[ome-devel] Fwd: experience with OME

[Will Moore]

Hi Curtis...

On 16 Sep 2009, at 23:09, Curtis Rueden wrote:

> We definitely want to encourage this sort of thing. My group (LOCI)  
> is in the middle of a similar effort, mapping all our acquisition  
> metadata to OME-XML, and working to produce valid OME-TIFF files in  
> every case.
>
> So yes, the documentation is supposed to help. I agree that the  
> documentation in the schema itself could use a lot of improvement.  
> My group has a graduate student in library sciences, Caitlin  
> Sticco, who is currently analyzing the schema and compiling a list  
> of suggestions and improvements; hopefully we can update the  
> documentation as well as we work to improve the schema.
>
> Caitlin and I are also discussing how to make better diagrams—one  
> idea we had is to generate them in Graphviz format from the XSD  
> file. Any other suggestions for ways to make useful pictures would  
> be welcome.

I've been using a combination of xsl, javascript (jQuery) etc to turn  
the ome.xsd into a browsable hierarchy.

http://cvs.openmicroscopy.org.uk/snapshots/omero/editor/omeXsd/ome- 
r373.xsd

Handy because it's instantly updated if you're editing the xsd, and  
hierarchy is easy to understand.

Use links on the top to expand/collapse all or show/hide docs.

Obviously this code could be extended to do a bunch of other stuff.  
E.g. JM suggested allowing the root element to be chosen, e.g.  
"Image" or "Instrument".


   Will.



>
> Your idea of a list of common use cases, and how to express them in  
> OME-XML, is a great one. We should add that to the OME-XML web  
> site. For that, we need A) a list of which common use cases to  
> include; and B) someone with enough time to work on writing it up.  
> But at the least we can file a ticket about it on the OME-XML Trac  
> at http://www.ome-xml.org/. And actually, you are welcome to file  
> such tickets too, using the ome/ome login. :-)  To be clear, we  
> want to encourage external suggestions through that mechanism.

William Moore
Division of Gene Regulation and Expression
College of Life Sciences
University of Dundee
Scotland
DD1 5PH

Tel 01382 386364

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