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Re: Evidence

From: William Bug <William.Bug@DrexelMed.edu>
Date: Wed, 13 Jun 2007 01:54:14 -0400
Message-Id: <A0967BDF-F6D2-45E1-95D9-559962822D51@DrexelMed.edu>
Cc: <samwald@gmx.at>, "Waclaw Kusnierczyk" <Waclaw.Marcin.Kusnierczyk@idi.ntnu.no>, <phismith@buffalo.edu>, <public-semweb-lifesci@w3.org>
To: "Skinner, Karen (NIH/NIDA) [E]" <kskinner@nida.nih.gov>
Hi Karen,

We're working on an expression of standard cognitive assessments and  
behavior tests in BIRNLex, as many of the functional imaging studies  
covered in the Function BIRN test bed make use of a whole battery of  
such tests - including the Fagerstrom Test for Nicotine Dependence.

Our goal is to express these using BFO and other OBO Foundry  
ontologies in such a way that the ultimate result can be incorporated  
into OBI.  To do so, requires we create a great many other entities,  
such as "Smoking Behavior".   Working through a few examples so that  
we can put these out on the BFO list for review is one of the current  
tasks on our plate.  In fact, I've got a meeting coming up soon with  
the FBIRN Project Manager Jessica Turner (http://www.nbirn.net/about/ 
personnel.shtm) who along with Christine Fennema-Notestine from the  
Morphometry BIRN and Angie Laird from the Brainmap.org group (Fox/ 
Lancaster) has been spear-heading this effort to compile a  
comprehensive list of the assessments and behavioral features we need  
to represent.  We'll also ultimately want to vet this with the folks  
at the fMRI Data Center (www.fmridc.org).

The ultimate goal is - built on a BFO + OBO-Relations foundation - to  
express evidence associated with executing these assessments using  
OBI and the PATO-associated Phenotype assertion formalism under  
development by NCBO+GO investigators.

We'd hoped to also make use of relevant terms in the CVs created by  
PsychInfo, but there have been licensing issues that have got in the  
way to date.

Cheers,
Bill

On Jun 12, 2007, at 4:41 PM, Skinner, Karen (NIH/NIDA) [E] wrote:

>
> This discussion on "evidence" makes me wonder if "inclusion" or  
> "exclusion" criteria for a study are considered as "evidence" or  
> are they something else?  For example, if "smokers" are to be  
> excluded from a study, a definition of a "smoker" must exist, and  
> then an interpretation of whether the subject satisfies the  
> definition  must exist. In the
> "Fagerstrom Test for Nicotine Dependence", the subject is evaluated  
> with respect to a series of questions, each of which requires its  
> own "evaluation."  http://ww2.heartandstroke.ca/DownloadDocs/PDF/ 
> Fagerstrom_Test.pdf
>
> Is there a definition for "evidence" that applies to any aspects of  
> this situation, and if so, what would it be?
>
> Karen Skinner
>
>
> -----Original Message-----
> From: samwald@gmx.at [mailto:samwald@gmx.at]
> Sent: Tuesday, June 12, 2007 3:53 PM
> To: Waclaw Kusnierczyk
> Cc: phismith@buffalo.edu; public-semweb-lifesci@w3.org
> Subject: Re: Evidence
>
>
> Hi Waclaw,
>
>
>> Matthias, if you look carefully at BFO, you'll see that roles are
>> entities.  This means that evidences, as roles, are entities.
>
> Of course. I just wanted to differentiate that an experiment is not  
> an instance of any class called 'evidence' (in other words, an  
> experiment 'is not' evidence). Instead, it should be associated  
> with an 'evidence-role'.
>
> cheers,
> Matthias
>
> cheers,
> Matthias Samwald
>
> ----------
>
> Yale Center for Medical Informatics, New Haven / Section on Medical  
> Expert and Knowledge-Based Systems, Vienna / http:// 
> neuroscientific.net
> --
> Psssst! Schon vom neuen GMX MultiMessenger gehört?
> Der kanns mit allen: http://www.gmx.net/de/go/multimessenger
>
>



Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)


Please Note: I now have a new email - William.Bug@DrexelMed.edu
Received on Wednesday, 13 June 2007 05:51:58 GMT

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