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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: Tue, 12 Jun 2007 13:00:57 +0200
Message-id: <466E7CE9.4090602@xxxxxxxxxxx>
Smith, Barry wrote:
> 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.
> 
> 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.    (01)

For more advanced:  I am working on X.  People who are working on Y are 
usually also working on X, but they tend not to use the term 'X'.  I 
want to retrieve literature on X.  Chances are that articles tagged with 
Y are relevant.  X does not have to be 'isa', 'partof', or the like, of 
Y.  MeSH, ICD etc. provide such help.    (02)

Obviously, when seen through ontological spectacles, such hierarchical 
terminologies are nonsense.  Not all of them were intended to be seen 
through such spectacles, though.  Some of them were intended to be 
organized collections of tags, and not ontologically correct 
descriptions of the reality.  Some of them, I agree, have the taste of 
wannabe-ontologies, and it may encourage their use as if they were 
ontologies, though they are not.  This is the problem, not necessarily 
that they are not.    (03)

vQ    (04)








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