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Re: [ontolog-forum] Two ontologies that are inconsistent but both needed

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: Waclaw Kusnierczyk <Waclaw.Marcin.Kusnierczyk@xxxxxxxxxxx>
Date: Sun, 10 Jun 2007 20:40:28 +0200
Message-id: <466C459C.80406@xxxxxxxxxxx>
Smith, Barry wrote:    (01)

> Some of the ontologies in the OBO Foundry, for 
> instance, work, as a very useful, flexible 
> framework for cataloguing the entities about 
> which biologists are collecting data and thereby 
> integrating this data and making it surveyable. 
> By serving this purpose they help research, e.g. 
> in the systematic analysis of the genetic 
> alterations involved in human cancers (e.g. in 
> Sj÷blom T, et al. The consensus coding sequences 
> of human breast and colorectal cancers. Science. 2006 Oct 
>13;314(5797):268-74.)    (02)

Many of those biomedical terminologies that you have severely criticized 
-- e.g., MeSH, ICD, etc. -- work as very useful, flexible (what did you 
mean by that, by the way) framework for cataloguing e.g., the data which 
biologists are collecting about the entities of their interest.  This 
somehow did not seem to you as serving the purpose of helping research.
While they are certainly not ontologies in the sense you advocate, I 
have been told many times by down-to-earth biologists that what they 
need are not philosophically correct (whatever this would mean, whatever 
doctrine one adopts) ontologies, but ontologies that are good enough to 
make their work easier.  I have heard complaints that overly 
philosophical ontologies are too distant from practical purposes, and 
make the work harder.    (03)

Not that I endorse those claims -- I merely report them here.    (04)

vQ    (05)


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