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RE: [BIONT-DSE] Inclusion versus exclusion criteria

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Wed, 12 Sep 2007 11:30:41 -0400
Message-ID: <DBA3C02EAD0DC14BBB667C345EE2D124841271@PHSXMB20.partners.org>
To: "Kavitha Srinivas" <ksrinivs@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>

> 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.

> 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.

[VK] I agree that whether you need to use OWA/CWA come from an understanding of
the domain. However, sometimes it could also be an artifact of the data
representation scheme. For instance, in Chintan's example above, one could have
negative assertions for drugs, i.e., patient not on drug X, in which case one
would use OWA instead of CWA.

> 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).
> this information.

[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 a polynomial time
reasoner (CEL) for the matching. I may be mistaken, but my initial sense is that
any CEL expression is likely expressed in SQL/Relational Algebra or vice versa. 

---Vipul


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Received on Wednesday, 12 September 2007 15:31:07 GMT

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