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: [EMAIL PROTECTED] [mailto:public-semweb-
lifesci-
[EMAIL PROTECTED] 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
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