[InterMine Dev] organism list
julie at flymine.org
Wed Mar 5 13:49:55 GMT 2014
That is a bit confusing! Whitespace is a valid delimiter in InterMine so
it's splitting the organism name into two. Example:
The code uses *both* the line break and the whitespace as delimiters
ending up with four strings: A., thaliana, H., and sapiens. To get the
upload to recognise each organism name, use double quotes e.g. "H.
You can also configure your mine to not recognise whitespace as a valid
Does that solve your problem?
On 04/03/14 23:24, Karamycheva, Svetlana A. wrote:
> Hi Devs,
> I tried to create a list of organisms on
> 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
> dev mailing list
> dev at intermine.org
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