[InterMine Dev] organism list

Karamycheva, Svetlana A. Svetlana at jcvi.org
Tue Mar 4 23:24:42 GMT 2014


Hi Devs,
I tried to create a list of organisms on http://www.flymine.org/release-38.0/bag.do
and was not able to do that despite of the organism name I used.
Based on intermine.log, name and shortName fields are used to "verify identifier matches".
An example of the query (for arabidopsis):

 SELECT a1_.id AS a2_, a1_.name AS a3_, a1_.shortName AS a4_ FROM Organism AS a1_ WHERE (LOWER(a1_.name) IN ('arabidopsis') OR LOWER(a1_.shortName) IN ('arabidopsis')) ORDER BY a1_.id LIMIT 10000

Based on data in the "organism" table (for taxonid=3702):

taxonid    | 3702
shortname  | A. thaliana
genus      | Arabidopsis
species    | thaliana
commonname | thale cress
id         | 46000000
name       | Arabidopsis thaliana
class      | org.intermine.model.bio.Organism

the above query can work only with "species" field, but it is not used for verification.

What should be changed to make "Create a new list" working for "Organisms"?

Thank you

Svetlana

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.intermine.org/pipermail/dev/attachments/20140304/fb3c94b3/attachment.html>


More information about the dev mailing list