[IAO] History of error (was: Defined classes vs. Universals)
Pat Hayes
>>
>>>> I agree. My fight is with the pseudo-Gruberians.
>>>>
>>>>>> It would indeed be odd to suppose, for instance, that when we say
>>>>>> that
>>>>>>
>>>>>> TLR2™-MyD88 ligand binding precedes TLR2™-MyD88 binding ig in the
>>>>>> TLR2
>>>>>> signalling pathway
>>>>>>
>>>>>> which is the sort of thing bio-ontologists do say, then they are
>>>>>> talking about some sort of temporal order among concepts.
>>>>>
>>>>> Of course, that would be ridiculous. Nobody has ever suggested
>>>>> such
>>>>> an
>>>>> idea, AFAIK.
>>>> There are government standards which say exactly
>>>> such things. I could give you a long, long list, but let these
>>>> suffice:
>>>>
>>>> Geographic Area isa Idea or Concept
>>>> Body Space or Junction isa Idea or Concept
>>>> Amino Acid Sequence isa Idea or Concept
>>>> Body Location or Region isa Idea or Concept
>>>> Body System isa Idea or Concept
>>>
>>> Ah, I stand refuted, indeed. I should never have said "Nobody...",
>>> forgetting the ubiquity of use/mention confusions in the wider
>>> world.
>>> But certainly Tom (and the rest of us in AI/KR) never suffered from
>>> this particular problem, as you can easily check by reading our
>>> writings (and some of the archived email discussions about reality
>>> and
>>> model theory, if you have the stomach for it.) So I don't think they
>>> are relevant to his definition of ontology.
>>
>> They are relevant to the phenomenal influence of
>> an (admittedly confused) reading of his
>> definition. Maybe you and he should join the
>> fight against the pernicious influence of this
>> confused reading, and against the use-mention
>> confusions in ontology circles which it promotes.
I don't believe that these confusions have been engendered by Gruber.
I doubt if most of their authors even know that Tom Gruber exists. Use/
mention confusions have been rife for centuries.
>>
>> Consider e.g. the Disease Ontology, which is an
>> open source ontology derived from the WHO's
>> international classification of diseases (ICD)
The error there is to conflate ontology with controlled vocabulary.
People are only just now beginning to distinguish between ontology,
vocabulary, taxonomy, and so on. BTW, I have been impressed by the
SKOS project, which quite explicitly accepts the constraints of
library science rather than natural sciences, and tries to work within
them. It is instructive to see how very different notions of hierarchy
and generalization arise when thinking in those ways rather than in
terms of scientific generalizations. For example, the equivalent of
is_a need not even be transitive, and (what we would consider to be)
use/mention confusion is no longer necessarily an error.
>> and contains dozens of terms like:
>>
>> senility without mention of psychosis
>> acute gastritis without mention of hemorrhage
>> acute monocytic leukemia without mention of remission
>> measles without mention of complication
>> toxic multinodular goiter with mention of thyrotoxic crisis or storm
>>
>> ICD itself is far worse even than this, though
>> it, I suppose, can defend itself by pointing out
>> that it is not aiming to be an ontology.
Quite.
>>
>>> BTW, one can treat such nonsenses with a little generosity,
>>> instead of
>>> taking them literally. They are obvious use/mention confusions, and
>>> can be repaired by a judicious use of something like quasi-
>>> quotation.
>>> If our formal logics were a little more accommodating, we should be
>>> able to take in stuff like this and make sense of it.
>>
>> Clever logicians can make sense of near-nonsense
>> in clever ways. Not, however, your standard
>> working scientist ontology user. Moreover, there
>> will often be multiple such clever ways; and so
>> allowing near-nonsense in through the front door
>> will promote precisely the sorts of forking
>> which ontologies, in science, are designed to
>> prevent.
True, but my point was that this is not all complete nonsense, but
rather has a single, systematic, fault, one that is so common and so
ubiquitous indeed that I fear it is impossible to teach the world not
to make it. So it is better to mend such stuff rather than mount a
campaign to teach the world better manners. (I do not mean to imply
that it may not have other faults as well, of course.)
>> I prefer, therefore, to do it right the
>> first time, and not have to distinguish, e.g.
>> two sorts of part relation: physical_part_of
>> between atrium and heart, and
>> conceptual_part_of, between heart and cardiovascular system.
I agree we should not just accept such stuff at face value.
>>
>> There are virtues, in ontology, of imposing a
>> certain degree of constraint on what people
>> should be allowed to say.
Maybe, but I am instinctively resistant to such ideas. The analogy
with cell phones is not reasonable. I think that at our current level
of understanding of the entire topic of ontology design and
utilization, it is premature in the extreme to believe that anyone has
a handle on the basic principles applicable to all ontologies. BFO,
just as one example, seems altogether a first attempt rather than a
final design, and has some obvious flaws. Moreover, I have been
constantly impressed by the way that users have found uses for
constructions that we would have (and in some cases did) ruled as
ridiculous or incoherent. My favorite example was the idea of a zero-
ary relation, which sounds dumb as a box of rocks but in fact turned
out to be the key to the design of IKL, which is a fully self-
descriptive logic that can handle all the apparently paradoxical
constructions within a single consistent logic. Often, the best ideas
are not the ones you think of first.
>> (Just as, when
>> building an international standard for telephone
>> networks it is good to impose certain
>> constraints on Sprint and Verizon technical
>> people.) I think, for instance, that it should
>> be impossible for people to say, e.g., 'aspirin
>> treats concept' (thousands of such assertions
>> follow axiomatically from SNOMED, which defines all diseases as
>> concepts).
>>
>> BFO is, indeed, a still ramshackle constraint,
>> but it is, I believe, improvable, and its users
>> seem to think it is better than existing
>> alternatives (though I am sure that there are
>> multiple non-existing alternatives which are way better).
Im sure BFO is better than nothing :-) But I really think that it can
be improved by simplifying it, and the result would be easier to use,
more supportive of interoperation, and give rise to far fewer email
debates and confusions. However, I will concede that it would have to
use something like Common Logic to reap the full benefits, and so
there would be some training/exposition required.
Pat
>>
>> BS
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Barry Smith
Again, I could provide you with bundles of
evidence to the effect that people have embraced
the (misunderstood) Gruber definition of
ontology, and thereafter committed use-mention
confusions, and used that definition as a cover for what they do.
You can spend your time cleaning up the various
messes, if you wish. I will work on improving table manners.
>>>I prefer, therefore, to do it right the
>>>first time, and not have to distinguish, e.g.
>>>two sorts of part relation: physical_part_of
>>>between atrium and heart, and
>>>conceptual_part_of, between heart and cardiovascular system.
>
>I agree we should not just accept such stuff at face value.
>
>>>
>>>There are virtues, in ontology, of imposing a
>>>certain degree of constraint on what people
>>>should be allowed to say.
>
>Maybe, but I am instinctively resistant to such ideas. The analogy
>with cell phones is not reasonable. I think that at our current level
>of understanding of the entire topic of ontology design and
>utilization, it is premature in the extreme to believe that anyone has
>a handle on the basic principles applicable to all ontologies.
Of course, that is why we need to work out
multiple standards and see which parts work best.
Empiricism. No one (sensible) claims to know
properly how to do this. That does not mean that
we should place an embargo on trying.
>BFO,
>just as one example, seems altogether a first attempt rather than a
>final design, and has some obvious flaws.
Of course. Suicide, then?
>Moreover, I have been
>constantly impressed by the way that users have found uses for
>constructions that we would have (and in some cases did) ruled as
>ridiculous or incoherent. My favorite example
>was the idea of a zero- ary relation, which
>sounds dumb as a box of rocks but in fact turned
>out to be the key to the design of IKL, which is
>a fully self- descriptive logic that can handle
>all the apparently paradoxical
>constructions within a single consistent logic. Often, the best ideas
>are not the ones you think of first.
Of course. So we shouldn't think first, because
someone else might think better, second?
>>>(Just as, when
>>>building an international standard for telephone
>>>networks it is good to impose certain
>>>constraints on Sprint and Verizon technical
>>>people.) I think, for instance, that it should
>>>be impossible for people to say, e.g., 'aspirin
>>>treats concept' (thousands of such assertions
>>>follow axiomatically from SNOMED, which defines all diseases as
>>>concepts).
>>>
>>>BFO is, indeed, a still ramshackle constraint,
>>>but it is, I believe, improvable, and its users
>>>seem to think it is better than existing
>>>alternatives (though I am sure that there are
>>>multiple non-existing alternatives which are way better).
>
>Im sure BFO is better than nothing :-) But I really think that it can
>be improved by simplifying it, and the result would be easier to use,
>more supportive of interoperation, and give rise to far fewer email
>debates and confusions.
It is as simple as it can be, to deal with the
rather complex domains (above all in the area of
information-driven experimentation) which it
needs to support. Clever people in those domains want it to become bigger.
>However, I will concede that it would have to
>use something like Common Logic to reap the full benefits, and so
>there would be some training/exposition required.
I agree.
There are those amongst us (one of them cc-ed
herewith) who are doing this already.
BS