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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