Re: Notes from informal Demo F2F

One final note, since my last few emails may have clouded this issue:

	1) However much I may believe we are closer than it may seem -  
despite the very real concerns Nigam points out below - to providing  
a means whereby domain expert scientists will be able to construct  
the manner of statements on that OBO Phenotype page, that is NOT what  
I'm suggesting for the demo.  Rather it comes down to exactly what  
EricN mentioned in his original email describing his off-line  
discussion on Monday.  As I state on that Wiki page, I believe  
creating these statements against real evidence would provide  
extremely effective semantic bridging between the less constrained,  
more abstract descriptions in SWAN, and the variety of RDF data  
sets.  Though I started out thinking it MIGHT be PRACTICAL for Gwen  
and Elizabeth to do this now in a small way, after discussing this  
with them back in early February, I became convinced that was not at  
all practical.  It would take folks such as Don, Vipul, Alan, myself,  
and others to slog through it (though I'm pretty certain I can  
considerably improve on the process using SWOOP).

	2) Using this formalism is NOT the same as committing to using OWL- 
DL.  As such, I'm not certain - and don't expect - in its current  
form it would support reasoning.  These assertions CAN be queried via  
SPARQL, however.

Cheers,
Bill

On Mar 6, 2007, at 9:47 PM, Nigam Shah wrote:

> Hi Alan,
>
> Tim and Steve (the other HyBrow guy) have discussed this in some  
> detail I believe. Its great to have formally structured  
> representations at the level of biological entities created by the  
> scientists themselves. However, right now (A) The ontologies and  
> relations for doing so might or might not exist (B) Most people  
> fall asleep when we start talking about BFO driven formal  
> representations (C) there are no incentives for someone to take  
> that much trouble (D) the UI's for creating the formal descriptions  
> are quite bad.
>
> Overall, I think it is more important to get people to curate  
> (however informal, disconnected from biological entities it might  
> be) and to get them to "donate" a few keystrokes and clicks towards  
> curation. IF this works, we can, in the next step think about  
> aquiring more deep, structured, formal descriptions of hypotheses.
>
> Regards,
> Nigam.
>
> 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