Chronological Thread 

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This scratches a couple of important pending issues:

1) I feel the term 'variant' is odd (even though I originally
suggested it). It was intended to mean that the model labelled as a
variant is a variation of the one it is a variant of. However, this
isn't really a very applicable definition, especially if one may
consider a model to be a variant of more than one other model. Since
variant is bound up in the URI and name then this makes for dilemmas.
My suggestion would be that we drop variants altogether. We can mark
relations in a better way through metadata.

I am also querying whether the flatness of our URI scheme is
appropriate for our uses.

e.g. perhaps:

http://www.cellml.org/models/bondarenko_szigeti_bett_kim_rasmusson_2004_version01

should be something like

http://www.cellml.org/models/bondarenko_szigeti_bett_kim_rasmusson/2004/ventricular?rev=1

(no that is not a formal proposal)

But this doesn't really help you now. The technically correct method
at the moment would be that the new models that are similar but
different only in their parameterisations are added as variants.

Another alternative in the short term would to simply name the models
as separate models (which they are) and we define now an rdf relation
scheme that is very explicitly about how different models at different
URIs relate to the one you are editing. This would mean that Tommy
needs to update the rendering of the pages for these models to reflect
this information.

2) These models should use imports so that we can at least point to
the generic model and then the specialised parameterised ones. But
that won't work right now because the repository can't handle 1.1
models.

cheers
Matt


On 4/12/07, James Lawson <j.lawson at auckland.ac.nz> wrote:
> Addendum:
>
> The model in the repository describes the apex cells only.
>
> James Lawson wrote:
> > Hi folks,
> >
> > I'm just fishing for some comments on how to handle cases where there
> > are models which describe, for example, the properties of multiple cell
> > types. Bondarenko et al. 2004 is a good example of this:
> >
> > "In the Bondarenko et al. 2004 publication described here, the authors
> > develop a computer model of the mouse ventricular action potential (see
> > below). The model includes parameters for both the apex and the septum
> > regions of the heart (the apex parameters have been substituted into the
> > CellML version of the model described in ), and this helps to illustrate
> > how there are regional differences in myocyte repolarisation in the
> > mouse heart."
> >
> > Penny Noble has just sent me a zip file containing the latest versions
> > of all the models she has curated for COR. I'm currently in the process
> > of comparing these versions to the latest versions we have on the
> > repository. In some cases, she has provided several variants of the same
> > model which describe different cell types, as above.
> >
> > Firstly, are these true 'variants'? If so, then the matter is relatively
> > simple. Unfortunately, if one goes through the repository list, variants
> > simply come up as a duplication of the model listing, with no
> > information concerning what the variant represents. This is something I
> > imagine will be fixed in time, but is presently rather frustrating
> > considering the issue at hand.
> >
> > Does anyone have any comments on this? Should I simply put the files up
> > as different variants, with a note in the documentation?
> >
> > Thanks,
> > James Lawson
> > _______________________________________________
> > cellml-discussion mailing list
> > cellml-discussion at cellml.org
> > http://www.cellml.org/mailman/listinfo/cellml-discussion
>
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion at cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-discussion
>

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• [cellml-discussion] Workshop presentations now available, David Nickerson, 04/11/2007
  • [cellml-discussion] model variants(?): e.g. where multiple cell types are described by the same model in different files, James Lawson, 04/12/2007
    • [cellml-discussion] model variants(?): e.g. where multiple cell types are described by the same model in different files, James Lawson, 04/12/2007
      • [cellml-discussion] model variants(?): e.g. where multiple cell types are described by the same model in different files, Matt , 04/12/2007
        • [cellml-discussion] model variants(?): e.g. where multiple cell types are described by the same model in different files, Tommy Yu, 04/12/2007
          • [cellml-discussion] model variants(?): e.g. where multiple celltypes are described by the same model in different files, David Nickerson, 04/12/2007
            • [cellml-discussion] model variants(?): e.g. where multiple celltypes are described by the same model in different files, Matt , 04/12/2007
              • [cellml-discussion] model variants(?): e.g. where multiplecelltypes are described by the same model in different files, David Nickerson, 04/12/2007
        • [cellml-discussion] model variants(?): e.g. where multiple cell types are described by the same model in different files, James Lawson, 04/12/2007
          • [cellml-discussion] model variants(?): e.g. where multiple celltypes are described by the same model in different files, David Nickerson, 04/12/2007
            • [cellml-discussion] curation annotation framework, James Lawson, 04/12/2007
              • [cellml-discussion] curation annotation framework, David Nickerson, 04/12/2007
              • [cellml-discussion] curation annotation framework, James Lawson, 04/12/2007
              • [cellml-discussion] curation annotation framework, Matt , 04/12/2007

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