Re: [Miase-discuss] Schema annotations

[Michael H. <mh...@ca...>]

  fbergman> if renaming is to be done, i think it should be
  fbergman> on the math-ML level.  I consider notes and
  fbergman> annotation for Sed-ML vital, but not at the
  fbergman> math- ml level. That would limit all changes to
  fbergman> the sbml-mathml.xsd file.  Maybe Mike could chip
  fbergman> in, how this feature is used in SBML.

Hi,

Do I understand it correctly that the 'annotation' we are
talking about is the following in the sbml-mathml schema?:

  <xs:complexType name="Annotation">
    <xs:simpleContent>
      <xs:extension base="xs:string">
        <xs:attributeGroup ref="AnnotationAttributes"/>
      </xs:extension>
    </xs:simpleContent>
  </xs:complexType>

If so, then this is not something we have much control over
-- it's part of the definition of MathML 2.0 (it's not even
an SBML issue).  The <annotation> and <annotation-xml>
constructs are involved in the definition of MathML's
<semantics> element.

At present, I don't think there is a lot of use of
<semantics> and its associated constructs in SBML software;
however, it *is* used by SBO, in the rate law MathML
expressions.  It's pretty vital in that role.  (Although,
now that I look at it, it doesn't seem that <annotation> and
<annotation-xml> per se are being used in the SBO terms I've
looked at, only <semantics>.)

I'm not sure what to suggest as far as the jaxb issue is
concerned.  I haven't looked at the jaxb code, but it seems
strange that jaxb would not let a person specify some sort
of prefix at the software level, so that it can be told to
generate alternate names for chosen elements.  One could
rename them to "mathml-annotation" or some such then.

MH