[ome-users] Question about XML schema for OME

[Graham Klyne]

My first step on the way to customizing OME for our project is to create a 
new  "semantic type definition" (I'm not yet seeing what's especially 
"semantic" about these type definitions, but that's another discussion) for 
the additional information we want to capture.  This isn't the end goal, 
since it ignores some existing values, but it seems to be a reasonable 
first step on the way.

To try and understand how additional annotations can be associated with an 
image, I'm looking at the XML schema for OME and custom annotations: 
ome.xsd and CA.xsd.

I'm looking at <xs:element name = "Image"> in ome.xsd, which has a content 
model that allows zero or more CA:CustomAttributes.  So far, so good.  I'm 
guessing that these are where additional values can be added into the 
content model.

Now I go to look at CA.xml, and my first surprise is that <xsd:element name 
= "Image"> is being redefined in the CA namespace.  What is the purpose of 
this <CA:Image> element thus defined?  The definition of 
CA:CustomAttributes is much as I'd expect.

It appears that many, but not all, of the top-level OME content elements 
are redefined in the CA namespace, also element OME, with reduced content 
models.  I find it's hard to see what's going on here.

[Later] I've found something in the documentation that says they cover the 
same information in hierarchical vs flattened forms.  Which raises a 
slightly different question: Why?  Or, more germane to my needs, which of 
these structures should I understand in order to understand how the changes 
I propose should fit into the overall structure?

It also seems odd that one form references the other for the 
CusatomAttrubutes definition.  The factoring (or naming) of definitions 
here seems confusing.  I would expect something like a hierarchical form 
and a flattened form, that both reference a separate schema for the 
definition of CustomAttribute.

Can anyone point out if I'm completely missing the point here, please?

#g
--

(Also, I note here an inconsistent use of namespace prefixes xs: and xsd: 
which, while correct XML, is mildly confusing.)


---
Graham Klyne
Image Bioinformatics Research Group (http://www.bioimage.org/)
Department of Zoology, University of Oxford
South Parks Road, Oxford OX1 3PS, UK
E-mail: <Graham.Klyne at zoo.ox.ac.uk>
Direct phone: +44-(0)1865-281991
Departmental fax: +44-(0)1865-310447