Re: [ontology-summit] [Quality] What means

[Pat Hayes <phayes@xxxxxxx>]

At 10:14 AM -0400 3/21/08, Barry Smith wrote:

> Patrich

Ah, if only I were...

> Hayes writes:
>
> We simply do not
> >yet know what 'well structured' can possibly
> >mean, as a general category or classification
> >applying uniformly to all ontologies. The world
> >has not yet even settled on a single class of
> >basic logics to write ontologies in, and notions
> >of 'well-structured' must be hostage to the
> >underlying language, since the same structure may
> >easily be an efficient and robust technique in
> >one language and a syntax error or worse in
> >another. Most of the criteria given for approval
> >in the OBO framework are controversial, for
> >example. (BTW, the reason I keep citing OBO is
> >that it is the only extant example to cite, not
> >that I wish it ill.)
>
> I hope that one OBO Foundry criterion, at least, is
> non-controversial
> to Patrick, this is the criterion to the effect that the
> ontologies
> use a common syntax.

Well, good question. While I agree that does make a lot of sense, I had formed the impression that the OOR would not impose this as a criterion, since one of the discussion points is that all ontologies in it must be in a language with an openly published specification. Presumably this is only meaningful if the OOR is intended to be, as it were, multilingual (no?).

A multilingual repository would be a lot more useful if it came with recommended ways to translate between the languages. For OWL and FOL/CL this is now thoroughly understood, for example. For things like UML it is much more problematic, as there is not even a common underlying semantic framework within which to compare such notations with logics.

> Currently this may be either OBO or OWL,
> but we
> would be happy to extend it to FOL / CL, and I personally
> would
> welcome the creation of FOL-based
> bio-ontologies.

One can define a sublanguage of CLIF which is virtually isomorphic to the OWL abstract syntax. If I ever get time (in a month or so, maybe) I will write this up in detail as an alternative OWL syntax.

> BFO, which is a related ontology project,
> exists in a FOL version, as
> well as in OWL and OBO versions.
> http://www.ifomis.uni-saarland.de/bfo/

Right; many 'professional' ontology projects seem to be created first in FOL and then projected into lesser languages for real-world service.

> For the other criteria see:
> http://www.obofoundry.org/crit.shtml
> This list is designed to evolve in light of lessons learned. The
> principles seem non-controversial at least to many biologists
> (hence
> the success in this community of the OBO Foundry experiment). But
> they are to be conceived as forming an experiment, designed to
> test
> potential answers to questions like: "what can 'well
> structured'
> possibly mean, as a general category or classification applying
> uniformly to all ontologies [or more precisely: to ontologies
> designed to serve the needs of life scientists]'.
>
> If Patrick finds some of them controversial, then the obvious
> suggestion would be for him to create an alternative experiment,
> using different criteria, and see what happens. If the
> selected
> criteria yielded better results, OBO
> Foundry would adopt them immediately.

I don't have anything remotely close to the resources needed to mount such an experiment.

> Patrick himself seems, however, to prefer
> the single principle of:
> anything goes.

More accurately, I see this as more like a free market, no doubt influenced by thinking about the semantic web. Of course there is a lot of dross out there, and indeed most of it is ignored by everyone except search engines. But I don't think there is a single 'perfect shopper', either. Different users communities, and sometimes different users, will have different demands to place upon ontologies. We are just at the beginning of finding out what ontologies might be useful for. It seems way too soon to be trying to create a single-product world, no matter how good the product is.

I think the main differences between our attitudes is that you see ontologies as representing a distillation of a common insight, ideally amounting to something close to a universally agreed scientific theory; whereas I see ontologies as much more like useful pieces of software. There are many text editors, and they all have their strengths and weaknesses, adherents and detractors. No size will fit all.

Pat

> Which is also, of course, perfectly acceptable.
> BS
>
>
>  
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