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

[Bill H. <ho...@gm...>]

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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