Re: [Miase-discuss] new namespace

[Nicolas Le n. <le...@eb...>]

Frank Bergmann wrote:
> By the way the example on the *official* site still has problems: 
> 
> - the mathml elements in the datagenerators won't work like that
> - referring to "time" is problematic, you should refer to the time of one of
> the tasks ... otherwise it's not clear which one to take (even though in
> this case they are identical)
> - (optionally we really could go with XPath 1.0)
> 
> All those changes have been made to the attached miaseFile. 

Frank, good catch. The dataGenerator time is still not right though. You write:

<dataGenerator id="time" name="Time">
   <listOfVariables>
     <variable id="time" taskReference="task1" XPath="time" />
   </listOfVariables>
   <listOfParameters />
   <math xmlns="http://www.w3.org/1998/Math/MathML">
   <!-- THERE IS TROUBLE HERE, refering to the time symbol this way is bad 
for a lot of reasons. -->
     <csymbol encoding="text" 
definitionURL="http://www.sbml.org/sbml/symbols/time">time</csymbol>
   </math>
</dataGenerator>

But the XPath "time" does not mean anything, even with the math pointing to 
the SBML special variable time. The problem is that 1) "time" is not the 
string representing the simulation time and 2) there are no links between 
the math and the variable. I am still unsure if this is a problem of 
SED-ML, SBML, XPath etc. In CellML, the time is a regular variable, so it 
is easier. For SBML, would the following be better?

<dataGenerator id="time"
                name="Time">
   <listOfVariables>
     <variable id="time"
               taskReference="task1"
               XPath="http://www.sbml.org/sbml/symbols/time" />
   </listOfVariables>
   <listOfParameters />
   <math xmlns="http://www.w3.org/1998/Math/MathML">
     <ci>time</ci>
   </math>
</dataGenerator>


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Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
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