Chronological Thread 

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On 4/12/07, James Lawson <j.lawson at auckland.ac.nz> wrote:
> So, for example in
> > http://www.cellml.org/models/tentusscher_noble_noble_panfilov_2004_version01_variant01
> > I'm guessing you have fixed the model to work in PCEnv (hence the star)
> > but the model status still states "This is the original unchecked
> > version of the model imported from the previous CellML model repository,
> > 24-Jan-2006". Given there is still no curation annotation framework I
> > think we still need to be using such a plain text description of the
> > status of each model and thus you should update the documentation to
> > reflect what you actually have done. This would also be the place to
> > justify the use of a variant rather than version.
>
> This particular model isn't one I've actually fixed - just one that I've
> checked and annotated with a star to denote that it runs in PCEnv. As
> such I don't know exactly where that version has come from - I can only
> assume that it came from the old repository.

So this is a variant of a version that does not exist anywhere? It may
have been that someone thought the default for name for a new model
needed to include a variant too.

> The presence of the star
> means that it shouldn't say that it is unchecked, however. I'll change
> that now. Of course the star system remains ambiguous because not all of
> the models that lack stars don't run in PCEnv - they simply haven't been
> checked, and not all of the models with stars have been fixed by myself
> personally - I have just certified that they run in PCEnv.

In my opinion the stars should be removed for this very reason.

>
> In the case that I have in fact created a new version, I have updated
> the model status. Since there's currently no annotation framework as
> such, and since I have really just started and am learning what needs to
> be said etc as I go, some of the annotation I've put to models that I
> fixed earlier isn't consistent with what I'm doing now. The model
> documentation can't be changed from the page - the file needs to be
> downloaded, changed and then reuploaded.

And that changes the version which is ok.

>
> At the moment I'm primarily saying what version the current version was
> updated from, by who, and when (if I know). Some of my earlier
> annotations included the error that the previous version was producing.
> This can produce a lot of text though, particularly when it requires
> listing scores of variables that couldn't be defined etc. I do have all
> this information (regarding how a particular model was fixed, that is,)
> documented on my computer, however.

I think include it anyway, it's basically your commit message for the
new version.

>
> Does anyone have any comments or proposals, formal or informal,
> concerning what information needs to be included in the model status
> documentation? The more consistent I can be now, the less I'll have to
> go back and redo in the future.

I presume you are talking explicitly about the element <section
id="sec_status"> in the http://cellml.org/tmp-documentation namespace?
e.g.:

<section id="sec_status">
<title>Model Status</title>
<para>
This is the original unchecked version of the model
imported from the previous
CellML model repository, 24-Jan-2006.
</para>
</section>


I would keep this brief as is, but those verbose changes that you
mentioned that described what the reason was for the change - i.e.
what it was fixing should use cellml metadata, specifically:

4.6 Modification History
The modification history lists changes that have been made to the
CellML document. Each separate alteration can be described in its own
<cmeta:modification> element. Each modification listed should also
include the name of the person who made the changes in a
<cmeta:modifier> element and the date the document was modified in the
Dublin Core date qualifier element, <dcterms:modified>. The definition
of modification history metadata is demonstrated in Figure 16

see
http://www.cellml.org/specifications/metadata/cellml_metadata_1.0#sec_general_metadata

cheers
Matt




>
> James
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion at cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-discussion
>

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• [cellml-discussion] model variants(?): e.g. where multiple cell types are described by the same model in different files, (continued)
  • [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
          • [cellml-discussion] curation annotation framework, David Nickerson, 04/12/2007
          • [cellml-discussion] curation annotation framework, David Nickerson, 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 celltypes are described by the same model in different files, David Nickerson, 04/12/2007

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