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 (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
Excitation-contraction coupling
Gene regulation
Mechanical constitutive laws
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.


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.


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.


Matt wrote:
On 6/6/07, David Nickerson <[EMAIL PROTECTED]> 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

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fn:Peter Hunter FRS
org:University of Auckland;Auckland Bioengineering Institute (ABI)
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