Re: [IAO] ICE and its concretizations

[Barry Smith]

At 08:53 AM 12/9/2009, Jonathan Rees wrote:
>I'm going to play Pangloss here, a bit...
>
>In what forum is BFO being critically appraised? As BFO seems to be
>shaping the whole foundry effort, including IAO and OBI, it would seem
>wise to attempt to predict whether it's going to serve the endeavor
>well, what its limits will turn out to be, and whether its reliability
>or applicability might be increased (or threatened) by changes to it.
>This is true even if a sunk cost argument convinces us all not to make
>any changes to it.
>
>Of course I mean an analysis with practical utility, not philosophical
>considerations, as the test (admitting of course that the latter are
>intended to predict the former).
>
>If an appraisal gives BFO high marks, then it should have the benefit
>of bringing skeptics like Pat and me into the fold.
>
>Such a forum might provide a place where we could continue to benefit
>from Pat's involvement, which I have found to be very valuable.
>
>Jonathan

There are four public domain top-level ontologies which are being
applied in support of scientific (and especially life-science)
research: BFO, DOLCE, SUMO, Upper Level CYC.
The ideal, from Jonathan's point of view, would be to take the same
ontology development problem, have it tackled by four independent
teams of equal competence, using each of these alternative
ontologies, and to measure e.g.:

1. training time taken,
2. quality of resulting ontology,
3. acceptability of resulting ontology to other users,
4. benefits brought by resulting ontology in supporting data
integration, reasoning, etc.

Unfortunately, we do not have the resources to carry out such an
experiment, and we do not have good measures, as yet, for 2.
(conformity e.g. to OWL is by no means a sufficient criterion of
ontology quality) and 4. (it is hard to find a domain which has not
already had ontology resources built, which are now infecting the
data which would be used in the integration; often tilting in a
direction prejudiced in favor of BFO).

However, I would be willing to commit to finding such resources (in
terms of both financing, expertise, and identification of an
independent arbiter) if the proponents of any other top-level
ontology would be willing to match one-on-one in terms of resources
and commitment to a clean experiment.

For the moment, we can note:

i. that matters are not as bad as they seem, given that BFO comes
close to approximating to a sub-ontology of DOLCE, and there is, I
believe, a potential for a comparable partial unification of BFO and SUMO
ii. BFO seems to be of the right size for cross-domain ontology
integration, since it does not overlap with the other sciences and
thus does not overlap with the scientific domain ontologies which
need to be built in integrated fashion
iii. re heading 1., BFO is much smaller than the others, so
(potentially) easier to learn
iv. BFO has demonstrated considerable responsiveness to the needs of
the scientists using it
iv. BFO seems to ahead under heading 3., given that we have some
approximation to a real-world experiment in the sense that people
have been voting with their feet. The list of independent projects
actively using BFO is growing by at least one per week:
http://www.ifomis.org/bfo/users
v. BFO seems to be ahead under a variety of other measures (though
this does not mean that we are satisfied with our performance along
any of these dimensions), including:
A. quality and extent of training resources available,
B. quality and extent of documentation,
C. size and expertise of team working on it, including what
is probably the most sophisticated user community (OBI), which has
already led to major changes in BFO; most of the oddities in current
BFO applications in IAO turn on the fact that IAO is a difficult
domain for which OBI needs a stable representation to deal with a
variety of different kinds of information artifact (I believe that
there is no competing representation of this domain that even comes
close to being able to make the needed distinctions)
D. size and activity of user-group, currently 117 members,
2745 messages
E. responsiveness to critics
F. longevity of engagement on the part of multiple specific users,
G. integration with the RO Relation Ontology, deeply
embedded within the bio-ontology field
(http://genomebiology.com/2005/6/5/R46) with 386 citations on google scholar.

BS

>On Tue, Dec 8, 2009 at 6:07 PM, Bjoern Peters <bpe...@liai.org> wrote:
> > Hi Pat,
> >
> > Getting used to BFO has been weird for me as well, but it worked
> well so far (for me at least). I would agree though that it will be
> better if you re-join this conversation at a later time when there
> is a higher degree of maturity, so that we don't have to develop
> already complicated enough issues using different frameworks.
> >
> > - Bjoern
> >
> >
> >
> >
> > ----- "Pat Hayes" <pha...@ihmc.us> wrote:
> >
> >> On Dec 8, 2009, at 3:29 PM, Bjoern Peters wrote:
> >>
> >> > Hi Pat - replies below
> >> >
> >> > ----- "Pat Hayes" <pha...@ihmc.us> wrote:
> >> >
> >> >>> 1) Every information content entity (ICE) is_concretized_as some
> >> >>> (physical) quality.
> >> >>
> >> >> Quality? Does that imply something other than the actual physical
> >> >> thing? I have been taking it that a concretization is something
> >> >> existing in physical time and space, something that could be
> >> >> destroyed
> >> >> by a physical process. Some of them (eg the Hollywood sign) might
> >>
> >> >> have
> >> >> physical properties such as mass. Is this understanding mistaken?
> >> >
> >> > 'quality' is referring to BFO:quality, which is tightly linked but
> >>
> >> > not the same as a independent continuant (='material entity' or
> >> > physcial entity for the discussion here). For example, a human being
> >>
> >> > that has different mass at different time points is considered the
> >>
> >> > same material entity with different mass qualities.
> >>
> >> OMG BFO obfusticationalism again. As far as I understand this (not
> >> very far), such a quality would be a property, or perhaps a fluent, ie
> >>
> >> a property varying with time, of the physical entity. Right? And a
> >> property, or property-like thing, is apparently not itself a physical
> >>
> >> thing. So, to answer my other question, a concretization which is a
> >> *pattern* of ink marks does not itself contain small particles of
> >> carbon, even though the marks themselves do. (Because a property, or
> >>
> >> quality, is not itself the kind of thing that can possibly contain
> >> particles of carbon.)
> >>
> >> I confess to being more confused now than I was before, in spite of
> >> your valiant efforts to explain.
> >>
> >> This is, for me, a perfect illustration of the reason why ontology
> >> should not be done by philosophers. I know what a piece of paper is,
> >>
> >> and I know what an ink mark is. I can understand the idea of an ink
> >> mark being a rendering of writing and hence of a message with content.
> >>
> >> I can make sense of talk which refers to properties of things like
> >> this. But I have absolutely no idea what continuants and qualities
> >> are, nor do I believe that I should need to, in order to understand an
> >>
> >> ontology of ICEs. (Evidence: I have been thinking about and working
> >> with ICEs for some time now, apparently successfully, without ever
> >> even being aware of the notions of continuant or quality.) I cannot
> >> believe that any ontology or even informal exposition that requires me
> >>
> >> to learn and accede to an alien set of philosophical abstractions can
> >>
> >> possibly provide any kind of enlightenment about the nature of part of
> >>
> >> reality.
> >>
> >> I think it might be best if I simply remove myself from this group.
> >> Almost every notion being discussed here is so alien to my way of
> >> thinking that it seems clear that I will only be sand in the bearings
> >>
> >> if I try to participate. For example, although I have been trying hard
> >>
> >> not to let this stand in the way, I simply do not believe that
> >> continuants exist, or are even possible. The very idea seems to me to
> >>
> >> be incoherent. I am already reconciled to not being able to understand
> >>
> >> or make use of anything which is rooted in BFO's strange, surreal,
> >> view of the world, and it would obviously be counterproductive to
> >> attempt to change it when this group has already decided to work
> >> within it.
> >>
> >> Good luck, y'all, in this mysterious wonderland of qualities and
> >> abstract concretion and independent continuants. I will stick to
> >> relationships between entities with spatiotemporal extents, where I
> >> know what I am talking about.
> >>
> >> Pat
> >
> > --
> > Bjoern Peters
> > Assistant Member
> > La Jolla Institute for Allergy and Immunology
> > 9420 Athena Circle
> > La Jolla, CA 92037, USA
> > Tel: 858/752-6914
> > Fax: 858/752-6987
> > http://www.liai.org/pages/faculty-peters
> >
> > --
> > informatio...@googlegroups.com
> > To change settings, visit
> > http://groups.google.com/group/information-ontology
> >
>
>--
>informatio...@googlegroups.com
>To change settings, visit
>http://groups.google.com/group/information-ontology

[Barry Smith]

At 10:01 AM 12/9/2009, Pat Hayes wrote:

>On Dec 9, 2009, at 7:53 AM, Jonathan Rees wrote:
>
> > I'm going to play Pangloss here, a bit...
> >
> > In what forum is BFO being critically appraised?
>

>Public acceptance in various scientific communities, I think is the
>answer. But there are not many competitors.

>
> > As BFO seems to be
> > shaping the whole foundry effort, including IAO and OBI, it would seem
> > wise to attempt to predict whether it's going to serve the endeavor
> > well, what its limits will turn out to be, and whether its reliability
> > or applicability might be increased (or threatened) by changes to it.
> > This is true even if a sunk cost argument convinces us all not to make
> > any changes to it.
> >
> > Of course I mean an analysis with practical utility, not philosophical
> > considerations, as the test (admitting of course that the latter are
> > intended to predict the former).
> >
> > If an appraisal gives BFO high marks, then it should have the benefit
> > of bringing skeptics like Pat and me into the fold.
> >
> > Such a forum might provide a place where we could continue to benefit
> > from Pat's involvement, which I have found to be very valuable.
>

>To clarify, I will not actually vanish, but simply become more of a
>lurker.
>
>And um... part of my purpose in deciding to withdraw from active
>participation was exactly to NOT have this forum get involved in re-
>examining the foundations of BFO. If I actively participate, my own
>predilictions will, I am quite sure, constantly rub against the BFO
>ground assumptions, causing irrelevant frictions in the discussions.
>Better to stick with the foundations y'all have chosen, and work
>within them, was my point. Please don't understand this as a threat to
>re-examine the foundations or else I will go home and take my ball
>with me; that would be entirely the wrong message.
>
>By the way, I am pretty sure that the result of, if I you will forgive
>the terminology, de-BFOing the final ontology would be largely a
>process of simplification at the 'upper' levels of the ontology,
>rather than a complete rejection of whatever is produced.
>
>Pat

Pat
Many communities find it useful to hide the top level, and
increasingly sophisticated tools are becoming available for this
purpose, thereby giving rise to the result you here describe. But
those same communities found using BFO useful for building the
ontologies. Thus de-BFOing would be unadvisable, unless an
alternative strategy for building is on hand. Good luck with that.
BS



> >
> > Jonathan

>------------------------------------------------------------
>IHMC (850)434 8903 or (650)494 3973
>40 South Alcaniz St. (850)202 4416 office
>Pensacola (850)202 4440 fax
>FL 32502 (850)291 0667 mobile
>phayesAT-SIGNihmc.us http://www.ihmc.us/users/phayes

[Phillip Lord]

Barry Smith <phis...@buffalo.edu> writes:
> At 08:53 AM 12/9/2009, Jonathan Rees wrote:
>>If an appraisal gives BFO high marks, then it should have the benefit
>>of bringing skeptics like Pat and me into the fold.
>>
>>Such a forum might provide a place where we could continue to benefit
>>from Pat's involvement, which I have found to be very valuable.
>>
>>Jonathan
>
> There are four public domain top-level ontologies which are being
> applied in support of scientific (and especially life-science)
> research: BFO, DOLCE, SUMO, Upper Level CYC.
> The ideal, from Jonathan's point of view, would be to take the same
> ontology development problem, have it tackled by four independent
> teams of equal competence, using each of these alternative
> ontologies, and to measure e.g.:

Five. You need a control. There is, as far as I can see, relatively
little evidence that use of a single upper ontology provides substantial
advantage over the costs that they involve. A base line would need to be
established.

> BFO is much smaller than the others, so
> (potentially) easier to learn

This is mistaken; by analogy to programming languages, for example, the
smallest complete language, lambda calculus, is extremely hard to learn
to use.

> v. BFO seems to be ahead under a variety of other measures (though
> this does not mean that we are satisfied with our performance along
> any of these dimensions), including:
> A. quality and extent of training resources available,
> B. quality and extent of documentation,
> C. size and expertise of team working on it, including what
> is probably the most sophisticated user community (OBI), which has
> already led to major changes in BFO; most of the oddities in current
> BFO applications in IAO turn on the fact that IAO is a difficult
> domain for which OBI needs a stable representation to deal with a
> variety of different kinds of information artifact (I believe that
> there is no competing representation of this domain that even comes
> close to being able to make the needed distinctions)

BFO lacks the ability to represent information. Hence, we end up with
the confusion of numeral with number, unit label with unit.

It's not the only area that BFO does not represent. Energy and force are
also missing. Processes that change are a problem. It's model of space
is still problematic.

Barry is right, BFO has strengths. It could be extended to cope with
areas for which it is not currently appropriate. But, even given the
issue above, it's small size is, generally, an advantage.

Stephen Jay Gould used the image of the Burgess shoe horn to describe
the perils of trying to force experimental data into a classification
where it does not fit. To my mind, trying to use BFO every would be a
mistake.

Phil

[Barry Smith]

At 12:03 PM 12/9/2009, Phillip Lord wrote:
>Barry Smith <phis...@buffalo.edu> writes:
> > At 08:53 AM 12/9/2009, Jonathan Rees wrote:
> >>If an appraisal gives BFO high marks, then it should have the benefit
> >>of bringing skeptics like Pat and me into the fold.
> >>
> >>Such a forum might provide a place where we could continue to benefit
> >>from Pat's involvement, which I have found to be very valuable.
> >>
> >>Jonathan
> >
> > There are four public domain top-level ontologies which are being
> > applied in support of scientific (and especially life-science)
> > research: BFO, DOLCE, SUMO, Upper Level CYC.
> > The ideal, from Jonathan's point of view, would be to take the same
> > ontology development problem, have it tackled by four independent
> > teams of equal competence, using each of these alternative
> > ontologies, and to measure e.g.:
>
>Five. You need a control. There is, as far as I can see, relatively
>little evidence that use of a single upper ontology provides substantial
>advantage over the costs that they involve. A base line would need to be
>established.

The control would be the empty ontology, would it not.
Perhaps we have this already in the very impressive mappings work
done by Olivier Bodenreider
<http://mor.nlm.nih.gov:8000/pubs/offi.html>http://mor.nlm.nih.gov:8000/pubs/offi.html

This shows that mappings can be done, even between large
ontology-like resources developed independently, but that they seem
always to be gappy, never completely error-free, very expensive to
build, and even more expensive to maintain.
It is not, I agree, clear that using a single upper ontology would
help. This is why BFO works with the OBO Foundry initiative, and its
orthogonality and cross-product strategy to ensure, as far as
possible, that mappings are not needed.

> > BFO is much smaller than the others, so
> > (potentially) easier to learn
>
>
>This is mistaken; by analogy to programming languages, for example, the
>smallest complete language, lambda calculus, is extremely hard to learn
>to use.

This may be mistaken. The fact that, in one domain, one small thing
is hard to learn, does not show that in all domains, smaller things
are not easier to learn than larger things.

> > v. BFO seems to be ahead under a variety of other measures (though
> > this does not mean that we are satisfied with our performance along
> > any of these dimensions), including:
> > A. quality and extent of training resources available,
> > B. quality and extent of documentation,
> > C. size and expertise of team working on it, including what
> > is probably the most sophisticated user community (OBI), which has
> > already led to major changes in BFO; most of the oddities in current
> > BFO applications in IAO turn on the fact that IAO is a difficult
> > domain for which OBI needs a stable representation to deal with a
> > variety of different kinds of information artifact (I believe that
> > there is no competing representation of this domain that even comes
> > close to being able to make the needed distinctions)
>
>
>
>BFO lacks the ability to represent information. Hence, we end up with
>the confusion of numeral with number, unit label with unit.

BFO helps to protect from the confusion of numeral with number, and
unit label with unit.
We are working hard to represent the information artifacts in
reality, and to represent the information in reality.

>It's not the only area that BFO does not represent. Energy and force are
>also missing. Processes that change are a problem. It's model of space
>is still problematic.

I agree that there are problems on each of these fronts, but they are
being addressed and we take them seriously.

>Barry is right, BFO has strengths. It could be extended to cope with
>areas for which it is not currently appropriate. But, even given the
>issue above, it's small size is, generally, an advantage.
>
>Stephen Jay Gould used the image of the Burgess shoe horn to describe
>the perils of trying to force experimental data into a classification
>where it does not fit. To my mind, trying to use BFO every would be a
>mistake.

We are attempting to extend it according to need; more will be
revealed when we are sure it works.
BS

>Phil
>
>
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>
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[Phillip Lord]

Barry Smith <phis...@buffalo.edu> writes:
>>Five. You need a control. There is, as far as I can see, relatively
>>little evidence that use of a single upper ontology provides substantial
>>advantage over the costs that they involve. A base line would need to be
>>established.
>
> The control would be the empty ontology, would it not.

I don't know what an empty ontology is. If you want to test whether an
upper ontology is good, you need to establish that it is better than
nothing. Is this what you mean?

>> > BFO is much smaller than the others, so
>> > (potentially) easier to learn
>>
>>
>>This is mistaken; by analogy to programming languages, for example, the
>>smallest complete language, lambda calculus, is extremely hard to learn
>>to use.
>
> This may be mistaken. The fact that, in one domain, one small thing
> is hard to learn, does not show that in all domains, smaller things
> are not easier to learn than larger things.

I said, by analogy. BFO is, because of it's size, simple. Our
experimental data is complex. Applying something simple (BFO) to
something complex (our data) is often pretty hard.

Lambda calculus has exactly the same problem; it's why we have invented
other programming languages.

>>BFO lacks the ability to represent information. Hence, we end up with
>>the confusion of numeral with number, unit label with unit.
>
> BFO helps to protect from the confusion of numeral with number, and
> unit label with unit.

Up to the point that you need to represent numbers. BFO doesn't do this,
so, instead, you represent numerals.

> We are working hard to represent the information artifacts in
> reality, and to represent the information in reality.

Why the problem with numbers then?

Phil

[Barry Smith]

At 12:03 PM 12/9/2009, Phillip Lord wrote:

>BFO lacks the ability to represent information. Hence, we end up with
>the confusion of numeral with number, unit label with unit.

BFO lacks the ability to represent information, just as it lacks the
ability to represent sugar or water or blood. This is because BFO
represents portions of information (and of sugar, water, blood).
This, in turn, is because BFO rests on the assumption that there is
no information except in the form of portions of information -- which
fall under what we call 'information artifacts', just as there is no
sugar except in the form of portions of sugar.

BFO insists on this because of the many errors people made, and are
still making, when dealing with mass nouns in their ontologies.
BS

[Robert Hoehndorf]

>>>>> "BS" == Barry Smith <phis...@buffalo.edu> writes:

Hi,

>> BFO lacks the ability to represent information. Hence, we end
>> up with the confusion of numeral with number, unit label with
>> unit.

BS> BFO helps to protect from the confusion of numeral with
BS> number, and unit label with unit. We are working hard to
BS> represent the information artifacts in reality, and to
BS> represent the information in reality.

As far as I can tell, the main feature of BFO, that helps to make it
applicable in so many domains, is its complete lack of clear criteria
as to what its categories are supposed to represent and how to apply
them within a domain. Consequently, there is nothing that prevents us
from including "number" in BFO:
- as generically dependent continuants that somehow depend on
collections or object aggregates of a certain size; 0 is not
representable that way? No problem, let us make it a defined class
(http://obi-ontology.org/page/Defined_classes) then.
- as specifically dependent continuants (qualities) that are
properties of things of a certain cardinality; similar to its use in
PATO, which has "count" as quality
- as independent continuant; numbers just exist at all times and
everywhere, need no other entities to exist, etc.
- as process boundaries: they exist at every process boundary
- roles: their bearer is the world, and they are in a special "social
set of circumstances" (whatever that means) in which they don't have
to be (whatever that means!) and the world is not changed when a
number ceases to exist (maybe they never cease, so this is trivially
satisfied)

There are probably further viable options, but these may suffice.
However, I don't see how BFO helps to prevent any confusion, not only
the confusion between numeral and number, when the meaning of its
basic categories is hidden behind obfuscated natural language
definition that are open to all kinds of interpretations.

(Example: Disposition:=A realizable entity that essentially (essence?
it is essential for an entity to cause a specific process for it to be
a disposition?) causes (what does "causes" mean? any specific theory
of causation, what are the implications? and where is this relation
mentioned, explicitly, formally described?) a specific process or
transformation in the object (so, a disposition can cause a specific
process (kind of process? an individual process?) or a transformation
in an object (how is this different from a process? if not, why is it
mentioned here?)) in which it inheres, under specific circumstances
(what kind of entity is a circumstance? state of affairs? fact?
situation? a world? And again, what does "specific" mean, does it mean
"individual"?) and in conjunction with the laws of nature (name
one thing that does not happen in "conjunction with" laws of nature!))

>> It's not the only area that BFO does not represent. Energy and
>> force are also missing. Processes that change are a
>> problem. It's model of space is still problematic.

BS> I agree that there are problems on each of these fronts, but
BS> they are being addressed and we take them seriously.

These are not really BFO's problems, I think, as BFO does not seem to
concern itself with energy, force, etc. But the very basic notions in
BFO still remain unclear: what is a dependent continuant in BFO
(explain the "necessary" part of your definition), what is its model
of space, of time, what is a continuant (not a continuant at a time
point, but "the" continuant), how are continuants different from
occurrents (it cannot be their relation to time, because time points
are occurrents; if it is persistence through time, what does this
mean?)?
I don't even mention realizables here, or what "universals" are
supposed to be.
But maybe you do not consider these things (which have been floating
around for years) as problems that are being addressed and taken
seriously...

Rob.

[Phillip Lord]

Barry Smith <phis...@buffalo.edu> writes:
> At 12:03 PM 12/9/2009, Phillip Lord wrote:
>>BFO lacks the ability to represent information. Hence, we end up with
>>the confusion of numeral with number, unit label with unit.
>
> BFO lacks the ability to represent information, just as it lacks the
> ability to represent sugar or water or blood. This is because BFO
> represents portions of information (and of sugar, water, blood).
> This, in turn, is because BFO rests on the assumption that there is
> no information except in the form of portions of information -- which
> fall under what we call 'information artifacts', just as there is no
> sugar except in the form of portions of sugar.

And it is this mistaken assumption that causes the problem. Talking
about this portion of zero or that portion of zero doesn't really make
much sense.

Very simple question. What kind of entity is a number?

My answer, it is an entity in it's own right, with special properties
which are not the same as the properties of sugar. Properties that we
understand pretty well from many thousands of years of mathematics.

In short, BFO lacks the ability to represent information because it is
lacking.

Phil

[Barry Smith]

At 07:06 AM 12/10/2009, Phillip Lord wrote:


>Barry Smith <phis...@buffalo.edu> writes:
> > At 12:03 PM 12/9/2009, Phillip Lord wrote:
> >>BFO lacks the ability to represent information. Hence, we end up with
> >>the confusion of numeral with number, unit label with unit.
> >
> > BFO lacks the ability to represent information, just as it lacks the
> > ability to represent sugar or water or blood. This is because BFO
> > represents portions of information (and of sugar, water, blood).
> > This, in turn, is because BFO rests on the assumption that there is
> > no information except in the form of portions of information -- which
> > fall under what we call 'information artifacts', just as there is no
> > sugar except in the form of portions of sugar.
>
>And it is this mistaken assumption that causes the problem. Talking
>about this portion of zero or that portion of zero doesn't really make
>much sense.
>
>Very simple question. What kind of entity is a number?

BFO is an ontology designed to support data integration in natural
science domains on the basis of the working hypothesis that the best
way to do this is to represent, as coherently as possible, physical
reality. From this perspective, your question is out of scope. (It is
also a very big question, belonging to a very sophisticated
discipline called the philosophy of mathematics; I do not believe
that it will bring benefits to the practical problems facing
bio-ontology to get embroiled in this discipline.)

>My answer, it is an entity in it's own right, with special properties
>which are not the same as the properties of sugar.

But I can agree with this much, at least.

>Properties that we
>understand pretty well from many thousands of years of mathematics.

That's what probably the greatest mind in logic thought when he wrote
his Foundations of Arithmetic. Bertrand Russell, in a 3-line
argument, proved him wrong. I truly don't want to get you embroiled,
but see e.g. here:
http://plato.stanford.edu/entries/frege-logic/

>In short, BFO lacks the ability to represent information because it is
>lacking.

We shall see.

[Barry Smith]

As I say, we are doing our best to improve the definitions of BFO
terms. We will be releasing some better definitions soon; though
these, too, will still surely be imperfect. Natural language is, for
these sorts of purposes, an imperfect vehicle. (But relying on a
formal language has its problems, too.) There is now a great deal of
experience of using BFO, and enough documentation explaining how it
is used, which Robert seems to be ignoring below. His post reminds me
of someone new to physics who says things like:

Well, numbers could be clusters of photons, couldn't they?

BS

[Phillip Lord]

Barry Smith <phis...@buffalo.edu> writes:
>>And it is this mistaken assumption that causes the problem. Talking
>>about this portion of zero or that portion of zero doesn't really make
>>much sense.
>>
>>Very simple question. What kind of entity is a number?
>
> BFO is an ontology designed to support data integration in natural
> science domains on the basis of the working hypothesis that the best
> way to do this is to represent, as coherently as possible, physical
> reality. From this perspective, your question is out of scope.

Exactly. As I said, BFO lacks the ability to represent numbers. And,
further, this is by design. You are arguing that data integration for
the natural sciences is best served, therefore, by not representing
numbers.

> (It is also a very big question, belonging to a very sophisticated
> discipline called the philosophy of mathematics; I do not believe that
> it will bring benefits to the practical problems facing bio-ontology
> to get embroiled in this discipline.)
>
>>My answer, it is an entity in it's own right, with special properties
>>which are not the same as the properties of sugar.
>
> But I can agree with this much, at least.
>
>>Properties that we
>>understand pretty well from many thousands of years of mathematics.
>
> That's what probably the greatest mind in logic thought when he wrote
> his Foundations of Arithmetic. Bertrand Russell, in a 3-line
> argument, proved him wrong. I truly don't want to get you embroiled,
> but see e.g. here:
> http://plato.stanford.edu/entries/frege-logic/

Sure. So, we could punt on the issue. It doesn't matter what numbers are,
it just matters that we put them somewhere consistent in the models that
we build.

You've done this with many other parts of the ontology; as you say, BFO
models physical "reality". I could send you links to some very long
discussions from physicists on the origin of mass in the universe; short
summary -- we don't know. But you don't have a problem with putting
entities which bear mass into BFO, nor does doing so require us to
answer the problems of physics. Likewise, the deep difficulties with
numbers does not prevent us from putting them into BFO, should we
choose.

This is fine. Ontologies should represent our shared confusion as well
as our shared understanding.

>>In short, BFO lacks the ability to represent information because it is
>>lacking.
> We shall see.

We already have seen. You've just said this above. BFO is lacking, by
design. Again, it's possible that this is good. You've argued that the
lack on multiple inheritance is a good thing also. Again, potentially,
you are right.

Personally, though, I think numbers would be good and are fairly useful.

Phil

[Janna Hastings]

Hi Phil,

I'm not sure I understand. Why would you like 'number' to be included in BFO? Is 'number' a class in an ontology you wish to align with BFO? Or do you mean that you wish to include properties such as mass which have numeric values?

Thanks, Janna

Phil

[Phillip Lord]

For example, a calculation process has an output of a number.

Numbers are one of the simplest forms of information, so if we can't do
numbers, then information in general is a problem.

The two options here are straight-forward; either we have numbers
because they are useful or, we don't have them because they introduce
more confusion than their utility. It's a cost-benefit issue.

Phil

[Janna Hastings]

Hi Phil,

I see. You want numbers _as forms of information_. That suggests the scope of the IAO. I see IAO already has 'measurement datum', which can be numeric, and have units associated, just as we would need to represent many numeric values in physics or biology. Surely something similar could accommodate calculated numeric values which do not correspond to measurements, something like 'calculated datum' perhaps?

Janna

[Michel Dumontier]

IAO's uses a datatype property (has measurement value) to relate a measurement datum (as the result of recording it) to its numeric value (currently restricted to a float). But units are *not* handled, they are referred to by their *labels* through the object property (has measurement unit label). 

-=Michel=-

--
Michel Dumontier
Associate Professor of Bioinformatics
Carleton University
http://dumontierlab.com

[Phillip Lord]

IAO has, for example, scalar measurement datum which consists of a
numeral and unit label. So, it covers the printed or visualised
representation. It does not cover the representation stored on a hard
drive, for instance.

Likewise, it has "conclusion textual entity"; conclusion is apparently,
like number, hard, but text about it is okay.

IAO demonstrates the problem with BFO. Barry argues that BFO clearly
differentiates between numbers and numerals; I say, that by considering
numbers out-of-scope, we are left with representing numerals instead, so
BFO is actually forcing us to conflate the two. I think that IAO is less
clear than it should be as a result.

>> bfo-discuss...@googlegroups.com<bfo-discuss%2Bunsu...@googlegroups.com>
>> .

>> For more options, visit this group at
>> http://groups.google.com/group/bfo-discuss?hl=en.
>>
>>
>>
>
> --
>
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>
>

--
Phillip Lord, Phone: +44 (0) 191 222 7827
Lecturer in Bioinformatics, Email: philli...@newcastle.ac.uk
School of Computing Science, http://homepages.cs.ncl.ac.uk/phillip.lord
Room 914 Claremont Tower, skype: russet_apples
Newcastle University, msn: m...@russet.org.uk
NE1 7RU

[Albert Goldfain]

[AG] Notice that IAO can be successful without ever answering "What
kind of entity is information?". IAO is more useful by ignoring this
question (or better, by letting the user answer it with their favorite
philosophical theory) and by instead focusing on those things in
reality that are the bearers of information or that depend to
information in some way (ICEs, information artifacts, ...) .
Similarly, an ontology of numerical artifacts could be constructed
without ever answering the question "What kind of entity is a number?"

[AG] Subclasses of number change with history: not just the historical
progression of the standard set: naturals, naturals + zero, rationals,
reals, and complex numbers, but also the stranger sorts of numbers
that have come out of mathematics: transfinite cardinal numbers
(Cantor), infinitesimals (Robinson), and quaternions. In fact, the
standard set of numbers are precisely those that find applications in
science (complex numbers, remember, have several applications
describing electricity. What kind of strange universal is supposed to
comprehend all of these?

[AG] Having said all that, we could do a whole lot with BFO to
describe circumstances where numbers and numerals are used (without
confusion!). Supposing I count to three by successively raising my
thumb, raising my index finger, and raising my middle finger. In BFO
terms, my middle finger is bearing the role of the cardinal number
three which is realized during my counting process. There are
problems with this number-as-role account (e.g., my middle finger
could have borne the role of the number one in the counting process if
I had started with it, so it is more of a generic dependence, or
better generic role...but starting with my middle finger would have
been vulgar :-), but the point is that we can in principle come up
with BFO compatible theories for different situations in which numeric
information is conveyed (street address enumeration, credit card
number assignment, ruler measurement, etc.), WITHOUT ever answering
the question "What kind of entity is a number?".

On Dec 10, 9:15 am, Barry Smith <phism...@buffalo.edu> wrote:
> As I say, we are doing our best to improve the definitions of BFO
> terms. We will be releasing some better definitions soon; though
> these, too, will still surely be imperfect. Natural language is, for
> these sorts of purposes, an imperfect vehicle. (But relying on a
> formal language has its problems, too.) There is now a great deal of
> experience of using BFO, and enough documentation explaining how it
> is used, which Robert seems to be ignoring below. His post reminds me
> of someone new to physics who says things like:
>
> Well, numbers could be clusters of photons, couldn't they?
>
> BS
>
> At 05:10 AM 12/10/2009, Robert Hoehndorf wrote:
>

[Alan Ruttenberg]

On Fri, Dec 11, 2009 at 12:32 PM, Phillip Lord
<philli...@newcastle.ac.uk> wrote:
>
> IAO has, for example, scalar measurement datum which consists of a
> numeral and unit label. So, it covers the printed or visualised
> representation. It does not cover the representation stored on a hard
> drive, for instance.

Measurement unit datum does not use numeral. Michel pointed out in a
previous mail that it uses a datatype property with a float value. Of
course, in OWL floats aren't numbers either ;-)

But we borrow (sort of) numbers from OWL rather than representing them
in IAO explicitly. This is cheating. But useful cheating for the
moment.

You point about alternate representations of numbers it interesting,
though, and deserves some thought. Please consider filing an issue.
http://code.google.com/p/information-artifact-ontology/issues/list

> Likewise, it has "conclusion textual entity"; conclusion is apparently,
> like number, hard, but text about it is okay.

We're more able to identify the textual entities and be clear about
identity criteria for them. Still waiting for a good proposal on how
to handle conclusions in general. I haven't been impressed by any so
far.

What's your strategy for dealing with hard things? My worry is that a
common way of dealing with hard things is to add a term to the
ontology with a label and no definition, and hope for the best. I
haven't found that to work very well.

> IAO demonstrates the problem with BFO. Barry argues that BFO clearly
> differentiates between numbers and numerals; I say, that by considering
> numbers out-of-scope, we are left with representing numerals instead, so
> BFO is actually forcing us to conflate the two.

Do you have an alternative that we should look at for inspiration?

> I think that IAO is less clear than it should be as a result.

Well, it's hard to argue that it couldn't use more clarity. But
frankly, I think IAO even as it is has made progress over what already
exists, and I credit BFO for bringing a perspective that I've found
helpful.

You said: "Numbers are one of the simplest forms of information".
Perhaps this makes sense to you, but I don't happen to find it very
illuminating. What definition of information supports the idea that
number is a subclass of it?

Elsewhere you say: "Ontologies should represent our shared confusion
as well as our shared understanding." How is representing our shared
confusion going to make IAO more clear?

-Alan