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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: Thu, 07 Jun 2007 23:55:20 +0800
I really don't like the idea of giving a model a keyword of "other".
Hopefully the repository will be smart enough to automatically add
models to the "other" listing if they don't have any of the other
predefined key words.

And then if "other" is taken out of this list of mandatory keywords you
can no longer make them mandatory - which I would also prefer. These
predefined keywords should simply be given as suggestions for the user
to choose from. I think we need to be careful not too present repository
users with the impression that only certain types of models are
acceptable in the repository - unless we *are* trying to restrict the
types of models going in there? One example that wouldn't fit any of the
current categories might be finite element basis function definitions
for use with fieldML models.


Andre.


Peter Hunter wrote:
> Dear All,
>
> The intention of this discussion was to decide on a list of items for a
> drop-down list of predefined terms that would be available when choosing
> 'key words' for a new model and which would be the list of terms used to
> display models on www.cellml.org/models (together with the default 'All
> models' item). The idea was that choosing one or more of these key words
> terms would be mandatory when defining model metadata but that one could
> also enter additional keywords for more advanced searching. It may be
> that the additional key words should adhere to terms from an ontology as
> Matt suggests and should use the predictive completion facility that
> Andre suggests. But I am keen to keep this first list of terms fairly
> short. My suggestion is the following list. I've checked through the
> repository and less than 10% of the models would end up solely under
> 'Other'. I am sure we will need to expand this list as the repository
> grows and I suggest we have a policy of keeping the number that end up
> solely in the 'Other' category to less than 10% of the total. We may
> also later need a policy to refine the classification when too many
> models are displayed under one term.
>
> Calcium dynamics
> Cell cycle
> Cell migration
> Circadian rhythms
> Electrophysiology
> Excitation-contraction coupling
> Gene regulation
> Mechanical constitutive laws
> Metabolism
> Myofilament mechanics
> Signal transduction
> Other (the default key word in the list of predefined terms)
>
> Let me know if you can think of other more appropriate terms or
> additional ones, then I'll ask Tommy to implement it. I'm happy to then
> go through and classify all current models in the repository into these
> categories.
>
> Cheers,
> Peter
>
> David Nickerson wrote:
>> One thing I have found useful in other taxonomy/keyword type web
>> interfaces (e.g., see drupal) is that when entering such keywords the
>> interface dynamically completes the terms and/or presents alternatives
>> based on what the user enters. I'd imagine such an interface would work
>> well at pulling terms out of the ontologies Matt is talking about.
>>
>>
>> David.
>>
>>
>> Tommy Yu wrote:
>>
>>> Just had a discussion with Peter, Randall and James about this.
>>>
>>> The keywords are in the metadata for the models, and there is no limit to
>>> what can go in there. The concern about that is the list could get too
>>> big (for minor categories), or variations in the name (electrophysiology
>>> vs electrophysiological), or just spelling in general. What was decided
>>> is to have the same category list, but it would act as a "blessed" list
>>> of keywords that will serve as a guide to what should be added to the
>>> model, and as a broad category filter for the main repository listing.
>>> Users would still be able to add or search by other keywords (from the
>>> advance search interface) if they wish.
>>>
>>> Tommy.
>>>
>>> Matt wrote:
>>>
>>>> On 6/6/07, David Nickerson <david.nickerson at nus.edu.sg> wrote:
>>>>
>>>>> James Lawson wrote:
>>>>>
>>>>>> David Nickerson wrote:
>>>>>>
>>>>>>> Would I be correct in assuming that these terms will be key words
>>>>>>> added
>>>>>>> to the model metadata and that the division into categories on the
>>>>>>> main
>>>>>>> repository page will be assembled from queries on each of these
>>>>>>> predefined key words?
>>>>>>>
>>>>>> Well potentially, there could be many many different keywords, so Peter
>>>>>> suggested that we might not necessarily want to base the categories on
>>>>>> just the keywords. At the moment, Tommy's sorting function is based on
>>>>>> keywords but he suggested that we could have both a keyword and a more
>>>>>> general category selection system.
>>>>>>
>>>>> not sure I like the idea of a separate category, seems to me adding some
>>>>> special piece of metadata to models just to make a repository dump look
>>>>> pretty isn't the way to go. It would be nicer to make use of the
>>>>> keywords (which are genuinely useful metadata to more than just the
>>>>> model repository), possibly with the addition of a guided part of the
>>>>> metadata editing workflow which prompts the user to choose at least one
>>>>> of the predefined "category" keywords and a filter smart enough to put
>>>>> models without one of the special keywords into an "other" category.
>>>>> This way the main repository page layout could be easily changed to add
>>>>> or remove keywords that get pulled out as categories without having to
>>>>> change the models.
>>>>>
>>>>> It would also be nice if we can analyse all the repository searching to
>>>>> keep track of the most popular keywords and adjust the categories on the
>>>>> main page accordingly :-)
>>>>>
>>>> Well, I'm hoping to steal all the keywords and lay them out in the
>>>> physiome ontology and then put them back in as bioentities (or math
>>>> related) metadata pointing into this. So the long term relationship
>>>> between keywords and this "ontology" metadata is where my thinking
>>>> lies. I like the idea of reflecting this information into keywords,
>>>> e.g. for 'cardiovascular' the bioentity would be some big long uri
>>>> pointing into the instance of the term 'cardiovascular' in the
>>>> ontology, so it would be nice if the keywords were at least
>>>> dynamically generated from the labels of these ontological term
>>>> instances.
>>>>
>>>>
>>>>
>>>>
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>>>>>
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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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