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Re: [ontolog-forum] Endurantism and Perdurantism - Re: Some Comments on

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: "Chris Mungall" <cjmungall@xxxxxxx>
Date: Wed, 18 Mar 2015 11:15:21 -0700
Message-id: <46ED6CD9-E5B8-458E-8FE0-8778A303D35E@xxxxxxx>

On 18 Mar 2015, at 9:23, Pat Hayes wrote:    (01)

> On Mar 18, 2015, at 9:17 AM, Thomas Johnston <tmj44p@xxxxxxx> wrote:
>> Could those of you who are involved in this thing vs. event 
>> (endurantism vs. perdurantism) exchange explain to me why, except as 
>> a bit of interesting metaphysical speculation, those of us building 
>> formal ontologies should be interested in it?
> Because if one is using almost any conventional representational 
> notation, from classical FOL through RDF and/or OWL, each of these 
> positions requires one to adopt an axiomatic style which is sharply 
> incompatible with the style the other one forces you to adopt. If your 
> ontology encompasses both kinds of entities, then you are obliged to 
> enforce a rigid top-level distinction between them, since all 
> assertions about one kind have to be made in one axiomatic style, 
> different from those mentioning the others. Basically, one style 
> prohibits attaching a temporal parameter to entity names (because 
> "continuants do not have temporal parts"), the other prohibits 
> attaching temporal parameters to relations (because relations are 
> timeless.) One sees this very sharply in the amount of work involved 
> in the OBO ontologies to keep continuants separated from occurrents. 
> The typical result is that many general facts have to be stated twice, 
> one using each notational style.    (02)

Can you give an example from some widely used OBO ontologies? I'm not 
really aware of work specifically to keep these separate.    (03)

I might agree that there is sometimes a general tendency of some 
ontologies to over-inflate the number of entities into different aspects 
corresponding to upper level categories. But the process vs physical 
entity distinction would be very hard to avoid (or perhaps we are too 
engrained in the mindset of biologists and bioinformaticians). It may 
_seem_ to be the case that facts are stated twice: for example, the GO 
ontology of biological processes (Occ.) will state about classes 'limb 
development', 'forelimb development' and 'hand development', whereas an 
anatomy ontology will also have facts stating facts about classes 'limb' 
'forelimb' and 'hand'. Similarly GO will include occurrent hierarchies 
of biochemical reactions and signaling pathways, and these will be 
related to but modeled distinctly from continuant ontologies about 
molecules and protein complexes and cell parts. What may appear to be 
redundantly stated facts are actually inferred from one hierarchy to 
another.    (04)

I'm all for collapsing distinctions and reducing the number of 
ontologies. I can imagine syntactic tricks that would allow classes from 
one category to proxy for classes in another, e.g. limb for limb 
development, or vice versa. But I don't think anything would be achieved 
here, other than completely baffling users. In addition, when you get 
down to the level of cells and below there are some subtle issues 
involving time and identity that could confound the use of the 
ontologies in query answering.    (05)

Perhaps I just have a hard time envisioning a different model. As I say, 
I believe the distinction is fairly hardwired into people's thinking. 
I'm not talking about ontologists here. Look at any datamodel that 
captures something like biochemical or signaling pathways, at its core 
you will see a bipartite graph of physical entities and occurrents. I'd 
be genuinely interested in seeing a non-handwavy attempt to model things 
differently.    (06)

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