On 18 Mar 2015, at 19:08, William Frank wrote: (01)
> Chris,
>
>
> *I do not think the issue is that there is no difference between
> things
> that happen and things that stay around for a long time. The issue
> is, as
> you say, people have to **decide** how most effectively to CAST the
> concept, from among some useful set of categories, given what they are
> trying to do. Only the decision is a human one, not one forced by
> nature. * (02)
no problem with that (03)
>
>
> *I am so **perplexed** by how what is easy in any rich logical
> representation with an expressive power even slightly close to that of
> a
> natural language, becomes a 'problem' that seems to plague
> ontologists.
> The problems are a result of starting by choosing an unexpressive
> language.
> * (04)
perhaps (05)
> *just for many examples from this thread, the excellent Mathew West
> says: **MW>]
> It sounds like you favour things like the President and such like as
> classes. I won’t say that you can’t do it, but I find it
> unattractive. I
> would want to be able to say that the President of the United States
> signed
> a treaty, but classes do not make good actors as abstract objects, so
> there
> are more contortions to be gone through.*
>
>
>
> **the* President would indeed be a poor class *
>
> *but *
>
>
>
>
>
> *'x is president of y' is a nice relation, with two roles, by adding
> the
> implicit constraint that *
>
>
> *at time t, for each y, there can be at most one x who is president of
> y *
>
> *then, *
>
>
>
> *using the iota operator (that object such that - an analog to the
> lamda
> operator for functions) *
>
> *let P = *
>
>
> *that object o such that at time t, o is the president of the United
> States
> *
>
> *and use the relation 'x signs y', so that *
>
>
> *for treaty T, *
>
>
> *at time t, P signs T. *
>
>
> *Tells this story, to me, completely naturally. Not a contortion,
> but an
> 'unpacking' of the complex, dense way in which people talk. * (06)
ok, not sure where this is going. I'm reasonably familiar with how to
translate natural language statements to FOL. (07)
> *Any such language will have from 5 to ten different categories of
> being,
> (hard to beat Aristotle's, I agree). *
> *And any good data model I have seen recently will let you say these
> kinds
> of things. And, if an 'ontological language' can't say them, or makes
> it
> hard to say them, then how is the ontology going to allow us to easily
> *translate* between these lowly data models? *
>
>
>
> *It is possible, in any such rich language, to RECAST something in one
> category into another. This does not mean they are 'really' the same.
> or
> that there is 'really' only one kind of thing. (when anybody says
> 'really', if you are a practical person, run.) Why would it be
> beneficial
> to recast everything into **one** category. I may be wrong, but I
> don't
> think anyone suggested that this was a good idea. Should we forget
> about
> money and integers and strings and only talk hexadecimal? Given a
> problem
> domain, casting things one way or another will prove to be the most
> useful. Sometimes, we want color to only be an attribute, say,
> talking
> about bears, sometimes, we want colors to be things, say, talking
> about the
> effects of colors on moods. *
>
>
>
>
>
>
> *So, the only 'problems' I see are that people 'code first, think
> later'.
> Let's start by creating a Procrustean bed ,an ontological straight
> jacket,
> in which, for example, you are not allowed to speak of times, maybe no
> states that things can be in during a time period, (such as a bannana
> that
> will be ripe for a given period of time, then rotten, then completely
> gone
> as it was consumed by microorganisms), where we are not allowed to
> treat
> the process of ripening as much of a first class citizen as the
> bannana, (08)
OK, now I'm not follow. What does "first class citizen" mean here? (09)
All I'm saying is that we treat 'banana' and 'banana ripening' as
distinct classes. I wasn't proscribing any kind of talk of the two at
the same time. (010)
> or
> are not allowed to treat the relation between the bannana and the tree
> it
> is growing on as a first class citizen, where probably no instances of
> relations are allowed, so that we are not allowed to refer to Tom and
> Linda's marriage, where being the officiator of that marriage can't be
> treated as a role in that marriage, or where the relational type
> marriage
> can't have roles like officiator, where for some reason, there are
> either
> no sets or no composites of other things - you have to choose which,
> Then
> we can happily say 'oh gee' we've got a real problem here (011)
This definitely sounds like a real problem. But it's not a problem that
maps to anything I'm familiar with. (012)
> -- how are we
> going to deal with the fact that customers come and go, and that when
> you
> say 'customer' you always mean the customer of something, and it
> becomes a
> 'problem' that the same company might be both a customer and a vendor.
> This can keep us employed solving 'problems', I guess. *
>
>
> *These are **manufactured** problems. I see similar kinds of
> 'problems'
> increasingly discussed among those following the fashion for 'Dogma
> Driven
> Development'. * (013)
Thanks. Sorry if I missed some of your points. I', certainly in favor of
driving development from practical requirements rather than dogma. (014)
> *Wm *
>
>
>
>
>
>
> On Wed, Mar 18, 2015 at 8:33 PM, Chris Mungall <cjmungall@xxxxxxx>
> wrote:
>
>>
>>
>> On 18 Mar 2015, at 14:30, Pat Hayes wrote:
>>
>>> On Mar 18, 2015, at 1:15 PM, Chris Mungall <cjmungall@xxxxxxx>
>>> wrote:
>>>
>>>>
>>>>
>>>> On 18 Mar 2015, at 9:23, Pat Hayes wrote:
>>>>
>>>>> On Mar 18, 2015, at 9:17 AM, Thomas Johnston <tmj44p@xxxxxxx>
>>>>> wrote:
>>>>>
>>>>>> Could those of you who are involved in this thing vs. event
>>>>>> (endurantism vs. perdurantism) exchange explain to me why, except
>>>>>> as
>>>>>> a bit of interesting metaphysical speculation, those of us
>>>>>> building
>>>>>> formal ontologies should be interested in it?
>>>>>
>>>>> Because if one is using almost any conventional representational
>>>>> notation, from classical FOL through RDF and/or OWL, each of these
>>>>> positions requires one to adopt an axiomatic style which is
>>>>> sharply
>>>>> incompatible with the style the other one forces you to adopt. If
>>>>> your
>>>>> ontology encompasses both kinds of entities, then you are obliged
>>>>> to
>>>>> enforce a rigid top-level distinction between them, since all
>>>>> assertions about one kind have to be made in one axiomatic style,
>>>>> different from those mentioning the others. Basically, one style
>>>>> prohibits attaching a temporal parameter to entity names (because
>>>>> "continuants do not have temporal parts"), the other prohibits
>>>>> attaching temporal parameters to relations (because relations are
>>>>> timeless.) One sees this very sharply in the amount of work
>>>>> involved
>>>>> in the OBO ontologies to keep continuants separated from
>>>>> occurrents.
>>>>> The typical result is that many general facts have to be stated
>>>>> twice,
>>>>> one using each notational style.
>>>>
>>>> Can you give an example from some widely used OBO ontologies? I'm
>>>> not
>>>> really aware of work specifically to keep these separate.
>>>
>>> ?? The basic ontology of every OBO ontology requires that they be
>>> kept
>>> separate, and the OBO discussion forums are constantly awash with
>>> discussions and questions about whether or not some new idea is a
>>> continuant or not. Just check the email archives.
>>
>> I'm on many of those lists. I'm aware of many upper ontology
>> discussions
>> that could be construed as time wasting. The people building the
>> ontologies are generally quite practical and may not be participating
>> in
>> some of the more obscure discussions.
>>
>> What I'm actually after is not waffle on a mailing list, but concrete
>> examples of a pair of classes P and C, taken from widely used OBO
>> ontologies, where P is a process and C is a continuant, where
>> maintaining the distinction between P and C involves work/effort, and
>> where there are pragmatic advantages to collapsing these. The
>> advantages
>> may be conceptual (easier to comprehend to domain scientists),
>> elegance,
>> advantages in inference, etc.
>>
>>>
>>>> I might agree that there is sometimes a general tendency of some
>>>> ontologies to over-inflate the number of entities into different
>>>> aspects
>>>> corresponding to upper level categories. But the process vs
>>>> physical
>>>> entity distinction would be very hard to avoid (or perhaps we are
>>>> too
>>>> engrained in the mindset of biologists and bioinformaticians).
>>>
>>> If you find it useful, by all means use it. But there are many cases
>>> where it is hard to classify something on either side of this
>>> divide.
>>> Is the flame of a gas torch a thing or a process? It has aspects of
>>> each. How about hurricane Katrina, or a tsunami wave, or a ripening
>>> banana?
>>
>> I have no opinion on tsunamis, flames.
>>
>> But bananas I like, because your example corresponds to classes in
>> two
>> ontologies I work on:
>>
>> "fruit ripening" from the process branch of the Gene Ontology:
>> http://amigo.geneontology.org/amigo/term/GO:0009835
>>
>> "fruit" from the plant anatomy ontology (continuants):
>> http://purl.obolibrary.org/obo/PO_0009001
>>
>> (banana ripening and banana would be trivial subclasses of these)
>>
>> AFAIK nobody has ever argued for merging these together. Or for
>> analogous merges, between anatomical structures and developmental or
>> physiological processes.
>>
>> I mean obviously I see how this *could* be done, I have no problem
>> conceptualizing the banana as a 4D worm and the ripening process as a
>> slice through the worm, and I could probably come up with the
>> required
>> axiomatization (there are subtleties, and some constraints imposed by
>> OWL). I have a harder time figuring out how to make the results
>> practically usable, and how to make my banana worms palatable to both
>> the ontology editors and users. I expect continuants would be
>> reintroduced through the back door, as some kind of 'maximal worm
>> slice'
>> class.
>>
>> Maybe this is just a conceptual prison we've locked ourselves into,
>> but
>> if so, I'd argue this is *not* due to philosophers imposing some
>> categorical distinction from above, but rather through the
>> perspectives
>> and modalities of different disciplines such as developmental biology
>> and classical anatomy and systematics.
>>
>>> All of these and many more can be viewed in either way; and
>>> prohibiting this, forcing users to make an artificial distinction
>>> between the flame-thing and the flame-process, serves no useful
>>> purpose. The point is not that the distinction is bad, but that
>>> being
>>> *forced* to make it can be harmful, or at the very least,
>>> time-wasting.
>>
>> Conversely, being denied the framework to make useful distinctions
>> may
>> be harmful and time-wasting.
>>
>> But this is all rather hypothetical. If there are particular cases in
>> the OBO world where we are wasting time making spurious distinctions
>> between physical entities and processes, I will be with you all the
>> way
>> in seeking to eliminate this.
>>
>>>
>>>> It may
>>>> _seem_ to be the case that facts are stated twice: for example, the
>>>> GO
>>>> ontology of biological processes (Occ.) will state about classes
>>>> 'limb
>>>> development', 'forelimb development' and 'hand development',
>>>> whereas
>>>> an
>>>> anatomy ontology will also have facts stating facts about classes
>>>> 'limb'
>>>> 'forelimb' and 'hand'. Similarly GO will include occurrent
>>>> hierarchies
>>>> of biochemical reactions and signaling pathways, and these will be
>>>> related to but modeled distinctly from continuant ontologies about
>>>> molecules and protein complexes and cell parts. What may appear to
>>>> be
>>>> redundantly stated facts are actually inferred from one hierarchy
>>>> to
>>>> another.
>>>
>>> I know that this all does actually work, and if one has become
>>> comfortable thinking of everything in this strictly segregated way
>>> then it may even seem obvious, but there are many ways in which the
>>> strict segregation is harmful. Other ontological standards use a
>>> basic
>>> framework which treats all spatiotemporal entities uniformly as far
>>> as
>>> their temporal description is concerned. Each, I am sure, seems as
>>> natural and motherhood and apple pie to those who have lived within
>>> it
>>> for an extended period.
>>
>> I have absolutely no problem with this, and I am happy for people to
>> model their domain in whatever way is most appropriate. I just
>> responded
>> because you said we were doing work (implied 'busy work') in the OBO
>> world maintaining a separation. If we can do less work and get a
>> leaner
>> and more intuitive model then I'm all for it. But it will take
>> concrete
>> examples to convince those of us doing the work. We need more than a
>> handful of edge cases like flames and tsunamis.
>>
>>>> I'm all for collapsing distinctions and reducing the number of
>>>> ontologies. I can imagine syntactic tricks that would allow classes
>>>> from
>>>> one category to proxy for classes in another, e.g. limb for limb
>>>> development, or vice versa.
>>>
>>> The fact that you insist upon treating these as fundamentally
>>> different suggests to me that you may be entirely happy in one way
>>> of
>>> thinking (not meaning to be ad hominem). It is possible to think
>>> differently, however. I think it is notable that apparently many
>>> users
>>> of OBO do not find the notion of continuant at all obvious, and
>>> indeed
>>> have extended debates about it, some of which are only finally
>>> resolved by an ex cathedra stipulation from Barry Smith.
>>
>> Right, I have no problem with the statement that users find notions
>> with
>> strange labels like 'continuant' unintuitive. But I think it's a leap
>> to
>> go from this to the fact that users find the distinction between a
>> physical entity (with a certain set of properties such as mass, and
>> spatial parts) and a process (with properties such as rate, and
>> process
>> parts) unintuitive, or to state that this distinction is unnaturally
>> forced on them from above by philosophers. (Personally, I think the
>> "picture" vs "movie" distinction is the only clear distinction in any
>> upper ontology, sometimes I'd happily throw the rest out).
>>
>> I mean we could try an experiment. You could make a request in CHEBI
>> (the OBO chemical entity ontology, continuants) for "phosphorylation"
>> using the tracker here:
>> https://sourceforge.net/p/chebi/curator-requests
>> After all, phosphorylation is just part of the life of a molecule,
>> and
>> the distinction between process parts and spatial parts is an
>> unintuitive one foisted on us by philosophers.
>>
>> It won't be a philosopher that rejects the request, it will be a
>> biochemist.
>>
>>> At the sub-cellular level, classifying between physical entities and
>>> processes becomes close to impossible to do on a principled basis,
>>> as
>>> far as I can see. Is a molecular pool (in SBGN) a continuant or an
>>> occurrent? (Does the question even make sense?)
>>
>> Well I guess if you want to be literal the question doesn't make
>> sense
>> in that SBGN defines squiggles and shapes on a diagram. And what the
>> diagram depicts exactly is not as straightforward as it might seem.
>> But
>> I'm not sure what the difficulty here is. Most pathway models,
>> including
>> SBGN boil down to bipartite graphs, with nodes in either the physical
>> entity category (e.g. ATP, or pools of ATP) or event/process
>> categories
>> (e.g. phosphorylation). The node pools in an SBGN process diagram (or
>> corresponding BioPAX or SBML model) would typically be annotated
>> using a
>> continuant ontology like CHEBI, and the transitions/events/processes
>> using GO or a vocabulary of reaction types. No one has a problem with
>> that as far as I know, and no one wants to start mixing these things
>> up.
>> There is no huge effort to maintain artificial distinctions here, as
>> far
>> as I'm aware. I mean in SBGN it's called a process diagram, it has
>> different properties than a structure diagram used to depict a
>> chemical
>> structure (continuant).
>>
>>>
>>>> But I don't think anything would be achieved
>>>> here, other than completely baffling users. In addition, when you
>>>> get
>>>> down to the level of cells and below there are some subtle issues
>>>> involving time and identity that could confound the use of the
>>>> ontologies in query answering.
>>>>
>>>> Perhaps I just have a hard time envisioning a different model. As I
>>>> say,
>>>> I believe the distinction is fairly hardwired into people's
>>>> thinking.
>>>> I'm not talking about ontologists here. Look at any datamodel that
>>>> captures something like biochemical or signaling pathways, at its
>>>> core
>>>> you will see a bipartite graph of physical entities and occurrents.
>>>> I'd
>>>> be genuinely interested in seeing a non-handwavy attempt to model
>>>> things
>>>> differently.
>>>
>>> With some colleagues I am trying to do this exactly on cellular
>>> pathways in oncology research. It is natural to write equations
>>> describing qualitative dynamics of chemical pools (abstracted from
>>> several sources including SBGN graphs) and then to instantiate the
>>> terms in such equations with temporal arguments when required, so
>>> one
>>> can speak of the quantity of-MEK hydrogenase at a certain time by
>>> simply adding a temporal argument to the relevant term denoting
>>> quantity of MEK-hydrogenase. All of which is elegant, natural and
>>> formally correct, but violates the OBO ontology conditions, since
>>> these quantities are classified, for reasons which are entirely
>>> opaque
>>> to me, as continuants.
>>
>> I couldn't care less if it violates current OBO ontology conditions.
>> If
>> your formalism is elegant, natural and formally correct then I'm far
>> more interested in that. I'm genuinely interested to hear more,
>> either
>> off list or after you're ready to publish on it.
>>
>>>
>>> Pat
>>>
>>>>
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