BIll:
(1) or (2) or none of the above is good enough for right now. I am
finding your proposal difficult to follow.
Tim
On TuesdayMar 6, 2007, at 7:43 PM, William Bug wrote:
Sorry, Tim.
Can't really go into more detail right now. I have a lot of
planning still to do on an all day meeting I must lead tomorrow.
I lay it out considerable detail on this proposal on that page I
cite below:
http://esw.w3.org/topic/HCLS/OntologyTaskForce/
OboPhenotypeSyntaxExperiment
It is just a suggestion. As I said a few weeks ago when I put it
out there, I welcome any feedback. Please amend, append, or
correct as you see fit.
As I mentioned to you a few weeks ago, I'd see this as a way of
providing much more structure to back up the "Concepts" and
"Claims" that are represented in SWAN. In fact, the "Concepts" (as
represented in RDF using community shared ontologies/terminologies)
provide a link into this more structure "bridge" I'm describing and
the wealth of detail contained in RDF converted versions of BioPAX,
SenseLab (BioPharm), ABA, MPO-based annotations from MGI & RDG, etc.
I hope this helps a little.
Cheers,
Bill
On Mar 6, 2007, at 4:33 PM, Tim Clark wrote:
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]
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]