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Re: Reviewing the Banff demo ontology infrastructure

From: Chimezie Ogbuji <ogbujic@ccf.org>
Date: Mon, 11 Jun 2007 08:40:53 -0400
To: samwald@gmx.at
cc: public-semweb-lifesci@w3.org
Message-ID: <1181565653.6543.23.camel@otherland>

On Sun, 2007-06-10 at 22:20 +0200, samwald@gmx.at wrote:
> Reviewing the Banff demo ontology infrastructure
> 1) What relations do we use to connect a biological entity with artificial entities describing it, e.g. ‘protein records’, ‘sequence records’, ‘Pubmed records’?

I've been using the DOLCE relation edns:about for this purpose.
edns:about is:

The relation between information objects and entities they are about.
The difference with 'expresses' is that the last requires a situation to
be about something. E.g. Dante's Comedy is about facts like Dante's
travel to the hereafter. The Comedy expresses a script as well as
various related meanings, while the facts talked about are not

The domain is inf:information-object and the range is dol:particular.
For example, a patient record is about a patient:

Class patient-record:
( ( edns:about only galen:Patient ) and ( obo:OBO_REL_has_proper_part
only cpr:clinical-description ) )

If we want to focus our attention to descriptions of biological reality,
then the range can be further constrained for this purpose
(dol:particular is really a catch-all, quite like owl:Thing)

> 3) How are information resources (e.g. the very abstract ‘database entry’, or the slightly less abstract ‘XML document associated with a database entry’) best represented in BFO-friendly ontologies?

In my most recent revision, I line [1] up clinical-description with
obi:OBI_342 (information_content_entity) - a subclass of obi:OBI_295

> These entities seem to be in conflict with the realism of BFO-friendly ontologies, yet we need to represent them somehow. This is probably a discussion for the BFO Google Group, but I could not get it started so far.
> Currently, we are classifying several such entities under bfo:Object, e.g. protein records, MeSH qualifiers, terms, notes and journal articles. I have the suspicion that this might be a problem.

Note, as a sibling to non-realizable_information_entity, we have the
notion of a "digital_entity".  These fall under the hierarchy of
"generically_dependent_continuants" instead of under
span:IndependentContinuant (where you'll find bfo:Object).  The
distinction is not completely clear to me.

clinical-description also lines up with the following terms from other
ontologies (which also have a notion of information resources - not
strictly in the TAG sense, however):

- cyc:InformationBearingObject (Cyc)
- inf:formal-expression (DOLCE)
- wn:synset-record-noun-1 (WordNet)

The DOLCE notion of a formal-expression is really meant for
information-objects 'ordered' with respect to a formal notation:

Class: inf:formal-expression
   ( edns:ordered-by some inf:formal-system )

[1] http://purl.org/cpr/mapping#clinical-description

Chimezie Ogbuji
Lead Systems Analyst
Thoracic and Cardiovascular Surgery
Cleveland Clinic Foundation
9500 Euclid Avenue/ W26
Cleveland, Ohio 44195
Office: (216)444-8593


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Received on Monday, 11 June 2007 12:41:11 GMT

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