Specifying a model description

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lenov

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Mar 1, 2012, 4:12:44 AM3/1/12

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Hello,

The example on the project page shows a NuML file containing the
concentration of three pools at two times. The pools corresponds to
species in an SBML model. This model is nowhere described. Shouldn't
we had a root address for the XPaths? Or do we assume this is always
provided by the format calling NuML (SBRML or SED-ML, or SBML/
distrib)?

That mean a NuML file cannot contains numerical values corresponding
to components of different models. (nothing wrong with that. Just
asking)

Frank Bergmann

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Mar 1, 2012, 7:29:22 AM3/1/12

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Good question,

It is vital to have headers for the data so that we can link it to the information. In SBRML the model is given explicitly via a model element and later in dimension descriptions the identifiers of the model is being used. In NuML we wanted to be as generic as possible and reduced it to contain just the results.

I can see that an xpath query to nowhere is not really helpful. Perhaps we should use an xlink/xpointer instead? So it would look like

xlink:href="http://somemodelsomewhere.xml#xpointer(id('species_1'))"

if we would restrict ourselves it would look much cleaner than the corresponding path expressions.