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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: Mon, 11 Jun 2007 16:36:42 +1200
I have concluded that they are now talking about the web site and not
keywords in general.

My assumption was that the category field selections are not persisted
in the model metadata at all.

I would have liked some indication that the 'categories' used also end
up in the model keywords attributed to the model in addition to the
keywords supplied by the author when creating or uploading the model.

I would like there to be as many keywords allowed as the
author/uploader wants (perhaps just a lines field will do for now for
this). Constraining them to a single extra keyword in addition to a
selected category makes no sense to me.


On 6/11/07, David Nickerson <david.nickerson at nus.edu.sg> wrote:
> I'm just wondering if we can clarify what this discussion is about? It
> started out as an attempt to define a minimal set of base keywords that
> would apply to most models currently in the repository. It now seems to
> be talking about modifications to the CellML metadata specification? If
> so then I would like to see a bit more in the way of justification for a
> new category metadata property and the proposed changes to the metadata
> specification to take this into account. (i.e., the specification of
> this property and the rules to which it must adhere.)
>
> I am also a bit confused as to what is meant by sorting? I would guess
> this refers to presentation of a complete (filtered?) repository
> listing? In this case is it safe to assume that there will be a testing
> phase to allow for feedback before the user interface to the live
> repository is changed?
>
>
> David.
>
>
> Peter Hunter wrote:
> > Dear All,
> >
> > Poul and I have looked at the discussion on this thread and to best
> > encompass the various suggestions we've decided to ask Tommy to do the
> > following:
> > 1. Include both a category field with predefined terms (Tommy has this
> > in now) and an additional general 'key word' field. A model can be in
> > multiple categories.
> > 2. The sort facility on the repository will have three ways of sorting:
> > The 1st is the above list of categories, the 2nd is a drop down list
> > that provides more options (see next point), and the 3rd is the curation
> > level.
> > 3. The 2nd sort facility will present several options such as keyword
> > search, species, cell type, etc, and access to more extensive boolean
> > searches (author, year, etc).
> >
> > Cheers,
> > Peter
> >
> > Matt wrote:
> >> On 6/8/07, James Lawson <j.lawson at auckland.ac.nz> wrote:
> >>
> >>> So for example someone's trying to build a large model but the only
> >>> components (or data to build components) available are from non-matching
> >>> species?
> >>>
> >>
> >> Yes.
> >>
> >>
> >>> So the LFID (I looked it up but it went over my head) provides
> >>> a way we can do that which is more precise and flexible than simply
> >>> referring to NCBI taxonomy?
> >>>
> >>
> >> Read the paper I referenced, it has a very simple breakdown of LSID
> >> and the taxonomy naming issue.
> >>
> >>
> >>>> 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.
> >>>>
> >>> _______________________________________________
> >>> 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
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> >>
> > _______________________________________________
> > cellml-discussion mailing list
> > cellml-discussion at cellml.org
> > http://www.cellml.org/mailman/listinfo/cellml-discussion
>
> --
> David Nickerson, PhD
> Research Fellow
> Division of Bioengineering
> Faculty of Engineering
> National University of Singapore
> Email: david.nickerson at nus.edu.sg
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