[ome-devel] OME-XML schema upcoming changes

[Andrew Patterson]

Hello,

Since the release of the April 2010 schema we have been working extensively with it to get it integrated into the OMERO server in time for our Paris users meeting. This process has thrown up some problems with it that we feel we should address sooner rather than later.

In SPW.xsd (Screen/Plate/Well, our HCS model) we're re-evaluating the fact that Timepoint, an attribute on WellSample, is recorded as an xsd:integer. This would be correct if the Timepoint was like a time in an Image, e.g. 0, 1, 2, etc. In actual fact it should be an absolute time so should be of type xsd:dateTime, e.g. 2010-03-02T10:01:15

In SA.xsd (Structured Annotations) we want to add support for Tags and Ontological Terms. The key changes here is the addition of 2 new types <TagAnnotation> and <TermAnnotation>.
We will also take the opportunity of making changes to this file to rename <StringAnnotation> to <CommentAnnotation> to better reflect it's intended use.

These changes, specifically the SPW change, are a major (breaking) change to the schema. We had not planned a major change until September but feel these changes are necessary so it is best to release them as soon as possible. 

So far they only affect the SPW and SA parts of the model. We are still working on integrating the new version of the model into Bio-Formats and OMERO so it is possible we may find some other snags. For this reason we are going to hold off on releasing the new model (likely to be called June 2010) until we have hit the code freeze date of OMERO.

Thank you to everyone who provided input on these changes. We welcome your suggestions for further improvements.
Comments can be emailed to us or added as tickets at:
http://www.ome-xml.org/

Thanks,

Andrew

Andrew Patterson
ajpatterson at lifesci.dundee.ac.uk
Software Developer, Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee