<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV>Hello Keith,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>I can provide an answer to your first question.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>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:</DIV><DIV><A href="http://cvs.openmicroscopy.org.uk/tiki/tiki-index.php?page=OME-XML+Evolution#id369323">http://cvs.openmicroscopy.org.uk/tiki/tiki-index.php?page=OME-XML+Evolution#id369323</A></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>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.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>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:</DIV><DIV><A href="http://www.openmicroscopy.org/use/">http://www.openmicroscopy.org/use/</A></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>I hope this information is helpful to you. Please get back to us and let us know how we can work with you further,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Thanks,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Andrew</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><DIV>On 9 Feb 2007, at 14:06, <<A href="mailto:Keith.Neil@sanofi-aventis.com">Keith.Neil@sanofi-aventis.com</A>> wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"> <DIV><SPAN class="573062713-09022007"><FONT face="Arial" size="2">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.</FONT></SPAN></DIV> <DIV><SPAN class="573062713-09022007"><FONT face="Arial" size="2"></FONT></SPAN> </DIV> <DIV><SPAN class="573062713-09022007"><FONT face="Arial" size="2">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</FONT></SPAN><SPAN class="573062713-09022007"><FONT face="Arial" size="2"> is tied to each image, when I would rather it be tied to the 'sample' in the well?</FONT></SPAN></DIV> <DIV><SPAN class="573062713-09022007"><FONT face="Arial" size="2"></FONT></SPAN> </DIV> <DIV><SPAN class="573062713-09022007"><FONT face="Arial" size="2">Did I read somewhere that you plan to re-use from the MGED ontology/xml the biomaterials element ? </FONT> </SPAN></DIV> <DIV><SPAN class="573062713-09022007"><FONT face="Arial" size="2"></FONT></SPAN> </DIV> <DIV><SPAN class="573062713-09022007"><FONT face="Arial" size="2">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. </FONT></SPAN></DIV> <DIV><SPAN class="573062713-09022007"><FONT face="Arial" size="2"></FONT></SPAN> </DIV> <DIV><SPAN class="573062713-09022007"><FONT face="Arial" size="2">Thanks for your help!</FONT></SPAN></DIV> <DIV><SPAN class="573062713-09022007"><FONT face="Arial" size="2"></FONT></SPAN> </DIV> <DIV><SPAN class="573062713-09022007"><FONT face="Arial" size="2">Keith</FONT></SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ome-users mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</A></DIV> </BLOCKQUOTE></DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV>Andrew Patterson</DIV><DIV>Software Developer, Open Microscopy Environment</DIV><DIV>Division of Gene Regulation and Expression</DIV><DIV>University of Dundee</DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN> </DIV><BR></BODY></HTML>