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Re: [ontolog-forum] Ontology and methodology

To: "[ontolog-forum] " <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "David Decraene" <David@xxxxxxxxxxxxxxx>
Date: Mon, 19 Mar 2007 16:49:22 +0100
Message-id: <28A0FFC7AEF0014AA8C2CE543AE13F5B8B89D1@xxxxxxxxxxxxxxx>
>JohnS:    (01)

>> Pet, for example, is in the sublattice under Role, but
>> it is also under Animal, since every pet is an animal.    (02)

>seems not so good as it supports the usual isa-overloading
>that confuses. A 'pet' is not an 'animal' in the same
>sense that a 'cat' is an 'animal', surely. Placing
>one of these under Role and the other not shows
>this.    (03)

>Why not:    (04)

 > pet is the name of the second participant in
 > a having-pet-relationship.    (05)

>In English, we have some minimal but productive
>morphology for such entities: e.g.,    (06)

 > employer, employee    (07)

>This provides more background to what it means
>to place something under 'Role'.    (08)

The problem I have however with keeping role-like concepts completely distinct 
(different hierarchy) from what many refer to as natural kinds is that you 
often have to make an ugly choice 
(I'll take proteins as an example again):    (09)

Either you maintain a huge flat list of proteins (tens of thousands) all 
directly related to protein (isa protein) because you are not allowed to 
organise it's children into role-like hierarchies.    (010)

Or you create artificial hierarchies that completely mimic & point to the 
role-hierarchy in question (e.g. protein as an enzyme, protein as a 
transferase, versus the role enzyme & transferase) in order to structure the 
ontology a bit more and make it more manageable.    (011)

None of these solutions strike me as elegant/aesthetic nor do they aid ontology 
development.    (012)

Internally we do integrate the role-like concepts into the regular hierarchies, 
but also (try to) define them through necessary and sufficient relations 
(enzyme: a protein with function-realisation catalysis) and (try to) establish 
guidelines that aid this as (try to) to avoid ontological misinterpretations to 
often rise from these situations.    (013)

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