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

[Andrew Patterson]

Hello Keith,

I can provide an answer to your first question.

We are in the process of introducing the Screen-Plate-Well concept  
into the OME XML data model. The changes that have been agreed and  
information about them is available here in our evolution document:
http://cvs.openmicroscopy.org.uk/tiki/tiki-index.php?page=OME-XML 
+Evolution#id369323

At the bottom of this page there is a link to the agreed screening  
data model. It is available to view in various file formats. I will  
be incorporating these changes into the OME XML schema over the next  
few months.

Bernd Jagla of Columbia University has implemented a plate viewer for  
the OME Server using this model that may be of interest to you. It  
has not been publicly released as yet. There is some information  
about his other work with OME and links at:
http://www.openmicroscopy.org/use/

I hope this information is helpful to you. Please get back to us and  
let us know how we can work with you further,

Thanks,

Andrew


On 9 Feb 2007, at 14:06, <Keith.Neil at sanofi-aventis.com> wrote:

> 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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> ome-users at lists.openmicroscopy.org.uk
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Andrew Patterson
Software Developer, Open Microscopy Environment
Division of Gene Regulation and Expression
University of Dundee



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