Re: [public-semweb-lifesci] AD/PD use case document

Yes - exactly - Vipul is correct.

Here's one other email from the weekend that goes into a little more  
detail regarding an experimental plan - if you will - toward actually  
describing what sort of balance between structured, nuanced, granular  
ontological seeds linked to community, shared semantic frameworks and  
straight-ahead RDF translation appears to provide the most value.

Again - the other important thing to remember is if we decide taking  
this approach is practical for the demo - the output of what we  
produce - including some significant portion of the BioRDF data  
sources relevant to the Use Cases might actually be in a form that is  
immediately useful to the Open Biomedical Data repository being  
accumulated by NCBO.  This may turn out to also be relevant to the  
NeuroCommons repository Jonathan Rees, Alan, and others are currently  
producing.

BTW - I didn't want to imply the folks working directly on the  
assembling and describing the scientific context for the Use Cases  
(June, Gwen, Elizabeth, et al.) shouldn't take a look at the page  
cited below by Vipul.  Their input will ultimately be critical on  
this task in vetting the veracity of the statements, should we decide  
to commit to this approach.  I only felt it may appear a bit opaque  
to those not familiar with some of the formalisms involved (some of  
which most folks would admit are pretty opaque).  This needs to also  
be vetted by those more deeply knowledgeable of the RDF tools &  
standards we are using to determine whether this can play the role in  
the demo that I'm proposing.

Should we decide to move in this direction, we also need to place  
this formal content into an RDF-compliant backend of some sort.   
Ideally, we'd want to use a tool that will enable us to construct  
these complex entities and assertions directly in some RDF-compliant  
backend.

Note the top of this page is rather old, but not irrelevant to the  
point I've been trying to make.  My feeling is there may be more  
payback from using the OBO phenotype syntax in this context.  Though  
this page looks complex and labor intensive, the work one needs to do  
constructing entities needed to build these OBO Phenotype Assertions  
quickly falls off, once you've assembled a lot of the basic building  
blocks.  It took quite a bit of time to construct the pieces required  
to represent the phenotype assertions associated with the first  
Research Statement in this list.  The next several Research Statement  
assertions came together in a matter of minutes.

Cheers,
Bill


On Feb 17, 2007, at 12:00 PM, William Bug wrote:

> Don is getting at the same point I've been trying to make here.
>
> The Dopamine-R1 & Dopamine-R2 scenarios he cites provide more hooks  
> into other highly connected graphs of relevant biological data  
> (gene networks & pathways) - which just goes to make his point at  
> the end about the value of SemWebTech.
>
> This was the point I was trying to make re: the use of the PATO  
> ontology and associated OBO phenotype syntax.  If we were to focus  
> in on one of the microdomains related to the Use Case, and distill  
> a few formal assertions from each article in the relevant  
> literature, we could use these as concentrating semantic "seeds" -  
> along with relevant models described using shared distilled  
> knowledge sources of various levels of semantic expressively  
> (terminologies --> formal ontologies expressed using a common,  
> community formalism).
>
> In fact, behind this was the thought of testing this  
> systematically.  In other words, if you identified 250 citations  
> relevant to specific, focussed topic (e.g., alpha-Syn relation to  
> second messenger enzymes, channels, and receptors associated with  
> molecular & cellular memory mechanisms in the hippocampus - still a  
> much too broad topic, actually), how well can one semantically  
> correlate BioRDF data entities if one created PATO-based formal  
> phenotype statements according combinations of the following  
> conditions:
> 	- 1, 3, 5, or unlimited number of formal OBO phenotype statements  
> for each article
> 	- 2%, 5%, 15%, 25% of that literature corpus
>
> Doing this as a part of the demo COULD provide a VERY SPECIFIC  
> example of how SemWebTech can help bring together the data & info  
> sources all biomedical researchers endeavor to unite in their daily  
> activities - the literature, distilled knowledge sources, data  
> repositories - in their lab, amongst their immediate collaborators,  
> within their restricted community, and across the entire community  
> of basic & clinical biomedical investigators.
>
> Cheers,
> Bill

On Feb 17, 2007, at 12:00 PM, Don Doherty wrote:

>> I'm assuming that "LTP in the corticostriatal connections" is  
>> enough plus
>> maybe one or two references (out of, for instance, 43 references  
>> just from
>> the Journal of Neuroscience)?
>>
>> Currently most neuroscientists agree that there are many different
>> subtleties underlying LTP giving it different characteristics in  
>> different
>> areas of the brain. The other thing is that it seems to be nearly  
>> everywhere
>> in one form or another. So, NMDA and AMPA receptors are key to LTP  
>> and they
>> are nearly ubiquitous. In the striatum, it is dopamine that  
>> provides the
>> local twist with implications in Parkinson's disease.
>>
>> For instance, activation of the D1 receptor increases the  
>> production of NMDA
>> receptor subunits (NR1, NR2A, and NR2B) in striatal neurons  
>> changing the
>> character and amount of NMDA receptors there and, therefore,  
>> influencing
>> LTP. In contrast, activation of D2 receptors results in Long Term  
>> Depression
>> (LTD) but under abnormal conditions (like in Parkinson's disease)  
>> their
>> activation results in LTP.



On Feb 19, 2007, at 2:55 PM, Kashyap, Vipul wrote:

>
>
> Matthias,
>
> This is exactly the approach Bill Bug has in mind, based on which  
> he has created
> these PaTO assertions.
>
> http://esw.w3.org/topic/HCLS/OntologyTaskForce/SeedOntology/ 
> SeedOntologyDetailed
> Followup#preview
>
> Do take a look and send feedback to Don whether this approach looks  
> feasible to
> you.
>
> Cheers,
>
> ---Vipul
>
> =======================================
> Vipul Kashyap, Ph.D.
> Senior Medical Informatician
> Clinical Informatics R&D, Partners HealthCare System
> Phone: (781)416-9254
> Cell: (617)943-7120
> http://www.partners.org/cird/AboutUs.asp?cBox=Staff&stAb=vik
>
> To keep up you need the right answers; to get ahead you need the  
> right questions
> ---John Browning and Spencer Reiss, Wired 6.04.95
>
>> -----Original Message-----
>> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb- 
>> lifesci-
>> request@w3.org] On Behalf Of Matthias Samwald
>> Sent: Monday, February 19, 2007 1:33 PM
>> To: public-semweb-lifesci@w3.org
>> Subject: [public-semweb-lifesci] AD/PD use case document
>>
>>
>>
>> Regarding the use case document Don sent to the mailing list today:
>>
>> Are some of the hypotheses already available in SWAN's RDF format? It
>> would be great to see an example of how they would look as RDF  
>> statements.
>> This would make it easier for the rest of us to judge how other RDF
>> datasources could be connected to the SWAN hypotheses.
>>
>> -- Matthias Samwald
>>
>
>
>
>
>
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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)
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215 843 9367 (fax)


Please Note: I now have a new email - William.Bug@DrexelMed.edu