Bill,
I am trying to understand your proposal. Which are you suggesting:
(1) we curate in to SWAN some existing published work hypothesizing
connection of, for example, MPTP/MPP+ mechanism to some forms of PD; or
(2) we build "our own" hypothesis of MPTP/MPP+ mechanism relationship
etc, not existing in the literature, and curate it in to SWAN?
or something else?
Tim
On TuesdayMar 6, 2007, at 7:25 PM, William Bug wrote:
Hi All,
Looks like a lot of substantive work was done at the F2F. Kudos to
all who participated!
I'd like to highlight one of the issues EricN mentioned.
On Mar 6, 2007, at 8:29 AM, Eric Neumann wrote:
As part of the scernario using the known aggregate of facts, add a
few *select* hypotheses (triple graphs), that would make major
connections with the rest of the graph that would function as a
"bridge" across the data and models; Show the new insights from
this merged compositeby re-applying queries that now retireve more
connections. One example Karen had was around the MPTP/MPP+
mechanism for some forms of PD.
This suggestion that came from the off-line discussion amongst
several call-in participants is EXACTLY the point I've been trying
to make since September with the proposal to use the OBO Foundry
PATO + Phenotype assertion syntax.
http://esw.w3.org/topic/HCLS/OntologyTaskForce/
OboPhenotypeSyntaxExperiment
I think this is critical to bringing together the various resources
around complex concepts such as LTP/LTD - which, as I've mentioned
before is a MODEL not a fact per se.
The advantage to using this approach is your assertions are based
on reported evidence from the literature - not on a high-level
encapsulation of an abstraction in the form of a complex model.
The strategy I'm proposing is only contrived in the sense you focus
in specifically on a collection of articles covering a particular
micro domain within the general use case. I've even proposed a way
in which one could determine a metric to decide exactly how much of
this sort of highly structured curation is required. The amount
will likely be a function of the complexity and abstraction in the
underlying hypothesis and the extent to which the underlying RDF
sources are already inter-liked via shared semantic frameworks such
as MeSH, GO, BioCyc, etc.
I would note the article I chose as an example was appropriate
given the PD use case as of September 2006. It was mainly put out
there to illustrate how to approach this task. We'd now want to
focus specifically on articles that cover the specific micro
domains in the most recent, narrowed version of the use case.
I have been working on how to use tools such as SWOOP to greatly
reduce the effort required to construct these phenotype assertions.
I'm afraid I'm busy for the next week with BIRN meetings - some of
which I need to lead - so I don't expect to be able to provide much
help on this until late next week.
Best of luck!
Cheers,
Bill
Bill Bug
Senior Research Analyst/Ontological Engineer
Laboratory for Bioimaging & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA 19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)
Please Note: I now have a new email - [EMAIL PROTECTED]
