Dear all,
Interesting connections -- one of the main developers of the CADIAG-2 system
(Prof. Klaus-Peter Adlassnig) was my PhD supervisor. While I was mainly
interested in crisp reasoning back then, I also played around with
fuzzy/probabilistic OWL reasoning. However, the scalability of these
reasoners (such as Pronto) seemed to be very limited back then (two years
ago). It is exciting to hear that this situation has seemingly improved in
the meantime.
The trend towards personalized medicine could generate some very interesting
use-cases, since the information about effects of certain SNPs, molecular
pathway alterations, lifestyle and demographic factors are still quite
incomplete and sometimes contradictory. One could extract the relevant data
for each disease/drug and each patient to yield a knowledge base fragment of
a manageable size, and then try to judge disease risk, drug efficacy or risk
of adverse events based on imprecise reasoning.
Cheers,
Matthias Samwald
// DERI Galway, Ireland
// Konrad Lorenz Institute for Evolution and Cognition Research, Austria
// http://samwald.info
--------------------------------------------------
From: "Joanne Luciano" <jluci...@cs.rpi.edu>
Sent: Wednesday, October 13, 2010 4:28 PM
To: "M. Scott Marshall" <mscottmarsh...@gmail.com>
Cc: "HCLS" <public-semweb-lifesci@w3.org>; "Andrey Rzhetsky"
<arzhe...@medicine.bsd.uchicago.edu>; <pkli...@cs.man.ac.uk>; "Deborah
McGuinness" <d...@cs.rpi.edu>; "Jim McCusker" <james.mccus...@yale.edu>;
"Dominic DiFranzo" <dif...@rpi.edu>; <div...@uchicago.edu>
Subject: Re: Representing conflicting evidence and refutation
Hi Scott,
Interesting you should being this up. Last week when I was at Manchester
I attended the DL (Description Logics) lunch talk by PhD Student Pavel
Klinov, The talk was on an analysis of CADIAG-2 KB. The aim of the
project is to analyze (in)consistency of CADIAG-2 -- the large medical
diagnosing system developed in Vienna in the 80s. The approach is to
translate CADIAG-2 into a P-SH KB and compute all (or most of) minimal
sets of conflicting rules. This is a joint work with David Picado from
the Technical University of Vienna, who provided the system and developed
its translation into P-SH.
Conflicting information in text is exactly what Andrey was working with.
His focus was in biological pathways.
After the talk I had a chat with Pavel and thought that there we other
applications of his work, but we'd need to identify some data sets. I
immediately thought of Andrey Rzhetsky's work on Geneways where he
addressed representing complementary data. I wrote to Andrey in hopes of
getting some data with inconsistencies to see what Pavel's methods would
uncover.
I've copied both Andrey and Pavel on this email as well as a few form the
TWC.
Cheers,
Joanne
On Oct 13, 2010, at 9:43 AM, M. Scott Marshall wrote:
Lilly recently halted development of of the Alzheimer's drug
"semagacestat" because it was making patients worse in two late stage
clinical trials. This type of knowledge seems like very valuable
information to researchers in Alzheimer's. However, in recent searches
of http://clinicaltrials.gov such as
http://clinicaltrials.gov/ct2/results?term=semagacestat, it seems that
the news hasn't been incorporated into the data on the website.
However, assuming that it had been added, I am curious how 'cancelled
clinical trials' can be found in the linked data. Has anyone looked at
this?
http://prescriptions.blogs.nytimes.com/2010/08/17/lilly-halts-alzheimers-drug-trial/?scp=2&sq=alzheimer's%20disease&st=cse
Another example of contradiction/refutation, this time found in
PubMed, is that Metformin apparently doesn't work (only) along the
pathways that previous research indicated:
"Metformin inhibits hepatic gluconeogenesis in mice independently of
the LKB1/AMPK pathway via a decrease in hepatic energy state"
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2898585/
Has anyone seen a way to deal with conflicting information like this
in text mining? If we were to represent this information in RDF, could
we do it in such a way that we could observe the change of the
Metformin association with LKB1/AMPK pathways over time in the
literature?
Cheers,
Scott
P.S. Oktie - It is pure coincidence that the first example is from
clinical trials. :)
--
M. Scott Marshall, W3C HCLS IG co-chair
Leiden University Medical Center / University of Amsterdam
http://staff.science.uva.nl/~marshall
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