Re: A question on the vocabulary for 'persons' - ACL level of granularity?

On Sep 14, 2006, at 10:36 AM, Drew McDermott wrote:

>
>
>> [Chimezie Ogbuji]
>>
>> Seems to me the biggest barrier is in coming to a consensus on
>> an appropriate placeholder vocabulary and not neccessarily on  
>> determining
>> all the various ways in which a person (and their related data)  
>> could be
>> expressed in a patient record.
>
> I'm not sure I'm agreeing or disagreeing with Chimezie (it depends on
> what's meant by "consensus" here), but I'd like to emphasize a point
> others have made in this discussion: Deciding to use a particular
> ontology is not like deciding who to marry.  It's just a _vocabulary_.

This is different from most definitions of ontology I am aware of. I  
think confusing ontology with vocabulary will get us into trouble.

> You can mix and match terms from different vocabularies, and you can
> make up a new class that's the intersection of two classes from
> different ontologies.
>
> Of course you don't want to (a) misuse an ontology; (b) duplicate what
> someone else has already done.  But it seems to me that if FOAF
> includes a term for Person (defined as broadly as Dan Brickley says it
> is),

This definition seemed to be along the same lines as the one in the  
HL7 RIM, for which a criticism was recently posted on this list

> then everyone in the world might as well use foaf:Person when
> they want to talk about persons.  If a person in a medical context has
> special properties, then subclass foaf:Person.  If you discover at
> some point that you (or HL7 RIM) has produced a class equivalent to
> one defined previously, then declare them equivalent (owl:sameAs).

Can two classes be declared identical if both their definitions are  
incoherent?

> [It seems to me that it would be good practice to use the earliest
> defined term for something, partly out of courtesy and partly so
> everyone will converge on the same term, but that's an orthogonal
> issue.]

Why should courtesy have anything to do with it? Surely everyone  
should converge on the best definition, not the first? Why is the  
first especially deserving of courtesy?

I think FOAF is an ideal application ontology for its stated goals -  
linking communities of people together, albeit with a bias towards  
computer science types.

I don't think it is appropriate for biomedical science, and I don't  
think your recommended practice of subclassing foaf:Person is a good  
idea. This will lead to a hodge-podge of non-disjoint classes. Others  
have recommended of separating a Person out from the roles a Person  
participates in - surely this is better?

I don't see the problem here as being particularly difficult - there  
are continuants, and there are biological continuants such as  
organisms. These continuants participate in different processes,  
taking on different roles at different times. See [1]

Aside from the very serious problem of lack of formal definitions for  
the central classes Person and Agent, there are a number of problems  
in using FOAF for science

Many of the properties such as foaf:geekcode are relevant for a very  
small proportion of human beings. Surely these should be separated  
out in a separate ontology of  
FOAFCharacteristicsRelevantToMaleComputerScienceUndergrads, in  
accordance with well-accepted principles of normalised design?

Here is something illustrative of the problem with FOAF; from the  
FOAF documention

http://xmlns.com/foaf/0.1/#term_dnaChecksum
"foaf:dnaChecksum -- A checksum for the DNA of some thing. Joke."

Whilst it is surely tempting to litter our ontologies with jokes -  
foaf:motherInLaw jokes, ChickenCrossingRoad in ontologies of animal  
behaviour, reasoning about the odor receptors of DogsWithNoNose and  
so on - I'm afraid I don't think jokes have any place in a reference  
ontology. Sorry to be so humorless. I'm sure the designers of GALEN  
regret adding "vomitus has_part carrot" to their ontology, after a  
certain ontologist uses this as a frequent point of criticism. I'm  
inclined to agree - in-jokes will cause problems for both human and  
computer users.

foaf then goes on to reverse its position, and states: "The  
foaf:dnaChecksum property is mostly a joke, but also a reminder that  
there will be lots of different identifying properties for people,  
some of which we might find disturbing."

...perhaps invoking a distant Gattaca-like dystopian future.

well obviously this is no joke in biomedical science where DNA  
checksums are commonly applied to database records, and a wealth of  
genotypic data is available for human and other organisms, and with  
individual genome resequencing around the corner. Obviously a per- 
human DNA checksum is a naive notion, but it's hardly inconceivable  
that we'd want to record euchromatic DNA sequences for samples of  
cells on a per human basis. This would have to be represented  
appropriately, to make sure the genotypes of cancerous cells are not  
mixed up with normal cells. The presence of a half-jokey half-serious  
dnaChecksum property is highly inappropriate and will add confusion.

How about a deal - we'll let FOAF define properties within the FOAF  
designers realm of expertise, like listing the different kinds of  
online chat accounts, and you leave the DNA stuff to us.

If there are aspects of FOAF that are of use to biomedical science  
(I'm not sure what these are), then these should be separated out  
into a minimal ontology. If people want to reason over databases to  
determine if genotypes correlate with foaf:OnlineGamingAccount then  
they can do so by linking the appropriate ontologies, but  
foaf:jabberID must be strictly separated from ontologies for doing  
science.

Sorry if this is discourteous but I really find it bizarre that FOAF  
is even being considered here.

Chris

[1] http://www.websemanticsjournal.org/ps/pub/2006-13

@ARTICLE{Smith2006,
   author = {Smith, B. and Ceusters, W.},
   title = {Referent Tracking for Treatment Optimisation in  
Schizophrenic Patients},
   journal = {Journal of Web Semantics},
   year = {2006},
   volume = {4},
   number = {3},
   abstract = {
The IPAP Schizophrenia Algorithm was originally designed in the form  
of a flow chart to help physicians optimise the treatment of  
schizophrenic patients. We examined the current version from the  
perspective of recent work on terminologies and ontologies thereby  
drawing on the resources of Basic Formal Ontology, and this with the  
objective to make the algorithm appropriate for Semantic Web  
applications. We found that Basic Formal Ontology is a rich enough  
theory to represent all the entities involved and that applying the  
theory to the IPAP schizophrenia algorithm results in a  
representation that can be used by software agents to perform  
monitoring and control in a referent tracking environment.
   },
}


>
> -- 
>                                                 -- Drew McDermott
>                                                    Yale Computer  
> Science Department
>
>
>

Received on Thursday, 14 September 2006 19:03:15 UTC