Thurs, September 13, 2007 Teleconference Agenda:
Time: 11:00 am EDT Sept 13, 2007 in America/New York for a duration of
1 hour
Phone: tel:+1-617-761-6200 (Zakim) conference #4257 (HCLS)
irc://irc.w3.org:6665/hcls
Chairs: Eric Neumann, Tonya Hongsermeier
Agenda:
a) Convene, take roll, review pr
Clinical Observations Interoperability Telcon
http://esw.w3.org/topic/HCLS/OntologyTaskForce/BIONTDSEDCM
Date and Time:
Spetember 18th, Tuesday 11:00am - 12:00pm EDT
Agenda
1. Sign off on the Use Case
2. Discuss next steps
Telcon Details:
Phone
+1 617 761 6200, conf
Clinical Observations Interoperability Telcon
http://esw.w3.org/topic/HCLS/OntologyTaskForce/BIONTDSEDCM
Date and Time:
Spetember 18th, Tuesday 11:00am - 12:00pm EDT
Agenda
1. Sign off on the Use Case
2. Discuss next steps
Telcon Details:
Phone
+1 617 761 6200, conf
> We perform a more simplistic set difference wherein we first find all
> patients that satisfy the inclusion criteria and then exclude
> patients that satisfy the non-negated exclusion crtieria. Sorry for
> the terse explanation, we describe our methodology in detail in this
> draft appearing in
> Just a quick correction -- the SHER reasoner is different from the
> CEL reasoner, because it is built on
> the standard tableau algorithm (internally SHER uses Pellet). It
> supports the SHIN subset of DL
> (in OWL DL terms, no nominals).
[VK] Thanks for the clarification. Now it falls into p
Kashyap, Vipul wrote:
I guess the issue then becomes for which data items/decision
criteria is
negation explicitly asserted (MRSA) vs it needs to be inferred (drugs)
Also, is it the case that one can make this statement about all
labs without
loss of generality? Or can this be said only in
At 08:06 AM 9/12/2007, Kavitha Srinivas wrote:
1. Yes, as Chintan said, in the case where you had explicit
negations in the data (e.g., the lab data rules out the presence of a
certain infectious agent), you clearly want to use open world
reasoning. However, if someone is not explicitly asser
[VK] It will be great if you could share specific examples of some
criteria that
were not expressible in SQL. We can then incorporate those into the
use
case and help make a case for SW technologies. On the other hand,
taking a quick
look at the SHER project at IBM, looks like you are using
Here's an early reminder for Monday's BioRDF telcon.
Cheers,
Susie
== Conference Details ==
* Date of Call: Monday September 17, 2007
* Time of Call: 11:00am Eastern Time
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.89.06.34.99 (Nice, France)
* Dial-In #: +44.117.370.6
> However, if someone is not explicitly asserted to be on
> some prescription drug, it is fair to assume that they are not taking
> the drug (closed world assumption).
[VK] The key issue is how well this assumption is likely to work in practice.
Guess we need some experimentation to get at this.
Hi Satya,
I believe the problem is even deeper. There is no unambiguous definition
for a pathway. Pathways are almost arbitrary groupings due to historical
and experimental reasons. Instances of pathway class in Biopax should be
treated as tags on interactions to enable easier querying.
The
1. Yes, as Chintan said, in the case where you had explicit
negations in the data (e.g., the lab data rules out the presence of a
certain infectious agent), you clearly want to use open world
reasoning. However, if someone is not explicitly asserted to be on
some prescription drug, it i
Chimezie Ogbuji wrote:
In SPARQL, the combined use of FILTER/!/BOUND effectively gives you a
mechanism for matching records with non-monotonic mechanisms without an
entailment regime. This is how we are able to *explicitly* ask for the
absence of an assertion based only on what the RDF dataset
> Agree. The assumption is that the user will choose whether it is
> closed world or open world. The key point that we've observed in
> terms of our clinical trials matching work using ontologies is that
> you need BOTH options to be available to correctly translate the
> exclusion criteria into
On Wed, 2007-09-12 at 09:31 +0100, Xiaoshu Wang wrote:
> You SHOULD not choose and you have to use open world reasoning because
> how someone can tell which part of the world is closed and which part is
> not.
Sorry, Xiaoshu, but I don't agree that you *have* to use open world
reasoning. That
> You SHOULD not choose and you have to use open world reasoning because
> how someone can tell which part of the world is closed and which part is
> not.
[VK] I think this is a good design principle we should consider when creating a
solution to the use case.
Open World Assumption + Local Clos
Chintan Patel wrote:
Regarding negation of exclusion criteria, it is interesting that you
mention open versus closed world reasoning. We have found that
depending on the underlying clinical data being queried, we might need
to choose between open and closed world reasoning.
You SHOULD not choo
> Note that it's impossible to answer the intended query above without
> SPARQL-DL - and the most intuitive syntax for this kind of query in
> SPARQL-DL may not be triple-based, cosmeticised or not. E.g. "ALL
> astrocyte develops_from SOME ?"
>
> I am heavily biased towards TBox queries -
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