- From: Joanne Luciano <jluciano@cs.rpi.edu>
- Date: Wed, 13 Oct 2010 10:28:52 -0400
- To: "M. Scott Marshall" <mscottmarshall@gmail.com>
- Cc: HCLS <public-semweb-lifesci@w3.org>, Andrey Rzhetsky <arzhetsk@medicine.bsd.uchicago.edu>, pklinov@cs.man.ac.uk, Deborah McGuinness <dlm@cs.rpi.edu>, Jim McCusker <james.mccusker@yale.edu>, Dominic DiFranzo <difrad@rpi.edu>, divoli@uchicago.edu
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 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Joanne S. Luciano, PhD Email: jluciano@cs.rpi.edu Research Associate Professor 110 8th Street, Winslow 2143 Tetherless World Constellation Troy, NY 12180, USA Rensselaer Polytechnic Institute Office Tel. +1.518.276.4939 Global Tel. +1.617.440.4364 (skypeIn) Office Fax +1.518.276.4464 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Received on Wednesday, 13 October 2010 14:29:56 UTC