@ -29,7 +29,7 @@ extends 'Catalyst::Model';
   with 'Catalyst::Component::InstancePerContext';

   # Config
  -has 'lookup_model' => ( is => 'ro', isa => 'Str', required => 1, default => 'DatabaseIDLookup' );
  +has 'lookup_model' => ( is => 'ro', isa => 'Str', required => 1, default => 'LongDatabaseIDLookup' );

   # Per instance variables
   has 'context' => (is => 'ro', weak_ref => 1);

That's all I can think of without seeing the way you have your server set up.

Regards,

Kieron

Kieron Taylor PhD.
Ensembl Developer

EMBL, European Bioinformatics Institute

> On 25 Nov 2016, at 11:06, Herzig, David <david.herzig at roche.com> wrote:
> 
> 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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> 
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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
> 
> _______________________________________________
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