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[cellml-discussion] PMR categories


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  • From: david.nickerson at nus.edu.sg (David Nickerson)
  • Subject: [cellml-discussion] PMR categories
  • Date: Mon, 11 Jun 2007 08:56:37 +0800
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.
>>>>
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>>>
>>>
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--
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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