Re: [GeneX-dev] Extra Species in the Database

[<ja...@op...>]

"Greg D. Colello" <gd...@nc...> writes:

> >Before anyone can add an array-layout into the DB the species for all
> >their USF must first exist in the DB. 
> >
> >I have no problem removing species without SF, and especially those
> >that we never will, like Red Kangaroo. They were put there to help the
> >CT folks test out the organism table.
> 
> Hmmm. I thought the point of the species table being rather thorough was to 
> avoid having to add species all the time as new dtasets appeared. Also looks 
> more professional. I though Carol vetted the list to be those species most 
> likely to succeed?

No, they were chosen so that one species from each
general_classification appeared in the pull-down menu in the CT.

> And, while we're talking about species, let's go the other direction
> towards more species. These species, which are not in our species
> table, have spots on the Stanford microarrays (they also have Homo
> sapiens, Escheria coli, and of course Arabidopsis thaliana):
> 
> Streptomyces hygroscopicus
> Bacillus thuringiensis
> Aequorea victoria
> Photinus pyralis
> 
> Can't load the data properly until these are in the species table
> and appear in the Control Bundle. In the short run I was thinking of
> taking an old Control Bundle and patching it by hand to include
> these new species, but I gotta fake the species id. Do we need to
> talk Jason?

That would be yes. The template XML file for adding a new species is
in CVS. 

On genebox that would be:

setenv CVSROOT gdc@genebox:/home/cvsroot/opengenex
cvs co analysis_scripts_install/Genex/data/db_tables/species.xml

Provide an XML file in that format, and it will be entered into the
DB.

jas.