[InterMine Dev] organism list

Julie Sullivan julie at flymine.org
Wed Mar 5 13:49:55 GMT 2014

Hi Svetlana

That is a bit confusing! Whitespace is a valid delimiter in InterMine so 
it's splitting the organism name into two. Example:

	A. thaliana
	H. sapiens

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
> 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
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