Re: [Miase-discuss] annotation/notes element

[Dagmar K. <da...@eb...>]

Hej Frank,
thanks a lot for your comments!
Some answers...

Frank Bergmann wrote:
> 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.

As far as I know UML, two entities with identical names in a UML schema 
represent the same (identical) class. So, in the UML you find two 
"drawings" of parameter/variable classes, but in fact they correspond to 
one "physical" class as they carry identical class names.

>
> - 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

Yes, I think that's what you mentioned before.
I think everybody agreed on changing it to the XML Schema type xs:double!?
If I don't get any complaints, I'll change it :-)


>
> - Other things I've noted with the schema: 
>
> - Inheritances differ in OM and schema, see for example curve and 
> surface.

Have to check.

> - 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:

Yes, I remember I've had that discussion with Mike.
My idea was to keep the notes/annotations as unrestricted as possible.
But I am sure you're right ;-)

>
> <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

I agree. Any comments, otherwise I'd change the data type.

> 	- changeAttribute: newValue should be of type xs:double
Not sure, could I - for example - change

<listOfProducts>
      <speciesReference species="PZ"/>

the species (XML) attribute "PZ" to some other species, e.g. to change 
the product in a reaction? Could that make sense? Or would we consider 
that as a completely different model then?

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

Thanks again!

Dagmar
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