[ome-users] question re OME XML semantic types for biological material + OME command line interface question/request

[Keith.Neil at sanofi-aventis.com]

Hi - First I am trying to see how I would best store in OME XML the
results of a phenotypic screen, and I'm not sure how to describe the
compound treatment and dose information and the positive and negative
control information in the XML correctly so that I can create templates
to display things nicely from OME.
 
What I want is to be able to properly annotate the compounds +
concentrations tested in each well of plates in a screen, and to flag
the wells that are control wells, and then to be able to use this
semantic information in querying, and creating a table view of the
screen.  I can create a category group called treatment, and then add my
treatments, but how to associate dose to the treatment?  Also if I use
category group, this is tied to each image, when I would rather it be
tied to the 'sample' in the well?
 
Did I read somewhere that you plan to re-use from the MGED ontology/xml
the biomaterials element ?  
 
Second, I saw that in an older version there was the possibility to run
command line scripts from the analysis engine but that it broke in
recent versions.  I'd be interested to have this working to incorporate
some non mathlab scripts, or scilab scripts.    
 
Thanks for your help!
 
Keith
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