Re: [Chebi-ontology] Oxygen-18 to isotope: instance or subclass?

[Alan R. <ala...@gm...>]

On Thu, Sep 4, 2014 at 8:28 AM, Alan Ruttenberg <ala...@gm...>
wrote:

> I've seen this usage "Elements that have no isotopes"
> http://digipac.ca/chemical/molemass/isotope1.ht
> <http://digipac.ca/chemical/molemass/isotope1.htm>m
>
> Now what they mean is that there aren't isotopes that are long moved
> enough or abundant enough to matter for some
>
s/moved/lived/

> purpose. But for the sake of argument suppose sodium-23 has no isotopes.
> Would there be a class sodium as distinct from sodium-23? Regardless of the
> answer, how would having no isotopes be expressed?
>
>
>
> On Thu, Sep 4, 2014 at 7:44 AM, Bill Hogan <ho...@gm...> wrote:
>
>> I've been lurking on this thread, but having thought through the ontology
>> in this area a bit myself a few years prior to this thread taking place, I
>> find myself in full agreement with Alan.
>>
>> One question I have is whether the following are correct English
>> statements:
>>
>> oxygen-17 is an isotope of oxygen
>> oxygen-18 is an isoptope of oxygen
>>
>> (I think those two are fairly non-controversial)
>>
>> oxygen-16 is an isotope of oxygen
>>
>> Or is it the case that oxygen-16 is the "typical" form, and thus the
>> following are correct:
>>
>> oxygen-17 is an isotope of oxygen-16
>> oxygen-18 is an isotope of oxygen-16
>>
>> Also, I take it from the discussion that the following is certainly
>> INCORRECT:
>>
>> oxygen-17 is an isotope of oxygen-18
>>
>> Thanks in advance,
>>
>> Bill
>>
>>
>> On Thu, Sep 4, 2014 at 1:19 AM, Alan Ruttenberg <ala...@gm...
>> > wrote:
>>
>>>
>>>
>>>
>>> On Thu, Sep 4, 2014 at 12:05 AM, Emw <emw...@gm...> wrote:
>>>
>>>> Alan,
>>>>
>>>> Start with the two problems I have identified
>>>>>
>>>>> 1) Discordance between isotope as relation versus class.  Use
>>>>> adjacent-to/adjacents as an analogy to help guide your thinking.
>>>>>
>>>>
>>>> I don't think the textbook's definition entails that isotope is a
>>>> relation and not a class.  Here is the full definition with some context:
>>>> "The number of neutrons in the nucleus of a particular element can vary.
>>>> Isotopes are two of atoms of the same element having a different number of
>>>> electrons." [1]
>>>>
>>>
>>> I don't see how the full definition adds anything. There is definitely a
>>> relation implied, otherwise there wouldn't be anything to be "different".
>>> Minimally there is the relation x is different from y for some x and y.
>>>
>>>
>>>>
>>>> Consider chemical element, which Wikipedia defines as "a pure chemical
>>>> substance consisting of a single type of atom distinguished by its atomic
>>>> number." [2]  We could equivalently define chemical elements as "two
>>>> substances of the same pure composition having a different number of
>>>> protons."
>>>>
>>>
>>> Not in my world. What you would we be defining with that would be a
>>> mixture not an element, at best. In the first definition "type" is used.
>>> This is also a problem - what is a type in that context?
>>>
>>> Another issue is that In the first definition, "pure" is a word that
>>> doesn't add anything to the definition. If anything the definition defines
>>> "pure". In the second definition pure is used rather than defined, and so
>>> you need to define what "pure composition" means.
>>>
>>> The definitions also need to be more careful to define atoms versus
>>> substance. If they are the same use the same word.
>>>
>>> Note that one of the practices that Barry recommends is never using mass
>>> nouns in class definitions because it makes it confusing to determine what
>>> the instances are. So the way I would approach it, as I understand things,
>>> would not be to define "element".
>>>
>>> Oxygen atom =def any atom that has a nucleus which contains 8 protons.
>>> Oxygen-16 atom =def an oxygen atom that has 8 neutrons
>>> Oxygen-17 atom =def an oxygen atom that has 9 neutrons
>>>
>>> Portion of pure oxygen: An aggregate of oxygen atoms.
>>> Portion of pure element = an aggregate of atoms where all have nuclei
>>> with the same number of protons.
>>>
>>> I don't know how you would define chemical element in terms of what the
>>> instances are, but one theory would be that you mean what I call "portion
>>> of pure element". If so, one could add "chemical element" as a synonym.
>>>
>>>  Does that make chemical element a relation and not a class?  I don't
>>> think it does.
>>>
>>> If you can rewrite isotope using the same pattern I have given for
>>> atoms, then we can see.  The pattern above is consistent with how one
>>> writes definitions using BFO. The definitions that you give for chemical
>>> element and chemical elements do not satisfy requirements for being
>>> adequate definition. There is a difference between a definition that one
>>> would find in wikipedia or a dictionary and one that would be in a BFO
>>> ontology. In the BFO ontology the class exists only by virtue of its
>>> instances, so you have to be clear on what the instances are.
>>>
>>> When I tried to define isotope in terms of instances was that any
>>> definition I tried for isotope was also a definition for atom.
>>>
>>>
>>>>  The same lexicographic technique is used in industry reference
>>>> material, e.g. when the IUPAC Compendium of Chemical Terminology defines
>>>> "isotopes" as "Nuclides having the same atomic number but different mass
>>>> numbers." [3]
>>>>
>>>
>>> A terminology is not an ontology. We work on ontology in part to remedy
>>> deficits in how terminologies are constructed.
>>>
>>>>
>>>> 2) Even in the (textbook) relational view, think about whether
>>>>> oxygen-18 *is isotope of* oxygen is a sensible statement, or whether
>>>>> only statements of the sort oxygen-16 is isotope of oxygen-17 are the right
>>>>> sort of statements.
>>>>>
>>>>
>>>> "Oxygen-18 *is isotope of* oxygen" is a sensible statement.
>>>>
>>> The statement "oxygen-16 *is isotope of* oxygen-17" is not; it is
>>>> incorrect.  Neither the textbook's nor IUPAC's definition entail the latter.
>>>>
>>>
>>> Please then define "oxygen" and isotope in terms of the  instances of
>>> the respective classes. If you can define oxygen and isotope of oxygen in
>>> terms of the instances of each of those classes, then it will be BFO
>>> compliant. If you can't then you may still be able to represent in a way
>>> that is representable in OWL2 and you can satisfy your queries. My best
>>> guess at the moment is that you should use an annotation property (or
>>> perhaps punning) to be able to satisfy the queries, once you've defined the
>>> classes in terms of the instances, which is the part that BFO can help you
>>> with.
>>>
>>>
>>>>
>>>> Some alternatives:
>>>>>
>>>>> "the relation between two atoms that are instances of the same type of
>>>>> element but which have a different number of neutrons"
>>>>>
>>>>> With the guideline that types of elements are classes all of whose
>>>>> members are atoms with the same number of protons in their nucleus.
>>>>>
>>>>> or
>>>>>
>>>>> "the relation between two types of atoms, with instances of both
>>>>> having the same number of protons in their nuclei and the differentia of
>>>>> the types being that respective instances differ in the numbers of
>>>>> neutrons"
>>>>>
>>>>
>>>> Oxygen, oxygen-17 and oxygen-18 are each a type of atom, i.e. a type of
>>>> chemical element.  Your alternatives both seem to suggest that *is
>>>> isotope of* would relate the latter two and not the former two.  So
>>>> they are quite problematic.
>>>>
>>>
>>> Sorry, I can't clearly resolve what you are referring to by the "latter
>>> two" and the "former two". Could you reply rephrasing what you are saying
>>> in a different way so I can do better?
>>>
>>>
>>>> The textbook and IUPAC definitions seem workable to me.  If use the
>>>> plural triggers parsing issues, then this definition might be better:
>>>> "isotope: a type of chemical element that has a constant number of protons
>>>> but a varying number of neutrons."
>>>>
>>>
>>> Here is how I would review this as I review other ontologies that are
>>> based on BFO:
>>>
>>> 1) The definition of isotope is in terms of chemical element. Please
>>> define chemical element.
>>> 2) Explain what the instances of isotope are - are they atoms? If so,
>>> rephrase the definition to not use the word "type".
>>> 3) As written, you have stated that a type "has" a constant number of
>>> protons. Types don't have protons, particular atoms or atomic nuclei do.
>>>
>>> We need to be careful to make clear what the instances of the class are
>>> so we can determine whether one class is a subclass of another. A subclass
>>> relation obtains between classes A and B when every instance of A is also
>>> an instance of B. If we can't say clearly determine what the instances are
>>> then we can't evaluate whether subclass relations are correct.
>>>
>>> I hope this helps. I am not trying to disagree with you or give you a
>>> hard time, but rather explain to you how one thinks of ontology within the
>>> BFO framework. My hope is that you can first respond with revised
>>> definitions that follow the practices I've tried to elucidate, and that
>>> based on those we can work out how to satisfy the queries that you want to
>>> be able to make.
>>>
>>> It might be helpful to look at some slides I call "introduction to
>>> ontology introductions", attached. I have another
>>> I'm-joking-I'm-just-being-serious slogan/heuristic: "language is your
>>> enemy". Of course we can't do anything without language, but on the other
>>> hand language can be confusing when it comes to ontology development. The
>>> fact that definitions in wikipedia are not ontological definitions is an
>>> example of that. Because the language looks like a definition, we assume it
>>> is a suitable definition of a term in an ontology. Analysis of the sort I
>>> give in this email shows that that's not the case.
>>>
>>> BTW, have you watched Barry Smith's tutorial videos on ontology? If you
>>> want to understand the perspective on ontology I am talking about, they are
>>> worth watching, though of course that is an investment of time. They are
>>> at: http://ontology.buffalo.edu/smith/IntroOntology_Course.html
>>>
>>> Regards,
>>> Alan
>>>
>>> note: The affiliation shown on the slides is my previous affiliation
>>> with Science Commons. I am currently affiliated with the University at
>>> Buffalo. Incidentally my job in the years 2002-2005 or so was building a
>>> pathway database for use in microarray analysis. So I think I do understand
>>> what you are trying to do with WikiPathways. My movement towards ontology
>>> of the type we're discussing was base in part on experiences trying to do
>>> that well. Representation is hard, and I concluded that BFO and its style
>>> of ontology was the most promising way to address the sorts of issues I was
>>>  encountering. I worked for some time on the development of BioPax but
>>> abandoned it when I concluded it wasn't going to solve the sort of
>>> representation and integration problems that I thought needed to be fixed.
>>>
>>>
>>>>
>>>> Eric
>>>>
>>>> 1.  Janice G. Smith (2006).  Organic Chemistry, 1st edition.  Page 7.
>>>> 2.  Chemical element on Wikipedia.
>>>> https://en.wikipedia.org/w/index.php?title=Chemical_element&oldid=623989378
>>>> 3.  IUPAC Compendium of Chemical Terminology, 2nd edition.
>>>> http://goldbook.iupac.org/I03331.html
>>>>
>>>>
>>>> On Wed, Sep 3, 2014 at 2:08 AM, Alan Ruttenberg <
>>>> ala...@gm...> wrote:
>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Sep 2, 2014 at 11:08 PM, Emw <emw...@gm...> wrote:
>>>>>
>>>>>> Alan,
>>>>>>
>>>>>>
>>>>>>> I think you first need to have a solid definition of what an isotope
>>>>>>> is. I offered a start of one from the perspective of BFO in my last email
>>>>>>> message. I think it would be good for you to offer an alternative. Simply
>>>>>>> saying the isotope is a metaclass of Oxygen-18 isn't an adequate definition.
>>>>>>>
>>>>>>
>>>>>> You provisionally define isotope as follows:
>>>>>>
>>>>>> to be an isotope is something like to be a mutation. To be a mutation
>>>>>>> is to be slightly different from the canonical, but of equal status except
>>>>>>> for perhaps the number of class members. To be an instance of an isotope of
>>>>>>> oxygen (atom) is to be a an atom with a different number of nucleons
>>>>>>> (protons and neutrons)  than the most abundant form (oxygen-16, with 8
>>>>>>> protons and 8 neutrons in its nucleus).
>>>>>>>
>>>>>>
>>>>>> I don't think that will work.  Oxygen-16 is an isotope of oxygen and
>>>>>> is referred to as such throughout the literature.  Any definition of
>>>>>> isotope must account for that.
>>>>>>
>>>>>> A typical textbook defines isotopes as "two atoms of the same element
>>>>>> having a different number of neutrons" [1].  Wikipedia defines isotope
>>>>>> similarly [2].  The textbook definition seems workable.
>>>>>>
>>>>>
>>>>> This is a relation, not a type. The clue is that it says "two atoms".
>>>>> A good idea would be to ask what the two atoms are in your statement
>>>>> "Oxygen-16 is an isotope of oxygen".
>>>>>
>>>>>
>>>>>> That definition in itself doesn't warrant modeling isotopes as
>>>>>> metaclasses.
>>>>>>
>>>>>
>>>>> Or even classes. What I don't understand is how you move from a binary
>>>>> relation ("two atoms") to a unary property (implicitly of one atom).
>>>>>
>>>>>
>>>>>> But criterion D from my 2014-08-27 message [3] arguably could.
>>>>>> Criterion D: "Avoid any potential subclasses of the isotopes in (A) and (B)
>>>>>> without relying on those subclasses being leaves in a subsumption
>>>>>> hierarchy."  See the criteria atop
>>>>>> http://sourceforge.net/p/chebi/mailman/message/32766380/ for context.
>>>>>>
>>>>>
>>>>> Actually I didn't understand that. However I think we should start
>>>>> with the discordance between considering isotope being a relation vs.
>>>>> isotope being a class. As a comparison, consider the relation of adjacency.
>>>>> Is there a class "adjacents"?
>>>>>
>>>>> Most of what comes below is phrased in terms of the unary
>>>>> interpretation of isotope. I'll not comment on it further until we sort out
>>>>> this unary versus binary thing, in the interest of not confusing things.
>>>>>
>>>>>
>>>>>> Such subclasses of a "particular" isotope are plausible, e.g.
>>>>>> carbon-14 in fossil fuels, carbon-14 in human bodies.  We could satisfy
>>>>>> criterion D by using SPARQL queries that do not use inference, e.g.
>>>>>>
>>>>>>    - Get *only* classes like oxygen-17, oxygen-18 and oxygen-19:
>>>>>>
>>>>>>    SELECT ?subject WHERE { ?subject rdfs:subClassOf oxygen
>>>>>>    . ?subject rdfs:subClassOf isotope . }
>>>>>>
>>>>>>
>>>>>>    - Get all subclasses of oxygen and isotope:
>>>>>>
>>>>>>    SELECT ?subject WHERE { ?subject rdfs:subClassOf* oxygen
>>>>>>    . ?subject rdfs:subClassOf* isotope . }
>>>>>>
>>>>>> (Note the asterisks in the latter.)
>>>>>>
>>>>>> That isn't enough, though.  It would still not filter out direct
>>>>>> subclasses of an element and isotope that are not "particular" isotopes
>>>>>> like oxygen-18, e.g. "stable isotopes of oxygen", "radioactive isotopes of
>>>>>> oxygen".  This complication could be addressed by using the statement "*instance
>>>>>> of* isotope" on "particular" isotopes like oxygen-17, oxygen-18 and
>>>>>> oxygen-19 but not subclasses of oxygen and isotope like "radioactive
>>>>>> isotopes of oxygen".  That is the motivation for representing isotope as a
>>>>>> metaclass.
>>>>>>
>>>>>> *is isotope of*, Chris Mungall's proposed BFO-compatible solution,
>>>>>> also has issues as described in
>>>>>> http://sourceforge.net/p/chebi/mailman/message/32658963/.  Simply
>>>>>> put, it is not valid in OWL 2 DL to declare "*is isotope of*
>>>>>> rdfs:subPropertyOf rdfs:subClassOf",
>>>>>>
>>>>> I don't see that as an issue of not being valid OWL 2 DL. To me it is
>>>>> an issue of whether it makes sense. To me it doesn't.
>>>>>
>>>>> Here is another question. How would you distinguish the class isotope
>>>>> from the class atom?
>>>>>
>>>>>> and the statement we'd thus be forced to make -- "oxygen-18 *subclass
>>>>>> of* oxygen and oxygen-18 *is isotope of* oxygen" -- is awkwardly
>>>>>> redundant.
>>>>>>
>>>>> Here again, even in the relational expression, the textbook definition
>>>>> can't be understood unless you say what the members of the class oxygen
>>>>> are. If the members of the class are all atoms with 8 protons in the
>>>>> nucleus, then in the above you would have instances of oxygen-18 being
>>>>> isotopes of oxygen-18.
>>>>>
>>>>> Aside from that, it isn't redundant - one of the axioms describes
>>>>> class membership and the other expresses a relationship between members of
>>>>> the class. The criteria of being awkward or not doesn't, to me, seem to be
>>>>> a relevant criteria at this point. First you have to make clear what you
>>>>> mean. Then we can discuss alternatives to representing that.
>>>>>
>>>>>> So none of the options here are good.  Option A -- "oxygen-18 *subclass
>>>>>> of* oxygen and *subclass of* isotope" -- is compatible with BFO and
>>>>>> ChEBI but requires brittle conventions to meet the querying and inference
>>>>>> requirements in [3]. Option B -- "oxygen-18 *subclass of *oxygen and
>>>>>> oxygen-18 *instance of* oxygen" is incompatible with BFO and thus
>>>>>> ChEBI.  Option C -- "oxygen-18 *isotope of* oxygen and *isotope of*
>>>>>> rdfs:subPropertyOf *subclass of*" or "oxygen-18 *subclass of* oxygen
>>>>>> and *isotope of* oxygen" is either incompatible with OWL or
>>>>>> awkwardly redundant.
>>>>>>
>>>>>> I see no way forward.  How can oxygen-18 be modeled as an isotope in
>>>>>> a way that is compatible with BFO and OWL 2 DL, and also meets the criteria
>>>>>> in [3]?
>>>>>>
>>>>>
>>>>> The way forward is to first get clear on what the ontology of isotope
>>>>> is, independent of OWL. Then we can work on OWL.
>>>>>
>>>>>
>>>>>>
>>>>>> You are free to use BFO or not.
>>>>>>>
>>>>>>
>>>>>> Wikidata is certainly free to use whatever upper ontology it
>>>>>> desires.  But I think compatibility among Wikipedia's ontology and BFO,
>>>>>> ChEBI and OBO would be a major boon to the Semantic Web.
>>>>>>
>>>>>
>>>>> I would tend to agree. One of the benefits of using BFO, in my view,
>>>>> is that it tries to force the user to be clear about what they are talking
>>>>> about. So let's work on that goal.
>>>>>
>>>>>
>>>>>>
>>>>>> Currently, Wikidata is not compatible with BFO or ChEBI.  There is a
>>>>>> tendency in the Wikidata community to use *instance of* in subjects
>>>>>> that are clearly classes, i.e. universals -- e.g. carbon *instance
>>>>>> of* chemical element, oxygen-18 *instance of* isotope, heart attack *instance
>>>>>> of* cardiovascular disease [4-6].   As we have established here,
>>>>>> such statements are not compatible or consistent with BFO, ChEBI and other
>>>>>> OBO ontologies.
>>>>>>
>>>>>
>>>>> More importantly, it isn't clear what they mean.
>>>>>
>>>>>
>>>>>>  But they do offer an easy way to solve important querying tasks --
>>>>>> like "how do I get a list of (elements | isotopes | diseases)?" -- even
>>>>>> though they contradict BFO's definition of instance as something with a
>>>>>> particular location in space and time.
>>>>>>
>>>>>
>>>>> My experience has been that by focusing first on ontology, afterwards
>>>>> the query problem tends to look much easier.
>>>>>
>>>>>>
>>>>>> I look forward to any more proposals on how to move through this
>>>>>> impasse!
>>>>>>
>>>>>
>>>>> Start with the two problems I have identified
>>>>>
>>>>> 1) Discordance between isotope as relation versus class. Use
>>>>> adjacent-to/adjancets as an analogy to help guide your thinking.
>>>>>
>>>>> 2) Even in the (textbook) relational view, think about whether
>>>>> oxygen-18 *is isotope of* oxygen is a sensible statement, or whether
>>>>> only statements of the sort oxygen-16 is isotope of oxygen-17 are the right
>>>>> sort of statements. I think you might gain some clarity by putting a
>>>>> critical eye on some of the problems with the definitions one might
>>>>> identify as an ontologist. Here I discuss the textbook definition, but the
>>>>> same problems are present in the wikipedia definition.
>>>>>
>>>>> original "two atoms of the same element having a different number of
>>>>> neutrons"
>>>>>
>>>>> This sounds like an isotope is an aggregate of two atoms, which of
>>>>> course is not what is meant, despite that being the most direct
>>>>> interpretation of the english.
>>>>>
>>>>> Some alternatives:
>>>>>
>>>>> "the relation between two atoms that are instances of the same type of
>>>>> element but which have a different number of neutrons"
>>>>>
>>>>> With the guideline that types of elements are classes all of whose
>>>>> members are atoms with the same number of protons in their nucleus.
>>>>>
>>>>> or
>>>>>
>>>>> "the relation between two types of atoms, with instances of both
>>>>> having the same number of protons in their nuclei and the differentia of
>>>>> the types being that respective instances differ in the numbers of
>>>>> neutrons"
>>>>>
>>>>> While these definition are perhaps not in the vernacular of the
>>>>> chemist, the explicit use of type/class/universal/relation in the
>>>>> definitions removes ambiguities (and therefore confusion) present in the
>>>>> natural english definitions.
>>>>>
>>>>>
>>>>> -Alan
>>>>>
>>>>>
>>>>>> Best,
>>>>>> Eric
>>>>>>
>>>>>> 1.  Janice G. Smith (2006).  Organic Chemistry, 1st edition.  Page 7.
>>>>>> 2.  Isotope on Wikipedia.
>>>>>> https://en.wikipedia.org/w/index.php?title=Isotope&oldid=623706639
>>>>>> 3.  http://sourceforge.net/p/chebi/mailman/message/32766380/
>>>>>> 4. Carbon on Wikidata.
>>>>>> https://www.wikidata.org/w/index.php?title=Q623&oldid=151858101
>>>>>> 5. Oxygen-18 on Wikidata.
>>>>>> https://www.wikidata.org/w/index.php?title=Q662269&oldid=84117617
>>>>>> 6. Heart attack on Wikidata.
>>>>>> https://www.wikidata.org/w/index.php?title=Q12152&oldid=155099715
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
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