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Re: Reviewing the Banff demo ontology infrastructure

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Mon, 18 Jun 2007 01:58:23 -0400
Message-Id: <E3871C36-19B9-4325-BF43-6C9EC91760BC@gmail.com>
Cc: samwald@gmx.at, public-semweb-lifesci@w3.org
To: ogbujic@ccf.org

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  

I'd probably push clinical description at least one level lower,  
below narrative object, where you also find report, clinical_finding,  

>> 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:

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 )
Received on Monday, 18 June 2007 05:58:29 UTC

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