W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > March 2007

Re: Notes from informal Demo F2F

From: Tim Clark <twclark@nmr.mgh.harvard.edu>
Date: Tue, 6 Mar 2007 21:10:30 -0500
Message-Id: <BDC53DD5-4B5A-470C-BACE-D3E884B2EE15@nmr.mgh.harvard.edu>
Cc: "Eric Neumann" <eneumann@teranode.com>, "Alan Ruttenberg" <alanruttenberg@gmail.com>, public-semweb-lifesci@w3.org
To: William Bug <William.Bug@DrexelMed.edu>
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 - 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
>
>
>
>
Received on Wednesday, 7 March 2007 02:10:57 UTC

This archive was generated by hypermail 2.3.1 : Wednesday, 7 January 2015 14:52:30 UTC