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

[Emw <emw...@gm...>]

Alan,


> I don't see how you come to the conclusion that it is not compatible with
> BFO to say so.... BFO doesn't prohibit anything....  In the framework of
> BFO, universals are not instances of anything.


If BFO states that universals are not instances of anything, then it seems
clear that BFO would prohibit the statement "oxygen-18 *subclass of* oxygen
and oxygen-18 *instance of* isotope".  By "prohibit" I mean "not be
compatible with" or "consider to be false".

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.

That definition in itself doesn't warrant modeling isotopes as
metaclasses.  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.

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", 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.
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]?

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.

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.  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.

I look forward to any more proposals on how to move through this impasse!

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