Re: Notes from informal Demo F2F

Meant to add I don't mean to imply the implicated models of cellular  
physiology (LTP/LTD) and of disease - or the hypotheses are not  
equally important.

I just feel there will be a "missing link" between those high level,  
abstracted views and the large data repositories (GENEBANK sequences,  
UniProt, UniGene, ABA, GENSAT, MGI & RDG data repositories) that a  
formal representation of observations from a focused selection of  
research articles can potentially help to fill.

I would add the literature curation performed regularly by MGI, RDG  
and others from the GMOD community has demonstrated the value of this  
research literature-based semantic "glue".  Taking the approach I'm  
proposing just provides much more fine-grained detail drawn from a  
more extensive set of community shared, semantic frameworks and  
represents the results in a Semantic Web compatible manner.  The  
latter is a given for the GO annotations created by the GMOD  
community now-a-days, as well (See the links on my "experiment" Wiki  
page cited below to the NCBO OBD repository).

Cheers,
Bill

On Mar 6, 2007, at 4:25 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