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RE: [ontac-forum] ISO 15926 and BFO

To: "ONTAC-WG General Discussion" <ontac-forum@xxxxxxxxxxxxxx>
Cc: "Paul J. Werbos" <pwerbos@xxxxxxx>, lander@xxxxxxxxxxxxx
From: "psp" <psp@xxxxxxxxxxxxxxxxxx>
Date: Sun, 20 Nov 2005 16:37:17 -0700
Message-id: <CBEELNOPAHIKDGBGICBGMEAPGOAA.psp@xxxxxxxxxxxxxxxxxx>


This discussion is really hard to follow.  One might assume that being able
to specify relationships between things within the same level of
organization would have an immediate agreement for anyone modeling
biological function.    (01)

It takes some experience to realize that the classical notion of
relationship might not apply well between levels of organization.    (02)

I know that the issue has to do with nested structures.  Time scale and
space granularity are used in most instances  - almost immediately ...    (03)

For example, individual synapses do not have a "relationsip" with the entire
system that is producing a single coherent mental event.  But the
relationship issue is a hard one, since a specific single synapse might be
given control over an emerging phase coherence as part of the phenomenon of
emergence (which happens to be a normal event in mental phenomenon.)  I can
cite the literature ... but this leads into the core of a science
"unrelated" to computer technology.    (04)

It would seem that the sturcture/function discussion would come up.  Does
it?  Is there an awareness by anyone involved in writting the paper at:    (05)

http://genomebiology.com/2005/6/5/R46    (06)

of Q-SAR (Qualitative Structure Activity Relationshp) analysis?    (07)

So this is about the fact that you do allow a relationship to be modeled?
Do you do this in OWL with RDF triples: < subject, verb, redicate >?    (08)


You state in the paper:    (09)

"Controlled vocabularies can be conceived as graph-theoretical structures
consisting on the one hand of terms (which form the nodes of each
corresponding graph) linked together by means of edges called relations. The
ontologies in the OBO library are organized in this way by means of
different types of relations. "    (010)

So you use controlled vocabularies as ontology terms and then establish
relationships between these terms.  So you use a more general triple < a, r,
b > ?  The elements of the vocabulary are not "concepts"?    (011)

But please can you comment, both of you on Gerald Edelman's paper at:    (012)

http://www.pnas.org/cgi/reprint/98/24/13763    (013)

Here the issue is that "a methodology for providing consistant and
unambiguous formal definitions of the relational expressions used in
<medical> ontologies... would violate the actual known behaviors of most
elements of boilogy.    (014)

Perhaps you have seen this issue and have a way to work with degeneracy?    (015)





-----Original Message-----
From: ontac-forum-bounces@xxxxxxxxxxxxxx
[mailto:ontac-forum-bounces@xxxxxxxxxxxxxx]On Behalf Of West, Matthew R
SIPC-DFD/321
Sent: Sunday, November 20, 2005 3:43 PM
To: ONTAC-WG General Discussion
Subject: RE: [ontac-forum] ISO 15926 and BFO    (016)


Dear Barry,    (017)


> -----Original Message-----
> From: ontac-forum-bounces@xxxxxxxxxxxxxx
> [mailto:ontac-forum-bounces@xxxxxxxxxxxxxx]On Behalf Of Smith, Barry
> Sent: 20 November 2005 20:00
> To: ONTAC-WG General Discussion
> Subject: RE: [ontac-forum] ISO 15926 and BFO
>
>
> At 11:51 AM 11/20/2005, you wrote:
> >Dear Barry,
> >
> >
> >
> > > Uniquely, among existing
> > > contributions, the BFO Relation Ontology allows the drawing of a
> > > clear distinction between relations on the level of
> instances (e.g.
> > > between your heart and your body) and relations on the
> level of types
> > > (e.g. between the type human heart and the type human body).
> >
> >MW: Just for the record, ISO 15926 also supports this.
> >
> >
> >Regards
> >
> >Matthew West
>
> ISO 15926 does indeed distinguish between relationships and classes
> of relationships:
>
> A <relationship> is an <abstract_object> that indicates something
> that one thing has to do with another.
>
> A <class_of_relationship> is a <class_of _abstract_object> whose
> members are members of <relationship>.
>
> However, it does not provide an account of the distinction between
> relationships BETWEEN CLASSES (for example in general assertions such
> as: human heart PART_OF human body, capital city PART_OF country) and
> relationships BETWEEN INSTANCES (such as Matthew's heart part_of
> Matthew's body; London part_of England).    (018)

MW: It does precisely this. We have class_of_composition_of_individual
for classes of relationship between classes (e.g. heart part of body)
and composition_of_individual for relationships between individuals,
e.g. Matthew's heart part of Matthew (which would of course be an
instance of the former example).    (019)

MW: We also recognise that in some cases there are relationships between
classes that are not classes of relationship. Specialisation would be
an example of this. Do you support this sort of distinction too? We even
have class_of_specialisation for saying that a member of one class has
a member of another class as a superclass.    (020)

> As is shown in
>
> http://genomebiology.com/2005/6/5/R46    (021)

MW: I've downloaded the PDF. I'll take a look when I get a moment. Its a
bit late now.
>
> these are formally two quite distinct sorts of relationships. And
> only if we provide an account of how they are connected one to the
> other can we understand how an ontology (which deals with
> relationships BETWEEN CLASSES) can be linked to the real world of oil
> rigs and generators.    (022)

MW: Indeed, which is why we do.    (023)

MW: For you not to have seen this I wonder
how you are looking at the model. Have you found the diagrams? If you
click on the little icon beside the entity type name in the list, you
will be taken to a diagram of the part of the model that entity type is
in. I find diagrams much easier than text, and since you use diagrams
in your ontologies you might too.
>
> BS
>
>
>
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