W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > October 2007

FW: [COI] Following up on your comment re "underlying model" in your reviewing the functional requirements spreadsheet

From: Forsberg, Kerstin L <Kerstin.L.Forsberg@astrazeneca.com>
Date: Mon, 29 Oct 2007 17:56:25 +0100
Message-ID: <00EF518168DD14409AA8DB92601D87360175B372@SEMLRDEMBX02.rd.astrazeneca.net>
To: <alanruttenberg@gmail.com>
Cc: <public-semweb-lifesci@w3.org>

Hi Alan,
my comment was about the need for a "underlying model". While the issue I raised is about our current focus on the mappings between specific terms in different terminologies. Instead I would like us to move beyond the mappings and focus more on how to specify different types/classes/kinds of clinical observations. 

      In the Power Points 1] Bo and I have put together we highlight the common interest for secondary use regardless if it is for primary use in Drug Development (i.e. secondary use of Health Care data in clinical research) or for health care actors as a knowledge base (see slide 2). A common model for sharing specifications of types/classes/kinds of clinical observations using applicable terminologies in health care and clinical research is in my mind a key enabler for secondary use. 

      CDISC SDTM is a standard for interchange of information resources describing clinical studies (so called trial parameters), describing study/trial design (e.g. inclusion/exclusion criterion) and describing observations made on subjects in studies (see slide 3). SDTM's information model assumes a flat file structure of variables for information interchange/submissions to FDA (see slide 7 and 8).

      So far, CDISC do not provide a common model to specify the different types/classes/kinds of observation descriptions: what observations of "real-world phenomenon" they describe using different terminologies, the contextual information required to interpret the observation results, alternative classifications and formats for the observation results etc.. Instead sets of terms / codes / "submission values" are published as CDISC's own controlled terminologies using terms such as "ALT", "CRP" and "DIABP" 2] defined in NCI Thesaurus (see slide 5).  

      CDISC SDTM include a trial design variable for inclusion/exclusion criterion rules "in computer-executable form" (see slide 3). This is very good, but as long as we lack a common way to specify, and identify, the different types/classes/kinds of clinical observations, I think it will be hard to express such rules.

- Kerstin																																					  

See: Initial SDTM Presentation by Kerstin and Bo, on http://esw.w3.org/topic/HCLS/OntologyTaskForce/BIONTDSEDCM

"ALT"   = Concept code in NCIt C64433, defined as 
        "A measurement of the alanine aminotransferase in a biological specimen."
"CRP"   = Concept code in NCIt C64548, defined as 
        "A measurement of the C reactive protein in a biological specimen."
"DIABP" = Concept code in NCIt C25299, defined as 
        "The blood pressure after the contraction of the heart while the chambers 
        of the heart refill with blood."

The first two defines the observations, while the last defines the "real-world phenomenon" being o.

Examples from CDISC's first package of controlled terminologies for lab tests and vital signs published as a Excel matrix 

-----Original Message-----
From: Alan Ruttenberg [mailto:alanruttenberg@gmail.com]
Sent: 26 oktober 2007 21:00
To: Forsberg, Kerstin L
Cc: public-semweb-lifesci@w3.org
Subject: [COI] Following up on your comment re "underlying model" in
your reviewing the functional requirements spreadsheet

Hi Kersten,

During the COI call this week you made some reference to the  
"underlying model" being an issue in filling out Vipul's functional  
requirements spread sheet.

Do you think you could say again what the issue was that you were  
referring to?

Received on Monday, 29 October 2007 16:56:34 UTC

This archive was generated by hypermail 2.3.1 : Wednesday, 7 January 2015 14:52:34 UTC