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

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

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 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...
<javascript:_e(%7B%7D,'cvml','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...
> <javascript:_e(%7B%7D,'cvml','ala...@gm...');>> wrote:
>
>>
>>
>>
>> On Thu, Sep 4, 2014 at 12:05 AM, Emw <emw...@gm...
>> <javascript:_e(%7B%7D,'cvml','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...
>>> <javascript:_e(%7B%7D,'cvml','ala...@gm...');>> wrote:
>>>
>>>>
>>>>
>>>>
>>>> On Tue, Sep 2, 2014 at 11:08 PM, Emw <emw...@gm...
>>>> <javascript:_e(%7B%7D,'cvml','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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