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Re: Evidence

From: Pat Hayes <phayes@ihmc.us>
Date: Thu, 21 Jun 2007 16:57:23 -0500
Message-Id: <p06230930c2a0a4b1a3af@[10.100.0.39]>
To: public-semweb-lifesci@w3.org
Cc: alanruttenberg@gmail.com, samwald@gmx.at, Dan Brickley <danbri@danbri.org>, <aldo.gangemi@istc.cnr.it>

>Hi all, Dan (Brickley) pointed me at these discussions on DOLCE.

Well, actually I only mentioned BFO. But you are 
correct in surmising that I had DOLCE partly in 
mind.

>I  tend to avoid too many emails and forums on 
>foundational ontologies, in favor of 
>constructive work, but this mailing list seems 
>oriented at doing real things, then I am eager 
>to come back to my old home in medical 
>ontologies :)
>
>Some comments and recap on the current status of 
>DOLCE and its utility for medical ontologies.
>
>(1) Continuant vs. Occurrent
>
>Pat, we already had this discussion at least two 
>times; the last one was very detailed and we 
>(apparently) agreed on the fact that we might be 
>free to adopt the distinction or not, even in 
>DOLCE: if you want to stay neutral, just use 
>Entity or SpatioTemporalEntity.

Yes, I know you can be 'neutral' in DOLCE. But 
this isn't using DOLCE correctly, as it was meant 
to be used. And I was intending to make a 
stronger point: not just that one can be 
continuant/occurrent neutral, but that having the 
distinction in a high-level ontology at all is 
actively harmful. The rest of your message makes 
my main point for me.

>The distinction can be useful in some domains 
>that share a common sense, linguistic 
>(Western-variety) intuition, but I will not 
>fight for it, as for any other.

If only everyone else had your laissez-faire attitude.

>The point of DOLCE and related ontologies is 
>having explicit *rationales* to justify 
>modelling choices, not to dictate how people 
>should think or model the world. As a matter of 
>fact, in the context of the NeOn project 
>(<http://www.neon-project.org>http://www.neon-project.org), 
>we are moving to a "design pattern" approach to 
>ontology reuse, which will probably change the 
>way foundational or reference ontologies should 
>be used or thought about.

That sounds interesting, indeed. Can you point to more on this topic?

>(2) Roles and occurrents
>
>Roles, as they are modelled in DOLCE-Lite-Plus 
>(<http://www.loa-cnr.it/ontologies/DLP_397.owl>http://www.loa-cnr.it/ontologies/DLP_397.owl) 
>and in 
>DOLCE-Ultralite (<http://www.loa-cnr.it/ontologies/DUL.owl>http://www.loa-cnr.it/ontologies/DUL.owl), 
>are applied to continuants, but this is just a 
>terminological choice that adheres to the usual 
>intuition of roles played by agents, substances, 
>etc.

But this is disingenuous. Maybe it was just a 
terminological choice when you made it, but now 
its in the foundational ontology it has the force 
of case law. It is virtually impossible for a 
user to deny it: if he or she tries to, all kinds 
of tools will give error messages, etc.. It 
really isn't possible to ignore the distinction 
under these circumstances. One has to be VERY 
careful when writing things that will get set 
into stone in a 'standard'.

>However, a similar intuition is provided for 
>occurrents by the classes Course and Task 
>in DOLCE-Lite-Plus and by the classes 
>EventStructure and Task in DOLCE-Ultralite.

A perfect illustration of my point. Why should 
anyone have to understand and remember all this, 
all these complicated distinctions about what 
goes with what but not with what other? What USE 
is any of this stuff? What would be lost if it 
were all simply swept away?

There are entities that occupy space and last for 
a time. One can use a single, uniform, set of 
concepts to refer to the spatial and temporal 
relations between such things, and their 
mereology and if necessary their geometry and 
topology, simply *because* they occupy space and 
time. There is no need to pay attention to all 
this clutter of terminological distinctions.

Now, of course, there are distinctions to be 
made: not all spatiotemporal things are in the 
same category. But they are all *contained in 
space and time* in the same way, which is why 
(you wanted a rationale, right?) any of their 
properties or relations *which arise from or 
refer to the nature of this containment* can be 
described in one way, and used for all of them. 
Which simplifies things enormously and means that 
busy, practical biologists don't have to keep 
wondering whether the Krebs cycle or a computer 
program is a continuant or an occurrent. And 
then, once that distinction goes away, all these 
other distinctions go away as well.

>In general, the class Concept is used to talk of 
>notions that are used to classify any entity at 
>some time for some reason.

Thats a nice definition. I presume it is OK to 
parse it as "...classify (any entity at some 
time) for some reason."

>If you want to use Evidence as a role for 
>(the result, execution of) an experiment, then 
>you can use EventStructure or directly Concept. 
>The distinction, where needed, makes sense: 
>roles of occurrents have usually a richer 
>structure than roles of continuants, because 
>they are used to suggest how events and their 
>temporal structure should be interpreted in some 
>context

How do you get that from the usual conditions on 
continuants? How do contexts come into the 
picture? Surely events have contexts too, no?

>; in order to be an evidence, the result of an 
>experiment should be obtained in a certain way, 
>e.g. with explicit methods and control 
>conditions.
>Pat, notice that in DOLCE-Ultralite you can 
>introduce experiment results as entities, 
>classified by an "EvidenceConcept"

I would suggest that anything that you can refer 
to using a name is an "entity" of some kind.

>: who cares about Brentano's theology (poor guy, 
>however, did he make anything bad to your 
>ancestors? :)).

No :-) I got fed up having Barry cite him at me 
every time we argued, so I went and checked out 
where his ideas really came from. In fact 
Brentano is one of the main sources for the 
'continuant' notion: both Barry and Peter Simons 
explicitly acknowledge him. It does not come from 
robust Western linguistic common sense, as you 
imply above and many people assume. (It is in 
fact a *very* peculiar notion.) And Brentano 
liked the idea because he was absolutely sure 
that he had a soul, and that souls had to be 
continuants for basically theological reasons. 
Makes you just love philosophy, finding out 
things like this.

OK, enough from me on this on this topic on this 
email list. I promised not to debate this stuff 
here. So Aldo, you get the last word, if you want 
it.

Pat

>
>Something else on another thread about DOLCE and 
>solutions for readability of horrible 
>foundational terms.
>Cheers
>Aldo
>
>>  >On Jun 12, 2007, at 3:53 PM, 
>><mailto:samwald@gmx.at?Subject=Re%3A%20Evidence&In-Reply-To=%253Cp06230907c29c6cae1e1a%40%5B10.100.0.39%5D%253E&References=%253Cp06230907c29c6cae1e1a%40%5B10.100.0.39%5D%253E>samwald@gmx.at 
>>wrote:
>>  >
>>  >>
>>  >>Hi Waclaw,
>>  >>
>>  >>>Matthias, if you look carefully at BFO, you'll see that roles are
>>  >>>entities.  This means that evidences, as roles, are entities.
>>  >>
>>  >>Of course. I just wanted to differentiate that an experiment is not 
>>  >>an instance of any class called 'evidence' (in other words, an 
>>  >>experiment 'is not' evidence). Instead, it should be associated 
>>  >>with an 'evidence-role'.
>>  >
>>  >The only problem with this is that roles inhere in continuants 
>>  >rather than in occurrents. One way around this is not to say that 
>>  >evidence is an experiment, but rather the results of an experiment.
>>
>>If I may interject, the fact that you need to find a way 'around' 
>>this illustrates what I have long found to be the case, that the 
>>continuant/occurrent distinction, and the resulting artificial 
>>restrictions that it places upon what one is allowed to say, is more 
>>harm than it is worth. One can take any ontology (such as BFO) that 
>>is based up on it and simply erase the distinction (and all its 
>>consequent distinctions) and nothing is thereby lost, only a 
>>simplification achieved and the need for artificial work-arounds 
>>diminished. It is in any case based on very debatable (and indeed 
>>debated) philosophical assumptions, arising chiefly from 
>>ordinary-language philosophy (and Brentano's theology) than from 
>>anything scientific. It carves nature at language's joints rather 
>>than nature's joints.
>>
>>Pat Hayes
>>
>>
>>-- 
>>---------------------------------------------------------------------
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>>40 South Alcaniz St.	(850)202 4416   office
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>><http://www.ihmc.us/users/phayes>http://www.ihmc.us/users/phayes
>>
>
>_____________________________________
>
>Aldo Gangemi
>
>Senior Researcher
>Laboratory for Applied Ontology
>Institute for Cognitive Sciences and Technology
>National Research Council (ISTC-CNR)
>Via Nomentana 56, 00161, Roma, Italy
>Tel: +390644161535
>Fax: +390644161513
><mailto:aldo.gangemi@istc.cnr.it>aldo.gangemi@istc.cnr.it
>
><http://www.loa-cnr.it/gangemi.html>http://www.loa-cnr.it/gangemi.html
>
>icq# 108370336
>
>skype aldogangemi


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IHMC		(850)434 8903 or (650)494 3973   home
40 South Alcaniz St.	(850)202 4416   office
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FL 32502			(850)291 0667    cell
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Received on Thursday, 21 June 2007 21:57:38 GMT

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