I took my Ph.D. in Chemistry and worked for 25 years doing biochemical
research in a pharmaceutical company. That leaves me with a warm spot in my
heart for chemistry. (01)
I have had occasion to dabble in representation of elements (and substances
generally), primarily to reassure myself that the concepts needed to build
the detailed technical representations are all represented in the Foundation
Ontology. But since the technical details of Chemistry are not vital to the
Foundation ontology itself, few of those details show up in the current
version of COSMO. To distinguish elements, one needs to get into the number
of protons in the nucleus, and for isotopes, the number of neutrons.
"Proton" and "Neutron" are in the COSMO, to provide the basis for those
distinctions. But this is not the sort of stuff that kids tend to talk
about - the same kids that can handle language well, and learn from it.
Supporting a basic language-understanding program is one of the
demonstration applications I think a widely accepted common FO is going to
need, so the focus of the FO is on the basic concept representations that
can support NLU with the basic vocabulary, as well as supporting creating
logical descriptions of more specialized things. (02)
Chemistry is one of the topics that would form a domain extension to the FO.
Unless there is a specific project to delve into it deeply and use the
result (project CALO, anyone?) any effort in that direction would appear to
be premature for me, or duplicative for many others. If, however, someone
is gearing up to create a *standard* or widely used domain ontology for
chemistry (with real applications that use automated reasoning), I would be
happy to contribute some effort. (03)
Pat (04)
Patrick Cassidy
MICRA, Inc.
908-561-3416
cell: 908-565-4053
cassidy@xxxxxxxxx (05)
> -----Original Message-----
> From: ontolog-forum-bounces@xxxxxxxxxxxxxxxx [mailto:ontolog-forum-
> bounces@xxxxxxxxxxxxxxxx] On Behalf Of Pat Hayes
> Sent: Friday, April 17, 2009 4:06 PM
> To: [ontolog-forum] ; John F.Sowa
> Subject: Re: [ontolog-forum] ISO merged ontology effort "MCO"
>
>
> On Apr 15, 2009, at 10:48 AM, John F. Sowa wrote:
>
> >
> > -------- Original Message --------
> > Subject: Your Ontology Summit discussion list
> > Date: 22 Jan 2009
> >
> >
> ...
> > The periodic table of the elements, for example, should be one of the
> > ontologies in the repository. It can be used by chemists, physicists,
> > pharmacists, etc., independent of any theory about the fundamental
> > nature of atomic particles.
>
> Recently Ive been talking to some chemists about this. They need to
> distinguish elements from isotopes, H2 from H and O2 from O from O3,
> etc.., and they need concepts such as 'isopropyl alcohol (AH) in which
> at least two carbon atoms are C14' and the like. They also need to
> distinguish oxygen-the-stuff from oxygen-the-element from oxygen-the-
> reagent from oxygen atoms (at least) (not proper chemical terminology
> here). And this is just for the elements: compound are a whole lot of
> other issues.
>
> >
> > A registry/repository that contains a large collection of such
> > modules/theories/ontologies (or whatever anyone might call them)
> > would be immensely valuable. I strongly recommend that we *begin*
> > with assembling and organizing such modules. This might not be
> > as theoretically exciting as debating the upper level ontologies,
> > but it would provide a valuable service with immediate benefits.
> >
>
> I agree. But (see above) we need subject-matter experts involved with
> this, as they have distinctions that we amateurs will fail to make,
> and thereby cause structural problems for others. So now we have a
> social/political/financial issue: how do we get the ontology writers
> into close collaborative contact with the SMEs?
>
> Pat
>
> PS. In my experience, this kind of work is much more intellectually
> exciting than anything in the 'upper' regions.
>
>
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>
>
>
>
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