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Re: Notes from informal Demo F2F

From: William Bug <William.Bug@DrexelMed.edu>
Date: Tue, 6 Mar 2007 19:35:10 -0800
Message-Id: <2EEE6FC2-1AD4-4461-9D50-195D6FC622FA@DrexelMed.edu>
Cc: Tim Clark <twclark@nmr.mgh.harvard.edu>, "Eric Neumann" <eneumann@teranode.com>, public-semweb-lifesci@w3.org
To: Alan Ruttenberg <alanruttenberg@gmail.com>
Many thanks, Alan.

I think you do an excellent job capturing most of the essential  
issues related to the effort depicted on that page - with two caveats:

	1) I'm not asking or expecting the SWAN group to change anything  
about what they are doing internally in SWAN.  I'm only suggesting  
this effort I've been pushing ahead can provide valuable semantic  
glue between what SWAN targets in its deign and what is being done  
elsewhere in annotating a broad spectrum of biomedical data  
repositories.  Tying it all together using shared community semantic  
frameworks is a critical part of the glue, as well, but this formal  
approach tied much more directly to the research literature works to  
distill a different source of information, and by nature of the  
approach, requires more formal constraints.  I've worked way too many  
complex software development projects to suggest the SWAN team make  
such a drastic change just as they are approaching a new release,  
though, as you indicate, I do think it is worth their CONSIDERING  
this for version 3.0.

	With that in mind, I was not envisioning the output of this proposed  
task would sit in SWAN but rather in the neurocommons repository.   
I'm only pointing to the "Claims" and "Concepts" in SWAN as the hook  
points via which this work would connect to what is constructed in SWAN.
	
	2) Though I agree with your general assessment of what the realist  
philosophers applying their approach in biomedical informatics  
(IFOMIS and other groups of which Barry is one of the most well known  
proponents), I would rather say what I am trying to do is INFORMED by  
their approach but not DRIVEN by it.  Even on this particular task, I  
would not characterize their perspective as "my perspective" - a  
perspective very much influenced by my years developing integrated  
bioinformatic infrastructures and working in the literature  
informatics industry (A&I industry).

	I do agree - as you intimate - that I too am learning as I go along  
in my attempts to apply this technique.  That's why I EXPLICITLY  
labeled it an experiment.  I would stress - I have not made up this  
technique from whole clothe.  It is derived rather - as that page  
makes clear - from a body of work in the GMOD and biomedical ontology  
development community, though, there too, it is still a work-in- 
progress.

Hope this helps to make things a bit more clear.

Cheers,
Bill

On Mar 6, 2007, at 6:59 PM, Alan Ruttenberg wrote:

> Here's my analysis:
>
> I think Bill wants (1). Bill is trying to convince the SWAN team to  
> curate to a level deeper than you are going now, by naming and  
> collecting relationships between the biological entities that are  
> being talked about in the paper SWAN curates. The page he  
> references is detailing his own effort to simultaneously learn for  
> himself and engage us (HCLS) to try to explicitly representing more  
> of the biological facts/hypotheses at the level of the  
> participating biological entities. PATO, the ontology he is trying  
> to learn how to use,  is just one of the OBO ontologies - its  
> domain is phenotypes (or qualities in BFO speak) of organisms and  
> properties of some sub-organismal biological material. He thinks  
> that there is a lot a work in the rest of the OBO ontologies and  
> other community efforts, and that this should be taking advantage  
> as much as possible in our efforts.
>
> He's also coming from perspective, which I think originates with  
> Barry Smith, that many of the problems we have had in managing and  
> making productive use of information related to biology and health  
> in recent history originate from not trying to represent reality,  
> and instead representing "concepts" which, because they don't  
> connect clearly enough to reality, don't land up having enough  
> shared meaning to make good use of when integrated or scaled.
>
> My understanding from discussions we (Tim and I)  have had is that  
> the SWAN project has, as a matter of setting scope, and addressing  
> its use cases, decided against doing this, at least for the moment.  
> This is an understandable choice - it's pretty hard work to learn  
> and do this kind of representation,  as practices and the  
> ontologies themselves are just developing. I think this is a  
> reasonable decision, given that what Bill is suggesting is by no  
> means easy. I'm curious to see what happens with SWAN. I suspect  
> that Bill is too!
>
> Still, Bill is hopeful that the SWAN team will change its mind,  
> because he thinks, as some subset of the people on this list, that  
> his kind of  representation will be what leads to the most  
> substantial payback in what it enables for science and medicine.
>
> Hope this helps,
>
> Alan
>
>
> On Mar 6, 2007, at 9:10 PM, Tim Clark wrote:
>
>> 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
>>>
>>>
>>>
>>>
>>
>

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 03:35:30 UTC

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