On Jun 11, 2007, at 8:40 AM, Chimezie Ogbuji wrote:
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
(non-realizable_information_entity).
In our case the database entry without commitment to format might be
reasonably considered to be an information_content_entity, whereas
the XML records etc, in the sense we mean them are digital documents
(OBI_352). OBI is making the distinction here between the information
in the record, in the sense that it would need to be interpreted by
some rational agent, and the digital document which contains that
information.
I'd probably push clinical description at least one level lower,
below narrative object, where you also find report, clinical_finding,
diagnosis.
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.
The information entities are what was said. The digitial_entities are
various sequences of bits. The former is encoded as the latter.
Both are dependent in that the what was said is carried by some
medium, as are sequences of bits. That's the connection to BFO
realism - the entities are to be traced back to things in the world.
For instance the bits are traced back to all the spots on the hard
disks(the independent continuants) that carry them. They are
"generically" dependent, in that the bit streams encoded on the disks
are identical as bits - any one of them could be the carrier. So the
bits could depend on any one of them as thing to trace back to. This
is different from quality particulars that inhere in exactly one
independent continuant.
The trick in the demo encoding was to shortcut this, because OBI/BFO
was in flux, and effectively identify the record with some single
independent continuant - a particular set of bits on a specific hard
disk. So that's how they landed there. However a rework of the demo
would follow the route indicated by Chimezie. And certainly the
"database entry without commitment to format" can't even claim to
remotely work as an independent continuant.
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)
I started to look at your table, which is nice. One thing I noticed
is that I don't think that galen:Person and cyc:Person are the same
thing. galen:Person maps either to one or both of cyc:Human or
cyc:HumanBody. compare:
Galen:
Person,
Synonyms:Human
Conventional (necessary) criteria:
hasFunction Growth
hasFunction OrganismReproduction
hasCountability discrete
Cyc:Person (extract)
Most currently known instances of person are instances of human but
there is no reason why all need be (consider Hobbits in the fictional
world of The Lord of the Rings trilogy). They need not even be
instances of living thing (consider the possibility of a person-like AI)
Though amusingly, despite this, the genls include Human.
Haven't looked carefully at more than person, but I will - this is a
very nice collection you've put together.
The DOLCE notion of a formal-expression is really meant for
information-objects 'ordered' with respect to a formal notation:
Class: inf:formal-expression
Necessary:
edns:information-object
( edns:ordered-by some inf:formal-system )
