Re: Notes from informal Demo F2F

Sorry to contribute to what appears to be an endless chain, here, but -

I see the relation between this OBO Phenotype Assertion Wiki page and  
SWAN EXACTLY as Tim describes it below.

Also - I would not expect working neuroscientists to go through what  
I did to produce what's on that page - HOWEVER - I do think it will  
be important to create systems that enable such scientists - in a  
very intuitive manner - to represent their largely manually  
assembled, expert knowledge in such a way.  I do not believe that is  
an intractable goal - either the UI engineering required or the  
informatics framework needed to support building and processing it.   
I do think it is far from a trivial effort, however.

I am sorry it's taken so much effort on everyone's part to get this  
across.

Cheers,
Bill

On Mar 6, 2007, at 7:15 PM, Tim Clark wrote:

> Alan,
>
> Thanks for that summary.
>
> SWAN is not a software project - it is a project for a technology- 
> mediated social infrastructure. Those fancy words mean we are  
> trying to get the working scientists themselves to curate the  
> material for their own benefit, self-understanding & "karma  
> points".  We think it is the only sustainable & scalableway to  
> represent hypotheses.
>
> Nothing in principle - and I hope we can test this out - should  
> prevent people who want to link very deep annotation of various  
> kinds to SWAN hypotheses, from doing so.  But that is not our  
> project. We are "just" providing the framework.  An essential  
> criterion is that whatever we do is doable by working scientists  
> and helps them to work.
>
> Best
>
> Tim
>
> On TuesdayMar 6, 2007, at 9:59 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