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Re: [ontac-forum] Surveyed Ontology "Library" Systems

To: nicolas.rouquette@xxxxxxxxxxxx, ONTAC-WG General Discussion <ontac-forum@xxxxxxxxxxxxxx>
From: Barry Smith <phismith@xxxxxxxxxxx>
Date: Sun, 30 Oct 2005 09:44:38 -0500
Message-id: <>
Responding to Nicolas and Denise:    (01)

> >I also do not think, though, that the relationships I have seen 
> defined by the
> >ontology community are sufficiently rigorous to meet the needs of individual
> >domains.
> >
>Do you have an idea about what's missing?
>Barry distinguishes 3 worlds of things:
>- concept systems (describing the meaning of terms w.r.t. relations
>among terms)
>- real-world entities (instances & types organized in an ontology)
>- information models about the world (e.g., an allegorical document)    (02)

Better not to call these three worlds. There is only one world, built 
up out of instances organized (in complex ways) by types.    (03)

>When we use 'part-of' at the instance level to be ontologically accurate
>in the sense of Barry,
>we are still vague about what is the criteria by which we adjucate on
>parthood. This goes
>back to issues of defining criteria of identity and unity.    (04)

Every descriptive/scientific endeavor will face cases where instances 
clearly stand in a given relation (e.g. my heart part-of me); other 
cases where they clearly do not stand in this relation (e.g. NOT: my 
heart part-of the Arc de Triomphe); and yet other cases where it is 
hard to tell (e.g. ?: my heart part-of ONTAC-WG)    (05)

My advice to all is to concentrate initially on the first group of 
cases (low hanging group). Certainly you should not allow the 
existence of the third group to block your efforts from the start.    (06)

>We need identity to make sense of "a123 part-of b456". How do I
>recognize 'a123' among all possible instances?    (07)

Typically it will be you who has baptised the relevant instance by 
using this designation. Thus you may have baptised your heart as 
'a123'. If you do not know what instance 'a123' stands for, then do 
not use this instance designator in your work!    (08)

>I have a feeling that, at a coarse level, we're more or less in agreement.
>At a practical level, there are wholes that are problematic w.r.t what
>should we be doing next.    (09)

Don't let worries about the problematic cases keep you from doing 
good work with the non-problematic cases.    (010)

>Whether we want to use an existing ontology build our own or some
>combination of the two,
>we need  to be practically clear about what it means to describe the
>meaning of a relationship.
>How many different kinds of 'worlds' do we need? thesauri, ontologies,
>contexts, etc...    (011)

There is only one world, but it is very complex. I think we need many 
different kinds of information artefact to deal with this one world, 
from scientific textbooks (containing information about types) to 
electronic health records (containing information about instances), 
and similarly in every other domain.    (012)

>In this example, suppose we want to practically account for the meaning
>of the 'part-of' relationship at the instance level
>(i.e., the 'part-of' relationship in the ontology of real-world entities)
>- in 'conventional' ontologies, we'd have things like:
>owl:Class A
>owl:Class B
>part-of: A -> B
>A a123
>B b456
>part-of(a123,b456)    (013)

The issue is how does the part-of relation between A and B, which we 
might write:    (014)

PART-OF(A,B)    (015)

relate to the part-of relation between given instances, say:    (016)

part-of(a123,b456)    (017)

My answer is as follows:    (018)

PART-OF(A,B) =def for every instance a of A there is some instance b 
of B which is such that part-of(a,b)    (019)

In brief: all As are part-of some Bs    (020)

This is simplified somewhat since it does not take account of time. 
However, the detailed (all-some) account is still quite simple (see 
http://genomebiology.com/2005/6/5/R46), and has the advantage that it 
applies in just the same way to all the so-called associative 
relations. Thus for example    (021)

LOCATED-IN(A,B) =def for every instance a of A there is some instance 
b of B which is such that located-in(a,b)    (022)

In brief: all As are located-in some Bs.    (023)

I believe that this all-some approach is consistent, too, with the 
underlying idea of Description Logic, where type-level relations must 
always be defined through the instance level.    (024)

But if any members of the list have a better account of how 
type-level relations are to be defined, I would be pleased to hear what it is.    (025)

With greetings
Barry    (026)

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