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Re: Representing conflicting evidence and refutation

From: Joanne Luciano <jluciano@cs.rpi.edu>
Date: Wed, 13 Oct 2010 10:28:52 -0400
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
Message-Id: <76BCF568-10EC-45F5-9605-630AB0946DB3@cs.rpi.edu>
To: "M. Scott Marshall" <mscottmarshall@gmail.com>
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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Joanne S. Luciano, PhD                   Email:   jluciano@cs.rpi.edu
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Received on Wednesday, 13 October 2010 14:29:56 GMT

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