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Re: Mapping SKOS into BFO

From: Alistair Miles <alimanfoo@googlemail.com>
Date: Fri, 8 Apr 2011 17:25:16 +0100
To: Jim McCusker <james.mccusker@yale.edu>
Cc: public-esw-thes@w3.org
Message-ID: <20110408162516.GB19816@aliman-desktop>
Hi Jim,

I can't see anything glaringly inappropriate in your suggestion, but I'm very 
far from being an ontological expert, so take that with a good dose of salt.

Coming at this from a very pragmatic point of view, I think I would suggest the 
following.

If it is in some way useful (i.e., adds some practical value) for someone to 
assert that skos:Concept is a sub-class of "generically dependent continuent", 
then I'd say go ahead and make the assertion. If any problematic inconsistencies 
are discovered further down the line, then we could deal with them as they 
arise.

The other thing to bear in mind is that, if two concepts in different concept 
schemes are found to share the same meaning (go with the fuzzy language here), 
then we *do not* recommend that owl:sameAs be used to link them. Rather, 
skos:exactMatch is recommended, as this avoids confusion over what concept is in 
what scheme and other problems like labelling inconsistencies e.g. ending up 
with two preflabels in the same language. I.e., we want to avoid breaking 
features of the data that most SKOS applications depend on for proper 
functioning.

If you think that making the link between skos:Concept and "generically 
dependent continuent" will not lead people into these practical problems, then 
go ahead.

Hth,

Alistair

On Wed, Apr 06, 2011 at 11:02:40PM -0400, Jim McCusker wrote:
> The Basic Formal Ontology is commonly used in biomedical semantics
> through OBO. I would like to propose a mapping of skos:Concept into
> BFO as a subclass of "generically dependent continuent". I believe
> this will help further the ongoing discussion surrounding definitions
> for the term "concept", and will also provide an ontological home for
> it in relation to non-conceptual ontologies. I chose "generically
> dependent continuent" for the following reasons:
> 
> The definition of "generically dependent continuent" is: "Definition:
> A continuant [snap:Continuant] that is dependent on one or other
> independent continuant [snap:IndependentContinuant] bearers. For every
> instance of A requires some instance of (an independent continuant
> [snap:IndependentContinuant] type) B but which instance of B serves
> can change from time to time."
> 
> This refers to entities that exist in relation to something, but it
> doesn't matter what, exactly, that something is. Ideas (and therefore
> concepts) have this property - an idea can exist in my head, I can
> write it down, someone else can read it, and in that process the idea
> is dependent on my brain, the media I write it down on, and then brain
> of the person who reads it.
> 
> A concept is not an occurrent (definition: "An entity [bfo:Entity]
> that has temporal parts and that happens, unfolds or develops through
> time. Sometimes also called perdurants."). While a concept can have a
> lifetime in which it is imagined, changed, and forgotten, in BFO this
> is considered distinct from the entity itself.
> 
> A concept is not an independent continuent (definition: A continuant
> [snap:Continuant] that is a bearer of quality [snap:Quality] and
> realizable entity [snap:RealizableEntity] entities, in which other
> entities inhere and which itself cannot inhere in anything.") These
> are things that exist in and of themselves, without any need for a
> substrate.
> 
> A concept is not a specifically dependent continuent (definition: "A
> continuant [snap:Continuant] that inheres in or is borne by other
> entities. Every instance of A requires some specific instance of B
> which must always be the same.") Concepts do not need some specific
> instance for it to be borne by, but can exist all the same in any
> suitable substrate.
> 
> That leaves generically dependent continuent. A concept needs to have
> some substrate to exist, but it doesn't have to be any one particular
> substrate.
> 
> Additionally, in the Information Artifact Ontology, "information
> content entity" is a subclass of generically dependent continuent. An
> information content entity is "an entity that is generically dependent
> on some artifact and stands in relation of aboutness to some entity".
> Some concepts are about particular things (universal classes and
> properties, for instance), which would make them information content
> entities, and therefore generically dependent continuents.
> 
> Thanks,
> Jim
> -- 
> Jim McCusker
> Programmer Analyst
> Krauthammer Lab, Pathology Informatics
> Yale School of Medicine
> james.mccusker@yale.edu | (203) 785-6330
> http://krauthammerlab.med.yale.edu
> 
> PhD Student
> Tetherless World Constellation
> Rensselaer Polytechnic Institute
> mccusj@cs.rpi.edu
> http://tw.rpi.edu
> 

-- 
Alistair Miles
Head of Epidemiological Informatics
Centre for Genomics and Global Health <http://cggh.org>
The Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford
OX3 7BN
United Kingdom
Web: http://purl.org/net/aliman
Email: alimanfoo@gmail.com
Tel: +44 (0)1865 287669
Received on Friday, 8 April 2011 16:25:47 GMT

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