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Re: [BIONT-DSE] Inclusion versus exclusion criteria

From: Kavitha Srinivas <ksrinivs@gmail.com>
Date: Wed, 12 Sep 2007 11:06:57 -0400
Message-Id: <8A697F91-E64E-4CB4-BAC3-DE838E5FD10C@gmail.com>
Cc: wangxiao@musc.edu, Alan Ruttenberg <alanruttenberg@gmail.com>, "Andersson, Bo H" <Bo.H.Andersson@astrazeneca.com>, Landen Bain <lbain@topsailtech.com>, Rachel Richesson <Rachel.Richesson@epi.usf.edu>, public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>, public-hcls-dse@w3.org, Stanley Huff <Stan.Huff@intermountainmail.org>, Yan Heras <Yan.Heras@intermountainmail.org>, "Oniki, Tom (GE Healthcare, consultant)" <Tom.Oniki@ge.com>, Joey Coyle <joey@xcoyle.com>, "Bron W. Kisler" <bkisler@earthlink.net>, Ida Sim <sim@medicine.ucsf.edu>
To: "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>

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 is fair to assume that they are not taking  
the drug (closed world assumption).
2.  I tend to think this comes from an understanding of the domain  
(unfortunately), and what you are modeling rather than the data  
characteristics per se.
3.  There is some elegant work by Boris Motik and others which has  
addressed the issue of combining the two although I don't know what  
the status is on implementation.  (http://www.webont.org/owled/2005/ 
sub12.pdf).  In terms of whether you can do this using SQL querying  
alone, based on our experience, its unlikely.  The problem is that  
the types of clinical exclusion and inclusion criteria we saw on  
clinicalTrials.gov cannot be easily reduced to SQL querying (at least  
with the structured medical records we got from Columbia).  From  
discussions with other institutions, we know this isn't unique to  
Columbia (i.e., there is a substantial "semantic gap" between what's  
in the structured record and what is being queried by investigators  
for clinical trials).

Kavitha
IBM Research


On Sep 12, 2007, at 9:14 AM, Kashyap, Vipul wrote:

>> 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 DL queries.
>
> [VK] The key issues we may want to explore in the context of a well  
> defined use
> case (which hopefully mirrors the real world to a significant  
> extent) are:
> 1. How do we decide when to use OWA vs CWA?
> 2. Is it possible to look at the data characteristics to determine  
> that? For
> instance, Chintan's lab example where negative statements are  
> explicitly
> asserted.
> 3. Use of appropriate technology for the same. For instance, we may  
> want to
> articulate the pros and cons of using a SQL querying based approach  
> as opposed
> to an OWL classification based approach.
>
> ---Vipul
>
>
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Received on Wednesday, 12 September 2007 15:17:44 GMT

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