Re: Notes from informal Demo F2F

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 - William.Bug@DrexelMed.edu