Re: Notes from informal Demo F2F

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 - William.Bug@DrexelMed.edu
>>
>>
>>
>>
>

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