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

To: "[ontolog-forum] " <ontolog-forum@xxxxxxxxxxxxxxxx>, "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "Smith, Barry" <phismith@xxxxxxxxxxx>
Date: Mon, 11 Jun 2007 16:22:12 -0600
Message-id: <20070611222909.15274109592@xxxxxxxxxxxxxxxxx>

At 12:40 PM 6/10/2007, Waclaw Kusnierczyk wrote:
>Smith, Barry wrote:
> > 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.)
>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.    (01)

For starters: I am working on X. Y and Z are 
subtypes of X, V and W are parts of. I need all 
the information about X, and so I need 
information about Y and Z and V and W, too. MeSH, 
ICD etc. will not necessarily give me this, at my 
command. A good ontology would.
BS    (02)

>Not that I endorse those claims -- I merely report them here.
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>    (03)

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