>Underspecication in the Relation Ontology. Let us recollect the deni-
>tion of the transformation of relation in the RO [4]: C transformation of
>C1 = [denition] C and C1 for all c, t, if Cct, then there is some t1 such that
>C1ct1, and t1 earlier t, and there is no t2 such that Cct2 and
>C1ct2. This def-
>inition reveals two issues. First, it is ignorant of the distinction
>between the
>cases of unidirectional transformations versus where some instance of C1 may,
>after transforming into C, transform back into C1;
the normal way of saying this is that it is neutral as between uni-
and bidirectional cases; this is not a defect, I believe, since the
both subcases can easily be defined in terms of the existing relation
>e.g., the transformations of
>erythrocytes (red blood cells) into echinocytes and back again, and
>of a healthy
>organ into a non-healthy organ and back again. Second, and more important for
>developing logic-based ontologies, the RO denition does not say how the enti-
>ties undergoing transformation are able to change and yet keep their identity,
>other than through the use of the same variable `c'. This under-specication
>can lead to unintended models of the theory; e.g., a given particular remains
>unchanged, but either C or C1 changes due to increased understanding or cor-
>recting a representation error in the domain ontology.
This is, surely, a confusion between ontology and epistemology. A
type does not change just because our understanding increases or
because we correct an error in some representation.
>Clearly, this does not meet
>the intention of the authors of the above denition. To exclude such unintended
>models, we have to make explicit in the definition that the individual changes
>somehow.
If we are working in first-order logic, or in anything (such as OWL
DL) weaker than first order logic, then there will always be
infinitely many unintended models. This does not, however, mean that
it is not good to attempt to exclude some of them, but the issue is
the price that one will need to pay (see below).
>Let a instantiate universals Cs and Ct|with s for source and t for
>target the source is transformed into|at the two dierent times, then we have
>to assert that `enough' properties are shared by a 2 Cs and a 2 Ct
>so that they
>can be identied as the same individual|in shorthand notation: as =i at|while
>other properties 1 : : : n are lost or gained so that after the
>transformation, a
>instantiates a dierent universal. A basis for a generic denition
>might then be:
>Denition 1 (Ct transformation of Cs). Let Ct be the target and Cs the
>source universal, x, y range over instances and t0; : : : ; tn range
>over points in
>time, then Ct(x) transformation of Cs(y) i for all x, there exist y,
>t0; : : : tn,
>if Ct(x; t0), then there is some t1 such that Cs(y; t1), t1 < t0, x
>and y have the
>same identity criterion (x =i y), x and y differ in at least one
>other property
>i, and there does not exist a t2 such that Ct(x; t2) and Cs(y; t2).
One goal of the RO is to provide a basic list of those relations
which can be defined in logically simple ways (to maximize the degree
that they will be used by multiple groups, and thus maximize the
degree to which they will serve interoperability). This definition
is, in my opinion, too complicated to meet this purpose.
The original definition uses 'identical with', which is, as we know,
problematic in some cases (yet still used everywhere by biologists,
including in those cases -- such as in discussions of erythrocytes --
where these problems are most severe). Marijke's solution is to talk
not of 'identity' but of 'identity criteria' -- but in the
problematic cases the problems arise precisely because we do not have
identity criteria (indeed I venture to claim that we do not have
identity criteria for any of the interesting sortals used in biology).
Further problems: Marijke does not define what she means by 'identity
criterion'. Moreover, her revised definition of transformation uses
'differ in at least one other property', but she does not provide a
definition of property (something that it is notoriously hard to do).
Would this criterion be met, e.g. if our understanding of x differs
from our understanding of y, or if we have correcting an error in our
representation of x but not of y? Moreover she does not provide an
account of what it would be to count properties. Is the property of
being red, for example, different from the property of being red and
such that 2+2=4? Is the property of a cell of having a membrane (if
this is a property) different from the property of having a cellular membrane?
BS
At 07:05 AM 4/23/2009, Marijke Keet wrote:
>Dear all,
>
>I, and so I've heard some other people, are not quite happy with the
>limitations that one can't really represent temporal stuff, yet some
>of the RO relations do allude to temporal things. The temporal-DL
>research is moving forward, but not rapidly in the sense that there
>will be implementation support for it anytime soon. There are
>several aspects of the temporality, however, that one can represent
>in an a-temporal setting. I gave that track a try taking RO's
>transformation_of relation as an example [1]. The additional
>constraints one can represent are fully backward compatible with
>RO's definition; i.e., they do not change the meaning, but instead
>seek to represent the intention of the relation in a more refined way.
>
>Comments are welcome (if you are a BFO-groupie, then one is advised
>to read the 2-sentence caution at [2] before commenting).
>
>[1] C. Maria Keet. Constraints for representing transforming
>entities in bio-ontologies. KRDB Research Centre Technical Report
>KRDB09-2, Faculty of Computer Science, Free University of
>Bozen-Bolzano, Italy. April 22, 2009.
><http://www.inf.unibz.it/krdb/pub/TR/KRDB09-2.pdf>http://www.inf.unibz.it/krdb/pub/TR/KRDB09-2.pdf
>[2]
>http://keet.wordpress.com/2009/04/23/refining-constraints-on-ro%e2%80%99s-transformation_of-relation/
>
>Best regards,
>Marijke
>
>C. Maria Keet
>KRDB Research Centre
>Faculty of Computer Science
>Free University of Bozen-Bolzano
>Via della Mostra 4
>39100 Bolzano
>Italy
>tel: +39 04710 161287
>fax: +39 04710 16009
>email: <mailto:ke...@inf.unibz.it>ke...@inf.unibz.it
>web: <http://www.inf.unibz.it/krdb/>http://www.inf.unibz.it/krdb/
>home: <http://www.meteck.org/>http://www.meteck.org
>
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aside from your minor comments, to which I have inserted replies below,
do you have any on the 17 constraints that, if one were interested,
could be added to ontology development software in an analogous fashion
that OntoClean was added (or else to use it as paper-based guidelines)?
Barry Smith ha scritto:
> Some quick first comments
>
>
>
>> Underspecication in the Relation Ontology. Let us recollect the deni-
>> tion of the transformation of relation in the RO [4]: C transformation of
>> C1 = [denition] C and C1 for all c, t, if Cct, then there is some t1 such that
>> C1ct1, and t1 earlier t, and there is no t2 such that Cct2 and
>> C1ct2. This def-
>> inition reveals two issues. First, it is ignorant of the distinction
>> between the
>> cases of unidirectional transformations versus where some instance of C1 may,
>> after transforming into C, transform back into C1;
>>
>
> the normal way of saying this is that it is neutral as between uni-
> and bidirectional cases; this is not a defect, I believe, since the
> both subcases can easily be defined in terms of the existing relation
>
ignorant, neutral, whichever. I do not say I hold it against the
transformation relation as a "defect", just mention that it does not
address it. By looking at more details of the temporal aspects, this
surfaces instantly. no more, no less.
>
>> e.g., the transformations of
>> erythrocytes (red blood cells) into echinocytes and back again, and
>> of a healthy
>> organ into a non-healthy organ and back again. Second, and more important for
>> developing logic-based ontologies, the RO denition does not say how the enti-
>> ties undergoing transformation are able to change and yet keep their identity,
>> other than through the use of the same variable `c'. This under-specication
>> can lead to unintended models of the theory; e.g., a given particular remains
>> unchanged, but either C or C1 changes due to increased understanding or cor-
>> recting a representation error in the domain ontology.
>>
>
> This is, surely, a confusion between ontology and epistemology. A
> type does not change just because our understanding increases or
> because we correct an error in some representation.
>
I am already aware of your point that you have made earlier, and I will
repeat again---as also mentioned in the paper, even emphasised in
italics---that what I describe there does not meet the intention of the
relation and its usage. It's an uncomfortable, but all to common, thing
that easily can happen when we deal with knowledge bases (see also next
comment). From a comfy philosopher's position, these things probably
ought to be ignored, but from a science & engineering perspective, one
can't just ignore it.
>
>> Clearly, this does not meet
>> the intention of the authors of the above denition. To exclude such unintended
>> models, we have to make explicit in the definition that the individual changes
>> somehow.
>>
>
> If we are working in first-order logic, or in anything (such as OWL
> DL) weaker than first order logic, then there will always be
> infinitely many unintended models. This does not, however, mean that
> it is not good to attempt to exclude some of them, but the issue is
> the price that one will need to pay (see below).
>
with a good theory (and I mean a theory in FOL or some fragment of it),
there will not be "infinitely many unintended models". Surely one would
want to reduce the amount of unintended models. With an ontology
representing more of reality in more detail (thanks to having the means
to represent it in more detail), then we have less unintended models
(call it higher precision and accuracy, if you wish), and, in principle,
can achieve more useful deductions and spot potential modelling errors
or inconsistencies in the theory more easily.
>
>> Let a instantiate universals Cs and Ct|with s for source and t for
>> target the source is transformed into|at the two dierent times, then we have
>> to assert that `enough' properties are shared by a 2 Cs and a 2 Ct
>> so that they
>> can be identied as the same individual|in shorthand notation: as =i at|while
>> other properties 1 : : : n are lost or gained so that after the
>> transformation, a
>> instantiates a dierent universal. A basis for a generic denition
>> might then be:
>> Denition 1 (Ct transformation of Cs). Let Ct be the target and Cs the
>> source universal, x, y range over instances and t0; : : : ; tn range
>> over points in
>> time, then Ct(x) transformation of Cs(y) i for all x, there exist y,
>> t0; : : : tn,
>> if Ct(x; t0), then there is some t1 such that Cs(y; t1), t1 < t0, x
>> and y have the
>> same identity criterion (x =i y), x and y differ in at least one
>> other property
>> i, and there does not exist a t2 such that Ct(x; t2) and Cs(y; t2).
>>
>
> One goal of the RO is to provide a basic list of those relations
> which can be defined in logically simple ways (to maximize the degree
> that they will be used by multiple groups, and thus maximize the
> degree to which they will serve interoperability). This definition
> is, in my opinion, too complicated to meet this purpose.
>
what do you find "too complicated" in the definition?
> The original definition uses 'identical with', which is, as we know,
> problematic in some cases (yet still used everywhere by biologists,
> including in those cases -- such as in discussions of erythrocytes --
> where these problems are most severe). Marijke's solution is to talk
> not of 'identity' but of 'identity criteria' -- but in the
> problematic cases the problems arise precisely because we do not have
> identity criteria (indeed I venture to claim that we do not have
> identity criteria for any of the interesting sortals used in biology).
>
we went through this before as well, and my reply is still that you
should read on after just Definition 1. There is both an introduction
and discussion on definition of and usability (or not) of identity
criteria in the "basic notions from OntoClean" paragraph, and examples
if ICs and \pi discussed in section 4. If you have a real problem with
ICs, then use that information in the argumentation instead of
simplifying it ("venture to claim") to a ping-pong exercise
yes-no-yes-no-yes-etc if ICs could be of any use. It is not easy to
establish, but modelling either the necessary or the sufficient
conditions, or both, actually does occur in bio-ontologies.
regards,
marijke
\begin{definition}
Let $\phi$ be a rigid property, $\Gamma$ the identity criterion and such
that $\neg \forall x,y,t,t^{\prime}( \Gamma(x,y,t,t^{\prime})
\leftrightarrow x = y)$, then $\Gamma$ is a {\em weak identity
criterion} iff either $\Gamma$ is a {\em necessary IC carried by} $\phi$
when:
\begin{equation}
E(x,t) \land \phi(x,t) \land E(y,t^{\prime}) \land \phi(y, t^{\prime})
\land x = y \rightarrow \Gamma(x,y,t,t^{\prime})
\end{equation}
\begin{equation}
\neg \forall x,y (E(x,t) \land \phi(x,t) \land E(y,t^{\prime}) \land
\phi(y, t^{\prime}) \rightarrow \Gamma(x,y,t,t^{\prime}) )
\end{equation}
or $\Gamma$ is a {\em sufficient IC carried by} $\phi$ when:
\begin{equation}
E(x,t) \land \phi(x,t) \land E(y,t^{\prime}) \land \phi(y, t^{\prime})
\land \Gamma(x,y,t,t^{\prime}) \rightarrow x=y
\end{equation}
\begin{equation}
\exists x,y,t,t^{\prime} \Gamma(x,y,t,t^{\prime})
\end{equation}
where $t$ and $t^{\prime}$ are points in time, so that for {\em
synchronic weak identity} $t = t^{\prime}$ and for {\em diachronic weak
identity} $t < t^{\prime}$, and $E$ denotes the existence of the objects.
\end{definition}
for my lack of creativity in word usage and looking towards some
operational description, then instead of using "identity criterion" one
perhaps could phrase it as a "collection of essential necessary or
sufficient conditions" (or /properties/attributes--depending on the
research community).
regards,
marijke
>
> Respectfully,
> BS
I approve of this general idea -- ontology development should be made
as easy as possible by building in constraints on what ontology
developers can do.
See more below.
I agree with you that those things should not be ignored. But they
need to be specified correctly -- scientists and engineers are not
helped if we tell them that a type changes when our knowledge of it changes.
>>
>>>Clearly, this does not meet
>>>the intention of the authors of the above denition. To exclude
>>>such unintended
>>>models, we have to make explicit in the definition that the
>>>individual changes
>>>somehow.
>>>
>>
>>If we are working in first-order logic, or in anything (such as OWL
>>DL) weaker than first order logic, then there will always be
>>infinitely many unintended models. This does not, however, mean
>>that it is not good to attempt to exclude some of them, but the
>>issue is the price that one will need to pay (see below).
>>
>with a good theory (and I mean a theory in FOL or some fragment of
>it), there will not be "infinitely many unintended models".
http://www.earlham.edu/~peters/courses/logsys/low-skol.htm
>Surely one would want to reduce the amount of unintended models.
>With an ontology representing more of reality in more detail (thanks
>to having the means to represent it in more detail), then we have
>less unintended models (call it higher precision and accuracy, if
>you wish), and, in principle, can achieve more useful deductions and
>spot potential modelling errors or inconsistencies in the theory more easily.
Agreed.
see below
>>The original definition uses 'identical with', which is, as we
>>know, problematic in some cases (yet still used everywhere by
>>biologists, including in those cases -- such as in discussions of
>>erythrocytes -- where these problems are most severe). Marijke's
>>solution is to talk not of 'identity' but of 'identity criteria' --
>>but in the problematic cases the problems arise precisely because
>>we do not have identity criteria (indeed I venture to claim that we
>>do not have identity criteria for any of the interesting sortals
>>used in biology).
>>
>we went through this before as well, and my reply is still that you
>should read on after just Definition 1. There is both an
>introduction and discussion on definition of and usability (or not)
>of identity criteria in the "basic notions from OntoClean"
>paragraph, and examples if ICs and \pi discussed in section 4.
I still do not find a definition of 'identity criterion'. It would be
interesting to have a definition which does not rely on any use of
the term 'identity'.
Respectfully,
BS
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> Just as you and I continue to maintain our identify while bend
> or stretch, molecules may also change their conformation (but
> not their configuration!) that yields new functionality. Thus,
> the use of ro:transformation_of seems most appropriate to describe
> the temporal relation from one conformation to another.
I concur, certainly for the protein complex case described by Alan.
> Unfortunately, the preRNA -> mRNA example provided in the
> ro:transformation_of description [1] is not consistent wrt
> to molecular identity championed above.
Hmm. Wearing both my chemist and Sequence Ontology hats, I would say that given that there is nothing inherent in the chemical structure of mRNAs that differentiates them from other kinds of RNA, I don't think molecular identity is appropriate here.
Or rather, the mRNA sequence may be a ro:transformation_of the preRNA sequence, but the mRNA molecule derives_from the preRNA molecule. As far as the OBO ontologies are set up, we have a rich description of transcript sequences but a very poor description of molecules.
But RNAs are a tricky edge case between molecular identity and biological identity anyway.
best wishes,
Colin.
--
Dr Colin Batchelor MChem MRSC, Team Leader, Informatics R&D
Informatics Department,
Royal Society of Chemistry, Thomas Graham House, Cambridge UK CB4 0WF
batch...@rsc.org t: +44 1223 432280
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Michel Dumontier writes:I concur, certainly for the protein complex case described by Alan.
> Just as you and I continue to maintain our identify while bend
> or stretch, molecules may also change their conformation (but
> not their configuration!) that yields new functionality. Thus,
> the use of ro:transformation_of seems most appropriate to describe
> the temporal relation from one conformation to another.
Hmm. Wearing both my chemist and Sequence Ontology hats, I would say that given that there is nothing inherent in the chemical structure of mRNAs that differentiates them from other kinds of RNA, I don't think molecular identity is appropriate here.
> Unfortunately, the preRNA -> mRNA example provided in the
> ro:transformation_of description [1] is not consistent wrt
> to molecular identity championed above.
Or rather, the mRNA sequence may be a ro:transformation_of the preRNA sequence, but the mRNA molecule derives_from the preRNA molecule. As far as the OBO ontologies are set up, we have a rich description of transcript sequences but a very poor description of molecules.
But RNAs are a tricky edge case between molecular identity and biological identity anyway.
best wishes,
Colin.
--
Dr Colin Batchelor MChem MRSC, Team Leader, Informatics R&D
Informatics Department,
Royal Society of Chemistry, Thomas Graham House, Cambridge UK CB4 0WF
batch...@rsc.org t: +44 1223 432280
DISCLAIMER:
This communication (including any attachments) is intended for the use of the addressee only and may contain confidential, privileged or copyright material. It may not be relied upon or disclosed to any other person without the consent of the RSC. If you have received it in error, please contact us immediately. Any advice given by the RSC has been carefully formulated but is necessarily based on the information available, and the RSC cannot be held responsible for accuracy or completeness. In this respect, the RSC owes no duty of care and shall not be liable for any resulting damage or loss. The RSC acknowledges that a disclaimer cannot restrict liability at law for personal injury or death arising through a finding of negligence. The RSC does not warrant that its emails or attachments are Virus-free: Please rely on your own screening.
> As i recall, pre-RNA indicates an RNA before it is chemically
> processed into another form... so there is definitely a change
> in molecular identity (according to structure-based molecular identity).
There is a change in molecular identity but the molecular structure doesn't by itself define what kind of RNA it is---one can imagine two atom-by-atom bond-by-bond identical RNA molecules M(eu) and M(pro) which have just been transcribed. M(pro), being in a prokaryotic cell, is already a messenger RNA, whereas M(eu), being in a eukaryotic cell, is a pre-mRNA.
Best wishes,
Colin.
--
Dr Colin Batchelor MChem MRSC, Team Leader, Informatics R&D
Informatics Department,
Royal Society of Chemistry, Thomas Graham House, Cambridge UK CB4 0WF
batch...@rsc.org t: +44 1223 432280
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Michel Dumontier writes:There is a change in molecular identity but the molecular structure doesn't by itself define what kind of RNA it is---one can imagine two atom-by-atom bond-by-bond identical RNA molecules M(eu) and M(pro) which have just been transcribed. M(pro), being in a prokaryotic cell, is already a messenger RNA, whereas M(eu), being in a eukaryotic cell, is a pre-mRNA.
> As i recall, pre-RNA indicates an RNA before it is chemically
> processed into another form... so there is definitely a change
> in molecular identity (according to structure-based molecular identity).
Best wishes,
Colin.
--
Dr Colin Batchelor MChem MRSC, Team Leader, Informatics R&D
Informatics Department,
Royal Society of Chemistry, Thomas Graham House, Cambridge UK CB4 0WF
batch...@rsc.org t: +44 1223 432280
DISCLAIMER:
This communication (including any attachments) is intended for the use of the addressee only and may contain confidential, privileged or copyright material. It may not be relied upon or disclosed to any other person without the consent of the RSC. If you have received it in error, please contact us immediately. Any advice given by the RSC has been carefully formulated but is necessarily based on the information available, and the RSC cannot be held responsible for accuracy or completeness. In this respect, the RSC owes no duty of care and shall not be liable for any resulting damage or loss. The RSC acknowledges that a disclaimer cannot restrict liability at law for personal injury or death arising through a finding of negligence. The RSC does not warrant that its emails or attachments are Virus-free: Please rely on your own screening.
> Hi all,
>
> As a starting point, I've always advocated molecular identity on the
> basis of molecular structure. Thus non-covalent complexes are formed
> from molecules that maintain their identity throughout the lifetime
> of the complex. Just as you and I continue to maintain our identify
> while bend or stretch, molecules may also change their conformation
> (but not their configuration!) that yields new functionality. Thus,
> the use of ro:transformation_of seems most appropriate to describe
> the temporal relation from one conformation to another.
What is your definition of molecule -- in particular does it include
large macromolecules? It seems counterintuitive for a single base pair
mutation to cause an entire DNA molecule to cease to exist and be
replaced by a new one.
> Unfortunately, the preRNA -> mRNA example provided in the
> ro:transformation_of description [1] is not consistent wrt to
> molecular identity championed above. I would argue that the
> configurational changes that occur between a preRNA to an mRNA is
> best described by ro:derives_from.
I agree this was a poor choice of example
> Furthermore, I believe that ro:transformation_of should be limited
> to where the changes results in a change in a sub-class membership,
Not sure exactly what you mean
> and never between disjoint classes.
I think the opposite - I think in many cases, transformation_of will
hold between disjoint classes. I'm assuming a definition of
disjointness for continuants as follows
C1 disjoint_from C2 iff not exists i, t such that i instance_of C1 at
t and i instance_of C2 at t
> --
> Michel Dumontier
> Assistant Professor of Bioinformatics
> http://dumontierlab.com
>
> --~--~---------~--~----~------------~-------~--~----~
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What is your definition of molecule -- in particular does it include
On Apr 23, 2009, at 12:14 PM, Michel Dumontier wrote:
> Hi all,
>
> As a starting point, I've always advocated molecular identity on the
> basis of molecular structure. Thus non-covalent complexes are formed
> from molecules that maintain their identity throughout the lifetime
> of the complex. Just as you and I continue to maintain our identify
> while bend or stretch, molecules may also change their conformation
> (but not their configuration!) that yields new functionality. Thus,
> the use of ro:transformation_of seems most appropriate to describe
> the temporal relation from one conformation to another.
large macromolecules? It seems counterintuitive for a single base pair
mutation to cause an entire DNA molecule to cease to exist and be
replaced by a new one.
I agree this was a poor choice of example
> Unfortunately, the preRNA -> mRNA example provided in the
> ro:transformation_of description [1] is not consistent wrt to
> molecular identity championed above. I would argue that the
> configurational changes that occur between a preRNA to an mRNA is
> best described by ro:derives_from.
Not sure exactly what you mean
> Furthermore, I believe that ro:transformation_of should be limited
> to where the changes results in a change in a sub-class membership,
I think the opposite - I think in many cases, transformation_of will
> and never between disjoint classes.
hold between disjoint classes. I'm assuming a definition of
disjointness for continuants as follows
C1 disjoint_from C2 iff not exists i, t such that i instance_of C1 at
t and i instance_of C2 at t
>On Wed, Apr 29, 2009 at 10:15 PM, Chris Mungall
><<mailto:c...@berkeleybop.org>c...@berkeleybop.org> wrote:
>
>
>On Apr 23, 2009, at 12:14 PM, Michel Dumontier wrote:
>
> > Hi all,
> >
> > As a starting point, I've always advocated molecular identity on the
> > basis of molecular structure. Thus non-covalent complexes are formed
> > from molecules that maintain their identity throughout the lifetime
> > of the complex. Just as you and I continue to maintain our identify
> > while bend or stretch, molecules may also change their conformation
> > (but not their configuration!) that yields new functionality. Thus,
> > the use of ro:transformation_of seems most appropriate to describe
> > the temporal relation from one conformation to another.
>
>What is your definition of molecule -- in particular does it include
>large macromolecules? It seems counterintuitive for a single base pair
>mutation to cause an entire DNA molecule to cease to exist and be
>replaced by a new one.
>
>
>In chemistry, a structural difference is sufficient to warrant a
>distinguished identity. I don't see why it shouldn't follow with
>chemicals of biological interest. A single base change is also
>sufficient to completely change the functionality of an nucleic
>acid, nevermind the evolutionary relationships.
bear in mind that the definition of transformation in RO rests on the
relation of identity at the level of particular (as for instance
Marietje on Wednesday is identical to Marietje on Thursday; my laptop
on Friday is identical to my laptop on Saturday). If my laptop is
immersed in water on Friday night, it will undergo a complete change
in functionality, but it will still be one and the same identical
particular object.
BS
><http://dumontierlab.com>http://dumontierlab.com
> >In chemistry, a structural difference is sufficient to warrant a
> >distinguished identity. I don't see why it shouldn't follow with
> >chemicals of biological interest. A single base change is also
> >sufficient to completely change the functionality of an nucleic
> >acid, nevermind the evolutionary relationships.
>
>bear in mind that the definition of transformation in RO rests on the
>relation of identity at the level of particular (as for instance
>Marietje on Wednesday is identical to Marietje on Thursday; my laptop
>on Friday is identical to my laptop on Saturday). If my laptop is
>immersed in water on Friday night, it will undergo a complete change
>in functionality, but it will still be one and the same identical
>particular object.
>BS
>
>
>I couldn't agree more - and i explained this further in the email.
>But what we are talking about is whether the transformation_of Barry
>can be made from Human to Elephant. The problem is that the very
>*definition* of transformation of is incredibly vague and subject to
>arbitrary interpretation.
>
>-=Michel=-
The definition of transformation is in fact very precise:
A transformation_of B = every instance of A was once [identical to]
an instance of B
The problem pertains to the 'identical to'. This is so basic that it
cannot be defined -- there are some areas where we can apply it
perfectly well, for example as regards particular human beings
undergoing normal metabolism; and then there are difficult,
borderline cases. Philosophers have learned that there is no way to
precisify the meanings of basic terms such as 'identity' in such a
way as to remove all such cases; fortunately, again in many areas,
the existence of such cases does not prevent us from using a term
like 'identity' perfectly successfully for the many, many cases which
are not borderline.
The issue, I think, is whether it is appropriate to use
'transformation' as defined above with regard to molecules. Perhaps
it is not appropriate at all. If so, this is not a problem with
transformation, or with its definition, I think.
BS
Michel Dumontier writes:
> let's start with glycolysis - please refer to the image at
> http://www.accessexcellence.org/RC/VL/GG/ecb/ecb_images/13_01Glycolysis-Steps_1-5.jpg
I like this example, for reasons I will list below.
> [...]
> My solution was that any difference in structure was an identity change.
What I would observe here is that glucose interchanging between ring and chain forms happens all the time in biological systems, not just in that particular reaction. In your connection table-based system, and let us remember that connection tables, which are based on a ball and stick model of molecules, are an administrative convenience for pharma companies rather than a realistic model of a wide range of molecules, we would have ring-glucose and chain-glucose popping into and out of existence all the time, to say nothing of the transition states between the two.
There are more equilibria to consider: acid--base equilibria for example. Amino acid residues will exist in biological systems in a variety of protonation states. I genuinely wouldn't want to argue that simply gaining or losing a hydrogen atom changes the entire protein. One of the strengths of ChEBI is that it represents these equilibria in a number of biologically-relevant cases.
I need to think a bit about how Marijke's S meta-property applies to the ring--keto-chain--enol-chain tautomerism case.
> Then nobody has to debate any given pair of structural transformations.
> The alternative is to make a social convention that any change over some
> arbitrary fraction, like 1/4, uses derives_from, otherwise it's
> transformation_of (if it can be applied as an instance level relation).
I don't think either of these alternatives are helpful. I don't believe this kind of thing can be modelled without thinking. I have some sympathy with the molecular identity criterion, but I would argue that it's naïve for the reasons listed above. Further, we are (non-multiplicatively, obviously) implicitly discussing many of these entities qua their participation in a biological process. Take a messenger RNA molecule M in your body and consider an atom-by-atom-identical molecule M' in a comet. The cometary one isn't, I claim, a messenger RNA. It wouldn't be in a universe where eukaryotes have never existed, so why would it be one in this?
Best wishes,
Colin.
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for the S, at first impression, CT14' and CT15' would then apply for the
tautomerism. That is, there are, in your email below, 3 structural
isomers, i.e., same molecular formula but different structural formulas
and because of the different structural formula they can have different
functions, melting points, and whatnot. Let's call these classes Cring,
Cketo, and Cenol; and any of the instances /a/ \in Cring can change to
an /a/ \in Cketo or an /a/ \in Cenol and, at a later point in time,
transform back to /a/ \in Cring (or vice versa).
The characteristic that does not change and, in this case at least,
contributes to identity of a subsuming class C (or a Cringketoenol class
as the union of the three), is the molecular formula, so that diachronic
identity can be guaranteed. If we'd put Cring, Cketo, and Cenol willy
nilly in different branches in the taxonomy, then identity of the
molecules across the transformations cannot be guaranteed (if, on the
other hand, you'd have a taxonomy of, say, functions or roles they play
then they could be at different places).
does this make sense w.r.t. the unmentioned example for the tautomerism?
Best,
Marijke
Colin Batchelor ha scritto:
> for the S, at first impression, CT14' and CT15' would then apply for the
> tautomerism. That is, there are, in your email below, 3 structural
> isomers, i.e., same molecular formula but different structural formulas
> and because of the different structural formula they can have different
> functions, melting points, and whatnot. Let's call these classes Cring,
> Cketo, and Cenol; and any of the instances /a/ \in Cring can change to
> an /a/ \in Cketo or an /a/ \in Cenol and, at a later point in time,
> transform back to /a/ \in Cring (or vice versa).
> The characteristic that does not change and, in this case at least,
> contributes to identity of a subsuming class C (or a Cringketoenol class
> as the union of the three), is the molecular formula, so that diachronic
> identity can be guaranteed.
There is something a bit stronger than just the molecular formula---nearly all of the molecule is the same in both forms---but yes.
(Incidentally, I've misremembered there being a Cenol! Cchain and Cring will do.)
> If we'd put Cring, Cketo, and Cenol willy
> nilly in different branches in the taxonomy, then identity of the
> molecules across the transformations cannot be guaranteed (if, on the
> other hand, you'd have a taxonomy of, say, functions or roles they play
> then they could be at different places).
>
> does this make sense w.r.t. the unmentioned example for the tautomerism?
Yes. This makes a lot of sense.
><http://www.obofoundry.org/ro/#OBO_REL:transformation_of>http://www.obofoundry.org/ro/#OBO_REL:transformation_of
seems ok to me
>the thymine-dimer <- thymine dinucleotide example is good (maybe
>give links to source / wikipedia?)
>
>now let's look at the derivation_of, which unlike transformation_of,
>puts the formal definition
>
>C derives_immediately_from C' if and only if: given any c and any t,
>if c instantiates C at time t, then there is some c' and some t',
>such that c' instantiates C' at t' and t' earlier-than t and c
>*derives_from* c'. C derives_from C' if and only if: there is an
>chain of immediate derivation relations connecting C to C'.
>
>after this description
>
>Derivation on the instance level (*derives_from*) holds between
>distinct material continuants when one succeeds the other across a
>temporal divide in such a way that at least a biologically
>significant portion of the matter of the earlier continuant is
>inherited by the later. We say that one class C derives_from class
>C' if instances of C are connected to instances of C' via some chain
>of instance-level derivation relations.
>
>and the example
>
>Example: osteocyte derives_from osteoblast.
>
>also lacks context (add pointer somewhere). I looked up osteocyte
>and osteoblast to figure out how they were *non-identical*, and
>here's what i found:
>
>"When <http://en.wikipedia.org/wiki/Osteoblast>osteoblasts become
>trapped in the matrix they secrete, they become osteocytes" - it
>pretty much stops contributing to bone formation. i looked around
>quite a bit, but i don't really see any convincing evidence that
>they are non-identical. I do certainly see it as transformation_of
>in this case. maybe a better example is something where
>there something either ceases to exist or now comes into existence
>as a result of a fusion/fission event.
I agree with you -- and I hope that this problem will be fixed in the
follow-up to the RO paper, which has finally been initiated. At that
stage we thought that there were examples of derivation which are
1-to-1 as in the osteoblast-osteocyte case; the best example (to me,
at least) is human corpse derives_from human organism. Since then,
however, I have been convinced that the corpse is in fact identical
to the organism which pre-existed it. (There is, in this sense at
least, survival after bodily death.) At the same time I have been
convinced that all the other seeming examples of 1-to-1 derivation do
not work. Hence -- with general agreement, I think -- in the new
version of RO we plan to insist that derivation is always either
n-to-1 or 1-to-n, for n > 1 -- i.e. that all derivation is either
fission or budding, or fusion or capture.
BS
>
>The issue, I think, is whether it is appropriate to use
>'transformation' as defined above with regard to molecules. Perhaps
>it is not appropriate at all. If so, this is not a problem with
>transformation, or with its definition, I think.
>BS
>
>The challenge is find a case where in every situation membership in
>class C occurs before C'. I can see it for things like "Product"
>transformation_of Substrate. or Enzyme transformation_of Protein (so
>is Protein transformation_of Enzyme ok because they aren't enabling
>chemical reactions?). These are just specialized terms, so they are
>fundamentally the same *kind*. so what about more radical
>transformations where the structure is changed?
>
><http://www.accessexcellence.org/RC/VL/GG/ecb/ecb_images/13_01Glycolysis-Steps_1-5.jpg>let's
><http://dumontierlab.com>http://dumontierlab.com
>
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> At the same time I have been
> convinced that all the other seeming examples of 1-to-1 derivation do
> not work. Hence -- with general agreement, I think -- in the new
> version of RO we plan to insist that derivation is always either
> n-to-1 or 1-to-n, for n > 1 -- i.e. that all derivation is either
> fission or budding, or fusion or capture.
I've been looking recently at mechanisms of chemical reactions. This all goes back to Ingold's work in the 20s and 30s, but it seems to hold good today.
Most of the reactions are 2-to-1 or 1-to-2 as you say, but there are some concerted processes which I would like to model as 2-to-2. One of them is the SN2 reaction:
http://en.wikipedia.org/wiki/Sn2
If we consider the potential energy surface (not shown), the reactants are in one basin, the products are in another basin, and the transition state is the col or pass through which the system moves. In general I would be wary of admitting transition states to a molecular ontology, but I would be happy to admit intermediates (basins in between cols).
Best wishes,
Colin.
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(Marijke added to the list as I haven't got round to joining bfo-discuss, sorry.)
I like this example, for reasons I will list below.
Michel Dumontier writes:
> let's start with glycolysis - please refer to the image at
> http://www.accessexcellence.org/RC/VL/GG/ecb/ecb_images/13_01Glycolysis-Steps_1-5.jpg
> [...]
> My solution was that any difference in structure was an identity change.What I would observe here is that glucose interchanging between ring and chain forms happens all the time in biological systems, not just in that particular reaction. In your connection table-based system, and let us remember that connection tables, which are based on a ball and stick model of molecules, are an administrative convenience for pharma companies rather than a realistic model of a wide range of molecules, we would have ring-glucose and chain-glucose popping into and out of existence all the time, to say nothing of the transition states between the two.
There are more equilibria to consider: acid--base equilibria for example. Amino acid residues will exist in biological systems in a variety of protonation states. I genuinely wouldn't want to argue that simply gaining or losing a hydrogen atom changes the entire protein. One of the strengths of ChEBI is that it represents these equilibria in a number of biologically-relevant cases.
I need to think a bit about how Marijke's S meta-property applies to the ring--keto-chain--enol-chain tautomerism case.
I don't think either of these alternatives are helpful. I don't believe this kind of thing can be modelled without thinking. I have some sympathy with the molecular identity criterion, but I would argue that it's naïve for the reasons listed above. Further, we are (non-multiplicatively, obviously) implicitly discussing many of these entities qua their participation in a biological process. Take a messenger RNA molecule M in your body and consider an atom-by-atom-identical molecule M' in a comet. The cometary one isn't, I claim, a messenger RNA.
> Then nobody has to debate any given pair of structural transformations.
> The alternative is to make a social convention that any change over some
> arbitrary fraction, like 1/4, uses derives_from, otherwise it's
> transformation_of (if it can be applied as an instance level relation).
It wouldn't be in a universe where eukaryotes have never existed, so why would it be one in this?
Best wishes,
Colin.
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I have no objection to 2-to-2, too.
We can just say: transformation is always 1-1; everything else is derivation.
BS
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"everything else"
In the puzzle I posed the other day (http://tinyurl.com/dasyrw), one
of the things buzzing around the back of my head was that it feels
like neither derivation nor transformation is appropriate at the
molecular level.
The problem with derivation is that it posits that after some point in
time the previous entities cease to exist. However, in (perhaps only
some) chemical reactions, at molecular granularity, it seems to me
that entities retain identity even as they come together because they
can later come apart and be what they were before.
I assume that existence is such that there can't be temporal gaps.
To argue against that they are the same entity as before would seem to
me to be a losing argument. (at least I can't figure out a way to win
it)
One might argue that the same (that constituents come together and
apart retaining identity) is true for macroscopic arguments. This
certainly seems to be true in some cases. If I build a car and later
take one of the wheels off, it is the same wheel I put on when I was
building the car.
However for many other entities this will not happen. The orange I eat
will not sometimes appear back as a whole orange. Statistically
speaking, it is possible, but very unlikely. Therefore I conclude that
questions of when identity is lost have something to do with entropy
and thermodynamics.
So back to Barry's "everything else"...
There are certainly changes that involve neither transformation nor
derivation. Even aside from the above examples, if we think that there
are thinks that retain identity and class over time (like person),
that nonetheless change in physical constitution, then we have cases
of materials merging and dissociating (n->1, 1->n) without the ceasing
of existence posited by derives_from, nor change in classification
posited by transformation_of.
In the case of my earlier post - proteins, protein complexes, ligands,
and implicitly chemical reactions (molecular granularity), and in the
case of car parts (some macroscopic granularity), are there not other
relations that are more appropriate than the two we have in hand
currently?
-Alan
> I suppose you have to ask yourself whether you think two
> molecular entities that differ even from by a single bond
> are in fact *different*.
What about hydrogen bonds? Some weak covalent bonds are weaker than some strong hydrogen bonds, and in any case hydrogen bonds may well have some covalent character. Your definition of ChemicalBond, "The attractive interaction between atoms.", includes van der Waals forces and other interactions which are not significant at body temperature.
My feeling is that biologists would consider the breaking of all of the hydrogen bonds between two strands of DNA to be a more significant change than the gain or loss of a proton. Energetically it's massively more significant.
Anyway, even taking the bonds that the MDL mol file knows about, consider ozone. Consider isotopically-substituted ozone, 17O16O2. The resonance structures for this are (in SMILES notation):
[17O-][O+]=O and [17O]=[O+]O.
Their bonding is different. Yet they are the same molecule. It's a case of mesomerism. Munchnones (http://goldbook.iupac.org/M04068.html) are the same. Nitro groups are the same. There has to be something to point to that is more subtle than an OWLification of the mol file.
> computationally, it is not feasible to look them up in ChEBI using some natural language description.
If ChEBI had natural language descriptions of (more of) its terms it would be much more useful!
But yes, obviously we want a computable version of ChEBI and I think your contributions have been tremendously helpful.
Best wishes,
Colin.
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> However for many other entities this will not happen. The orange I eat
> will not sometimes appear back as a whole orange. Statistically
> speaking, it is possible, but very unlikely. Therefore I conclude that
> questions of when identity is lost have something to do with entropy
> and thermodynamics.
I wonder whether the important quantity here isn't kT. What counts as a chemical entity at 3 K certainly doesn't count as a chemical entity at body temperature, and very little inside me would count as a chemical entity inside a star.
The only difference between changes that break bonds and changes that rearrange atoms in space but preserve bonding is one of energy, and what we think of as a bond is conditioned by the temperature we do our experiments at.
This is a bit like granularity. Could it even be a different sort granularity?
Best wishes,
Colin.
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there is a good case to be made to the effect
that the existence of artifacts can have temporal gaps:
Poland in the era 1795–1918
your watch when it is lying in bits in different places in the repair shop
BS
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There are enough cases to warrant fixing.
I can't reason well about countries. The case of the watch is
interesting, though I note that your language still identifies the
watch with the bits. "your watch when".
What happens to the parts when they are part of the watch. Do they
cease to exist? If not, continuing my question, what is the relation
between the bits and the watch that is part of the family of relations
that include derives_from and transformation_of?
In the case of molecules we aren't dealing with "artifacts". Did you
mean to suggest that the compelling argument doesn't apply in that
case?
>On Tue, May 5, 2009 at 1:33 PM, Barry Smith
><<mailto:phis...@buffalo.edu>phis...@buffalo.edu> wrote:
>
>At 12:06 PM 5/5/2009, Alan Ruttenberg wrote:
> >On Tue, May 5, 2009 at 11:23 AM, Barry Smith
> <<mailto:phis...@buffalo.edu>phis...@buffalo.edu> wrote:
> > >
> > > At 11:18 AM 5/5/2009, Colin Batchelor wrote:
> > >>Barry Smith writes:
> > >>
> > >> > At the same time I have been
> > >> > convinced that all the other seeming examples of 1-to-1 derivation do
> > >> > not work. Hence -- with general agreement, I think -- in the new
> > >> > version of RO we plan to insist that derivation is always either
> > >> > n-to-1 or 1-to-n, for n > 1 -- i.e. that all derivation is either
> > >> > fission or budding, or fusion or capture.
> > >>
> > >>I've been looking recently at mechanisms of chemical
> > >>reactions. This all goes back to Ingold's work in the 20s and 30s,
> > >>but it seems to hold good today.
> > >>
> > >>Most of the reactions are 2-to-1 or 1-to-2 as you say, but there are
> > >>some concerted processes which I would like to model as 2-to-2. One
> > >>of them is the SN2 reaction:
> > >><http://en.wikipedia.org/wiki/Sn2>http://en.wikipedia.org/wiki/Sn2
> > >
> > > I have no objection to 2-to-2, too.
> > > We can just say: transformation is always
> > 1-1; everything else is derivation.
> >
> >"everything else"
> >
> >In the puzzle I posed the other day
> (<http://tinyurl.com/dasyrw>http://tinyurl.com/dasyrw), one
> >of the things buzzing around the back of my head was that it feels
> >like neither derivation nor transformation is appropriate at the
> >molecular level.
> >
> >The problem with derivation is that it posits that after some point in
> >time the previous entities cease to exist. However, in (perhaps only
> >some) chemical reactions, at molecular granularity, it seems to me
> >that entities retain identity even as they come together because they
> >can later come apart and be what they were before.
> >
> >I assume that existence is such that there can't be temporal gaps.
>
>there is a good case to be made to the effect
>that the existence of artifacts can have temporal gaps:
>Poland in the era 1795–1918
>your watch when it is lying in bits in different places in the repair shop
>BS
>
>
>What happens if you pick up different parts than
>you had before? In only a select few cases
>would the same atoms actually be reincorporated into the molecule...
I can well imagine that artifacts have special features in this respect;
BS
Derivation on the instance-level is a relation holding between
non-identicals. More precisely, it holds between distinct
material continuants when one succeeds the other across a
temporal divide in such a way that at least a biologically sig-
nificant portion of the matter of the earlier continuant is
inherited by the later. Thus we will have axioms to the effect
that from c derives_from c1 we can infer that c and c1 are
not identical and that there is some instant of time t such that
c1 exists only prior to and c only subsequent to t. We will also
be able to infer that the spatial region occupied by c as it
begins to exist at t overlaps with the spatial region occupied
by c1 as it ceases to exist in the same instant.
Alan Ruttenberg writes:
> However for many other entities this will not happen. The orange I eat
> will not sometimes appear back as a whole orange. Statistically
> speaking, it is possible, but very unlikely. Therefore I conclude that
> questions of when identity is lost have something to do with entropy
> and thermodynamics.
I wonder whether the important quantity here isn't kT. What counts as a chemical entity at 3 K certainly doesn't count as a chemical entity at body temperature, and very little inside me would count as a chemical entity inside a star.
The only difference between changes that break bonds and changes that rearrange atoms in space but preserve bonding is one of energy, and what we think of as a bond is conditioned by the temperature we do our experiments at.
This is a bit like granularity. Could it even be a different sort granularity?
> Doesn't quite feel the same. With granularity we have different
> perspectives on the same stuff, whereas with temperature you are
> either hot or cold, so to speak, but not both at the same time.
> The arrangements of matter can be different at different temperatures
> (or in solution), and as objects are subjected to these different
> conditions, changes to them may occur.
Agreed.
The conundrum as I see it is that, disregarding the thermal background, at the molecular granularity, all changes are reversible. Irreversibility only arises when we start looking at ensembles. But if we pick a temperature then we can look at the energy landscape for a particular system and point to relatively-shallow, symmetric barriers which we expect to be recrossed all the time, like tautomerisms, and barriers which are asymmetric and relatively steep on one side which we don't expect to be recrossed. I'm not suggesting this is a good way of modelling this! But I am suggesting that this might be one of the many unstated assumptions in the way that people try to model molecular entities in biological systems.
Best wishes,
Colin.
--
Dr Colin Batchelor MChem MRSC, Team Leader, Informatics R&D
Informatics Department,
Royal Society of Chemistry, Thomas Graham House, Cambridge UK CB4 0WF
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David
I think South Korea is derived from Korea
I think East Germany, God bless its soul, derived from Germany
>I was hoping that I was getting clearer on what
>the problem is, and that you might address it
>more directly. But I'll try again. We have two
>types of relations for representing temporal
>change in entities in an overall process where
>total material is approximately conserved:
>derivation and transformation. According to the
>documentation of these relations, each has
>consequences - in transformation there is a
>class change and in derivation entities cease to exist and come into existence.
>
>Neither of these seem appropriate for
>representing the kind of change where something
>becomes a part and yet retains its identity, as
>evidenced by the ability to have the part later
>become dissociated and be the same thing as it was before.
I think on the instance level (where we can talk
simply of identity, rather than transformation), the matter is clear:
A heart undergoes two successive transplants; the
same heart (instance) in 3 successive ; so
identity. Can you think of a case where the story
you tell above would not realizably be described in terms of identity?
BS
>Given the above, I see two choices currently.
>Either a) such a change is not represented by a
>relation at all, as neither derives_from or
>transformation_of appears appropriate or b)
>There is some other relation to be used.
>
>If the choice is v, the other relation should
>imply (at least) that one of the relata goes
>from being a part to being not a part, and that
>the now-not-part-then-part continues to exist
>and retain identity. Subtypes of this relation
>could be created for the case where the other
>relatum a) comes into existence during the
>transition, as is the case with the synthesis of
>small molecules or b) retains identity during
>the transition, as is the case with cars and
>wheels, or c) Undergoes a transformation (not
>coming up with a good example atm, but I suspect this is a valid case).
>
>There would be a corresponding relation going in
>the other direction, for the now-part-then-not-part case.
>
>-Alan
>
>
>
>BS
>
>
>
>-Alan
>
> >
> >> In the case of molecules we aren't dealing with "artifacts". Did you
> >> mean to suggest that the compelling argument doesn't apply in that
> >> case?
> >
> > I am just not sure.
> > BS
> >
> >
> >
>
>
I think on the instance level (where we can talk simply of identity, rather than transformation), the matter is clear:I was hoping that I was getting clearer on what the problem is, and that you might address it more directly. But I'll try again. We have two types of relations for representing temporal change in entities in an overall process where total material is approximately conserved: derivation and transformation. According to the documentation of these relations, each has consequences - in transformation there is a class change and in derivation entities cease to exist and come into existence.
Neither of these seem appropriate for representing the kind of change where something becomes a part and yet retains its identity, as evidenced by the ability to have the part later become dissociated and be the same thing as it was before.
A heart undergoes two successive transplants; the same heart (instance) in 3 successive ; so identity. Can you think of a case where the story you tell above would not realizably be described in terms of identity?
assembled_from holds between material continuants when one comes into existence at a certain time in such a way that it has the others as parts. Thus we will have axioms to the effect
that from c assembled_from c1 and c2 we can infer that c1 part_of c at t, c2 part_of c at t, etc, and that the spatial region occupied by c contains the spatial regions of c1.. cn at t
c gains_part c1
gains_part holds between material continuants when one becomes part of the other at a certain time. Thus we will have axioms to the effect that from c gains_part c1 we can infer that c1 part_of c at t, that the spatial region occupied by c contains the spatial region of c1 at t , and that for any e > 0, there exists a time te st. t-te < e and it is not the case that c1 part_of c at te and the spatial region occupied by c does not overlap the spatial region of c1 at te.
loses_part holds between material continuants when one ceases being part of the other at a certain time, but both entities continue to exist. Thus we will have axioms to the effect that from c loses_part c1 we can infer that not(c1 part_of c at t), that the spatial region occupied by c does not overlap the spatial region of c1 at t , and that for any e > 0, there exists a time te st. t-te < e and c1 part_of c at te and the spatial region occupied by c contains the spatial region of c1 at te.
-Alan
breaks_into holds between material continuants when one ceases to exist at a
certain time and some of its parts come to be self standing.
Thus we will have axioms to the effect that from c disassembles_into
c1 and c2 we can
infer that c1 part_of c just before t, c2 part_of c just before t,
etc, that the spatial region
occupied by c contains the spatial regions of c1.. cn just before t,
that c does not exist
after t, and c1, c2.. exist at t.
-Alan
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-Alan
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derives from is a primitive relation. I believe we should always start with
primitive relations. The is_result_of_disassembly_from and the others Alan
proposes can be defined using simple processes. For derivation, there is no
such simple process (hence the still ongoing discussion on what goes under
it and what not).
I think I'm stuck on what it means to be a "primitive relationship"
and what a "simple" process is. Maybe you could give me some ways to
think about that.
-Alan
Yes, it sounds a little like this, except that the fission case
implies that the entities that are created in the fission process
didn't exist as themselves before the fission process started, whereas
in the case of is_result_of_disassembly_from they did.
Fission: A drop of water splits into two upon bouncing on the ground.
Disassembly: The 3 parts of a yoyo body (side1, side2, post) come apart.
As I understand these, a process might result in there being both
derivation *and* disassembly relations, e.g. in the case of container
made of two parts that snap together holding some material which
expands rapidly causing to come apart with the contents fissioning.
-Alan
>On Fri, May 8, 2009 at 4:14 PM, Barry Smith <phis...@buffalo.edu> wrote:
> >
> > Except that 'breaks-into' (or better: is_result_of_disassembly_from
> > -- since otherwise we lose the all-some relation) sounds just like a
> > fission subcase of derives_from.
>
>Yes, it sounds a little like this, except that the fission case
>implies that the entities that are created in the fission process
>didn't exist as themselves before the fission process started, whereas
>in the case of is_result_of_disassembly_from they did.
See section VI of http://ontology.buffalo.edu/smith/articles/16Days.pdf
>Fission: A drop of water splits into two upon bouncing on the ground.
>Disassembly: The 3 parts of a yoyo body (side1, side2, post) come apart.
>
>As I understand these, a process might result in there being both
>derivation *and* disassembly relations, e.g. in the case of container
>made of two parts that snap together holding some material which
>expands rapidly causing to come apart with the contents fissioning.
Disassembly, it seems to me, is a subcase of derivation
BS
>> be defined using simple processes. For derivation, there is no
>> such simple process (hence the still ongoing discussion on what
>> goes under it and what not).
AR> I think I'm stuck on what it means to be a "primitive
AR> relationship" and what a "simple" process is. Maybe you could
AR> give me some ways to think about that.
Usually, a primitive relation is a relation that is not defined, but
characterized axiomatically. Derivation seems to be a defined relation
based on primitives like identity and "biologically significant
portion of matter" (which may be definable using part-of).
R
Yes. A richer account than we have in RO. In those terms assembly =
unification, disassembly = separation. I don't see the cases
corresponding to gains part/loses part. Here's a summary, in short
hand. -> marks the temporal divide. If you don't see a variable on one
side, the entity it denotes doesn't exist at that time.
The {} is a kind of signature, even shorter version to emphasize the
changes in existence. "," marks the temporal divide. "-" means
something ceases to exist. "*-" means all denoted entities ceases to
exist. "+" means something comes into existence.
derivation {*-,+}
a -> b c
b c -> a
transformation {,}
a,C(a) -> a,C'(a)
gains part {,}
a,b, not has_part(a,b) -> a,b, has_part(a,b)
loses part {,}
a,b, has_part(a,b) -> a,b, not has_part(a,b)
unification/assembly {,+}
a,b -> c, has_part(c,a),has_part(c,b)
separation/disassembly {-,}
c, has_part(c,a),has_part(c,b) -> a,b
>
>>Fission: A drop of water splits into two upon bouncing on the ground.
>>Disassembly: The 3 parts of a yoyo body (side1, side2, post) come apart.
>>
>>As I understand these, a process might result in there being both
>>derivation *and* disassembly relations, e.g. in the case of container
>>made of two parts that snap together holding some material which
>>expands rapidly causing to come apart with the contents fissioning.
>
> Disassembly, it seems to me, is a subcase of derivation
Still don't see it. In terms of the signatures I've listed above,
derivation is {*-,+} and disassembly/separation is {-,}.
-Alan
I guess my proposal is that derivation should be viewed as the
superordinate relation, of which all cases except transformation [and
(perhaps) loses part and gains part] would be subcases.
BS
The only issue I see with this is that the relation "derives_from" is
already out there and this would be an incompatible change.
-Alan
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