>>
>>If we are building ontologies to support kosher science, then the
>>ontologies should be compatible with the results of kosher science
>>(and evolve as we learn more from doing kosher science and from
>>discovering how ontologies can best help with kosher science).
>
>No argument. But supporting kosher science isn't the only use for
>ontologies. For example, Im very interested in using ontologies to
>help artists search for images more effectively. Others are more
>concerned with engineering, or commerce, or management. (01)
Of course. (02)
>>The point of ontologies, in all of this, is to help solve an
>>increasingly severe problem of data siloing (I am tempted to call
>>it data silage), by providing convergence on single,
>>algorithmically useful representations of the domains from which
>>data are collected. For this to work ontologies have to be as far
>>as possible unique.
>
>Almost an aside, but I am not convinced of this. They have to be
>compatible in well-understood ways. Uniqueness is just the easiest
>way to achieve such compatibility at present. (03)
Biologists like easy ways. Also biologists need guidelines as to what
they should be doing when they first recognize the need for
ontologies. Alternatives (drive on the right; drive on the left; it's
up to you) defeat this need. (04)
>>Hence where you characterise our differences as:
>>
>>>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.
>>
>>I would say:
>>
>>I see scientific ontologies as being involved in a necessary
>>convergence on a single scientific-evidence-based representation
>>for each domain. From these, reference ontologies, many application
>>ontologies (your 'products') are being formed; but the reference
>>ontologies are needed to keep the products in line with each other
>>(otherwise the silage problem arises once again).
>
>I see many, perhaps most, uses of ontologies as having nothing at
>all to do with correct science, or indeed with science of any
>description or quality. The general area you are concerned with is
>important, of course, but the scope of ontology deployment is far
>wider than this. (05)
I hope OOR will have a special metadata field labeled 'ontologies
Patrick Hayes is pleased to recommend to others without blushing'. (06)
>>>>>And any such implication of 'scientific' authority must be
>>>>>examined especially carefully when the, er, foundry is
>>>>>controlled by the philosophers themselves
>>
>>>>One philosopher, one computer scientist, two computer
>>>>scientist-biologists, one immunologist, one world-class geneticist.
>>>>
>>>>>, and its gatekeepers are mandated to only allow ontologies
>>>>>which conform to the somewhat arbitrary philosophical views of
>>>>>its founders (for example, by requiring consistency with a
>>>>>single 'base' ontology).
>>>>
>>>>Actually not -- the single base ontology we started with has
>>>>already been modified because it did not fit the science.
>>>
>>>I applaud that kind of a move, but it does not really counter my
>>>point. Would you allow an ontology which explicitly denied the
>>>continuant/occurrent distinction?
>>
>>It is an empirical question. When we see a good one for a specific
>>area of biology we will examine it, see whether it works better
>>than what we have.
>
>Perhaps I have made too hasty a judgement :-) (07)
We will be publishing our procedures in due course, and you will see
that we are bending over backwards to be very careful in these and
related respects. (08)
>>>>> I do not mean this to be a criticism of OBO itself, but I do
>>>>> claim that OBO hardly qualifies as anything like an "open"
>>>>> ontology repository. In the contrary, in fact: it is quite
>>>>> firmly closed to an entire approach to ontology construction
>>>>> which, while successfully deployed elsewhere, happens to not
>>>>> conform to the philosophical views that Barry has so nobly
>>>>> defended in so many publications.
>>
>>OBO is open in the sense you require, I think. The OBO Foundry is
>>constrained, to some degree, in the sense you describe. But I am
>>not by any means all powerful in the OBO Foundry. Many views were
>>accepted by what turned into the main OBO Foundry ontologies before
>>I came along. Some views I (and others) have to argue for
>>strenuously. Sometimes I (we) lose those arguments. Evidence-based
>>ontology is involves getting many things right which are not
>>addressed at the level of OBO/OWL/RDF formatting questions.
>
>Fair enough. I still insist however that there is a role for
>repositories which have much broader, and more varied, criteria of
>'quality' than those appropriate for accurate representations of
>scientific fields. (09)
Yes. No argument here. I still think that syntactic (and even
semantic) correctness is too weak a criterion, however. (See Fabian's
proposals posted earlier.) OOR will be used only if users feel that
it is useful. Not every syntactically correct ontology is useful for
anything (as is proved by the gazillions of them stranded on the web
which have not been accessed since, say, 2006).
BS (010)
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