Re: [Miase-discuss] annotation/notes element

[Frank B. <fbergman@u.washington.edu>]

Apart from validation, i rarely look at schema files. For my purposes  
looking at the PDFs of the OM is more productive. So first of all  
thank you for keeping them in sync. There are however some issues that  
need addressing:

- Variable & Parameter:

	- in the OM it does look like we have two separate variable and  
parameter objects, after a look at the schema this is not the case.

	- Of course to make variables work in the ChangeMath case, a variable  
now can refer directly to a model, where before we would only refer to  
variables based on a taskreference. I'm not exactly sure why we did it  
that way. However having these two (possibly different) ways to  
describe where a variable comes from seems troublesome to me. If  
possible we want to avoid tables in the specification telling people  
what to use when. (Anyone not feeling pain, just look at the SBML  
specification and Table 5 or how to interpret constant / boundary  
condition). We still have time to sort things out ... or is this a non- 
issue, and it is an error to use modelReferences in variables for  
datagenerator, while using a taskreference is an error for variables  
in ChangeMath. If so they need to be renamed :) ... the schema  
currently lists both as optional, which does not do this situation  
justice :)
	
	- parameter value type should be xs:double rather than xs:string

- Other things I've noted with the schema:

	- Inheritances differ in OM and schema, see for example curve and  
surface.
	- for notes and annotations, which are currently strings, it might be  
nice to use more than simple strings. If I were to use annotations,  
I'd rather use a block of xml ... good news, mike has gone through the  
trouble before and the sbml schema has the needed specification:

<xsd:sequence>
             <xsd:element name="notes" minOccurs="0">
                 <xsd:complexType>
                     <xsd:sequence>
                         <xsd:any namespace="http://www.w3.org/1999/xhtml 
"
                                  processContents="skip"
                                  minOccurs="0" maxOccurs="unbounded"/>
                     </xsd:sequence>
                 </xsd:complexType>
             </xsd:element>
             <xsd:element name="annotation" minOccurs="0">
                 <xsd:complexType>
                     <xsd:sequence>
                         <xsd:any processContents="skip"
                                  minOccurs="0" maxOccurs="unbounded"/>
                     </xsd:sequence>
                 </xsd:complexType>
             </xsd:element>
         </xsd:sequence>

	- for ChangeXML a structure like  "annotation" above should be used  
for newValue, rather than xs:string
	- changeAttribute: newValue should be of type xs:double

That's all i could find for now ....

cheers
Frank

On Jan 28, 2009, at 7:46 AM, Dagmar Köhn wrote:

> Hej Richard (and everybody),
>
> I have changed the XML schema so as notes/annotations are now  
> applicable
> to all schema elements.
> All complex types are now extensions of the SED-Base type.
>
> /Dagmar
>
>
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