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RE: drug-drug interaction scientific discourse

From: Rich Cooper <rich@englishlogickernel.com>
Date: Thu, 5 May 2011 09:20:51 -0700
To: <rdb20@pitt.edu>, <public-semweb-lifesci@w3.org>, "'Gardner, Gregory'" <gardnerga@upmc.edu>
Message-ID: <E1QI1J1-0006C3-Sd@lisa.w3.org>
Hi Rich B,

What kind of data do you anticipate getting as inputs?  Will it include free
text descriptions, comments, observations, measurements, or will those
things be quantized, digitized or otherwise mapped into structured database
columns?

My question is whether the data will be linguistic in nature, as compared to
mostly structured, as in a relational database?

Curiously,
-Rich C
 
Sincerely,
Rich Cooper
EnglishLogicKernel.com
Rich AT EnglishLogicKernel DOT com
9 4 9 \ 5 2 5 - 5 7 1 2

-----Original Message-----
From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Richard Boyce
Sent: Thursday, May 05, 2011 8:45 AM
To: public-semweb-lifesci@w3.org; Gardner, Gregory
Subject: drug-drug interaction scientific discourse

Hi All,

We are working on creating a linked-data version of an academic 
drug-drug interaction (DDIs) knowledge-base called the DIKB that 
contains assertions about DDIs observed in clinical studies as well as 
assertions about drug mechanisms that can be used to infer DDIs. DIKB 
assertions are linked to supporting and refuting evidence (see 
<http://www.pitt.edu/~rdb20/data/DIKB-lightning-summary-05262010.pdf>). 
Additionally, each use of evidence is linked to "evidence-use 
assumptions"; other DIKB assertions that represent assumptions made by 
the knowledge base curator when inferring a drug mechanism claim from an 
evidence item. We have questions about how to best represent this 
assertion/evidence structure as scientific discourse. We have been 
looking at the SWAN discourse ontology and it seems possible to use its 
elements but have ran into some issues that we are unsure about. For 
example, we are not sure if we should map DIKB assertions to research 
statements qualified as hypotheses or claims and it is not clear to us 
if we should represent DIKB evidence-use assumptions using SWAN 
elements. Would anyone have any thoughts based on their experience 
representing discourse? Also, has anybody used elements from the OBO 
Information Artifact Ontology w/ SWAN to represent scientific discourse?

We also are interested in representing DDIs that are computationally 
inferred from assertions in the DIKB but are not sure if there is an 
ontology for algorithmic inferences. Would anyone have a suggestion?

Thanks in advance,
-Rich

-- 
Richard Boyce, PhD
Assistant Professor of Biomedical Informatics and
Intelligent Systems
Scholar, Comparative Effectiveness Research Program
University of Pittsburgh
rdb20@pitt.edu
412-648-6768
Received on Thursday, 5 May 2011 16:21:38 GMT

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