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[cellml-discussion] PMR categories


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  • From: matt.halstead at auckland.ac.nz (Matt )
  • Subject: [cellml-discussion] PMR categories
  • Date: Fri, 8 Jun 2007 13:45:15 +1200
Yes, species attributes are important - especially where a model
contains mixed data. We can use the species metadata, however I would
like to extend the specification of that property to have other
resources as possible values, not just simple strings, and to use
something like the LSID formalism outlined in the following paper:

TAXONOMIC NAMES, METADATA, AND THE SEMANTIC WEB : Biodiversity
Informatics, 3, 2006, pp. 1-15

The paper explains in a pretty straightforward way why this is better
than using names from a single source such as the NCBI Taxonomy (which
we advocate in the metadata spec).

The critical thing for us is that a single model will quite often
contain elements that derive their mechanism or parameters from
studies on different organisms, so we need to be quite rigorous in
looking at all components in a model and identifying their origin.
This is obviously one facet where imports should be helping us to put
circles around species specific submodels.

cheers
Matt


On 6/8/07, James Lawson <j.lawson at auckland.ac.nz> wrote:
> Actually, I'd venture to say that the majority of them aren't models of
> human biological systems. A lot of them are animal models or based on
> experiments done in non-human cell lines (for example Xenopus oocytes
> (frog) are commonplace for cell cycle experiments,) and there are also a
> number of bacterial models.
>
> I agree, I think the metadata field for species (a lot of the models
> already have this, I think,) would be a useful value to sort by. Perhaps
> this should be on the advanced search page rather than on the front
> page, however.
>
> Eventually, the plan is to be able to sort by pretty much any metadata
> field that is contained in the models.
>
> In the future, perhaps we'll actually have specific sections devoted to
> particular species. For example, the nematode work Caenorhabditis
> elegans has only ~1000 cells, and every single cell and its function has
> been mapped. The C. elegans neural system in particular has been mapped
> in a lot of detail, with work by White, Brenner et al. (1986) mapping
> all the synaptic connections between all of the neurons. Although I
> haven't checked, I imagine there are efforts to model the whole
> organism. While this isn't a human physiome project, animal models like
> this are really important in developing frameworks to use for
> modelling/studying larger systems.
>
> Randall Britten wrote:
> > A separate phylogeny attribute is probably also needed.
> >
> > It is not clear whether all the models are meant to pertain to human
> > physiology. One example certainly does not: "# Baylor, Hollingworth,
> > Chandler, 2002, 'Comparison of Simulated and Measured Calcium Sparks
> > in Intact Skeletal Muscle Fibers of the Frog'".
> >
> >
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