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

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

Stefan, Janna,

My original question, i.e. whether the model

    oxygen-18
        *subclass of* oxygen
        *instance of* isotope

      (where *instance of* is rdf:type and *subclass of* is rdfs:subClassOf)

is compatible with ChEBI, seems to depend on whether class-instance punning
is valid in BFO.  If it is, then this negates the foundational definition
of "instance" in Smith and Rosse 2004 [7]: "Instances are individuals
(particulars, tokens) of special sorts... bound to a specific... location
in space and time."

Is class-instance punning compatible with BFO, and thus ChEBI?

Since this question also concerns BFO, I've copied Alan Ruttenberg on the
conversation.  The following response explores this further.


"Punning" is possible in OWL Full, but it is first of all a syntactical
feature. Description logics reasoners ignore it, and its semantics is
undefined.

Punning is possible in OWL 2 DL and supported in description logics
reasoners like Pellet [1, 2].  The formal semantics of punning are defined
in Motik 2007 [3], which describes a decidable extension of SROIQ(D) using
contextual semantics.  Motik 2007 is the basis of the class-instance
metamodeling supported in OWL 2 DL.

[Metamodeling an entity as a class and an instance, as in the cited UniProt
example] may be motivated by pragmatic reasons, but is no recommendable
solution as long as we envisage ontologies as interoperable descriptions of
segments of the world, and not just as logical models that support specific
use cases.

Part of me agrees with this.  But how is that recommendation tenable when
most authoritative explanations of punning in OWL 2 DL use precisely the
kind metamodeling that UniProt does, i.e. "human *instance of *taxon, human*
subclass of* primate?  Here is a representative example from Horrocks and
Patel-Schneider 2010 [4]:

In contrast, OWL 2 allows the same name to be used to refer to different
types of entity; for example, ex:Eagle might be used to denote both the
class (a subclass of ex:Bird) and an individual (an instance of ex:Species):

    Class: ex:Eagle
        SubClassOf: ex:Bird
    Individual: ex:Eagle
        Types: ex:Species

(See also the canonical "Harry the Eagle" example used in Motik 2007 [3],
Grau et al. 2008 [5], Krötzsch 2014 [6], etc.)

This poses a dilemma for those wanting to interoperate in letter and spirit
with BFO.

The dilemma emerges from the fact that BFO and OWL 2 DL seem to have
conflicting definitions of "instance".  BFO states that instances are
particular tokens with a unique location in space and time, while classes
are universal types [7].  However,  the motivating example for one of OWL 2
DL's major new features contradicts this: as an instance of "species",
"Eagle" is *not* a particular thing with a unique location in space and
time.

Such metaclasses pop up in numerous domains: "human *instance of* taxon,
human *subclass of* primate"; "Ford Focus *instance of* car model, Ford
Focus *subclass of* compact car"; "Nimitz-class aircraft carrier *instance
of* ship class, Nimitz-class aircraft carrier *subclass of* aircraft
carrier".  These examples are based on classification discussions in
Wikidata.

I see two options to resolve this dilemma:

   1. Allow class-instance metamodeling in BFO.  This entails broadening
   the definition of "instance" in BFO to account for classes being
   instances of metaclasses.  It would clarify that statements like those in
   the canonical OWL 2 DL examples, UniProt, and the preceding paragraph are
   all compatible with BFO.  This has a cost in that would, as Stefan puts
   it, detract from our ability to "envisage ontologies as interoperable
   descriptions of segments of the world, and not just as logical models that
   support specific use cases."

   2. Prohibit class-instance metamodeling in BFO.  This would preserve the
   foundational definition of "instance" in Smith and Rosse 2004 [7]:
   "Instances are individuals (particulars, tokens) of special sorts... bound
   to a specific... location in space and time."  However, it would also
   prevent BFO ontologies from using a major feature in OWL 2 DL.

Stefan notes another possibility:

> If one wants to represent types differently from classes it has been
> proposed to represent them as OWL individuals.
>
However, that would have the same philosophical cost as Option 1 above,
because -- ontologically, at least in BFO -- classes are types [7].  If we
use *instance of* to relate two types, then it seems we are treating the
"instance" and "class" constructs in OWL as just syntactic features with no
philosophical meaning.

I have searched for literature on how BFO accounts for class-instance
punning in light of the Smith and Rosse 2004 definition of "instance", but
have not found anything relevant.  This might be because
philosophically-oriented BFO literature, e.g. Smith and Ceusters 2010 [9],
tends to predate the publication of OWL 2 in December 2012, which brought
punning from the controversial OWL Full vocabulary into the mainstream OWL
2 DL vocabulary.

Thanks,
Eric

P.S.: Janna, thanks for correcting my misunderstanding about ChEBI.  I see
now that chebi.owl [8] defines object properties which have rdfs:domain
values, but avoids modeling classes as instances by using those properties
only in OWL restrictions.
1.  http://www.w3.org/TR/owl2-new-features/#F12:_Punning
2.   "Pellet supports reasoning with the full expressivity of OWL-DL
(SHOIN(D) in Description Logic jargon) and has been extended to support the
forthcoming OWL 2 specification (SROIQ(D)), which adds the following
language constructs: ... vocabulary sharing (punning) between individuals,
classes, and properties ..."
http://clarkparsia.com/pellet/features#standard
3.  Boris Motik (2007).  *On the Properties of Metamodeling in OWL*.
https://www.cs.ox.ac.uk/Boris.Motik/pubs/motik07metamodeling-journal.pdf
4.  Ian Horrocks and Peter Patel-Schneider (2010). * Knowledge
Representation and Reasoning on the Semantic Web: OWL*.
http://www.cs.ox.ac.uk/ian.horrocks/Publications/download/2010/HoPa10a.pdf
5.  Bernardo Cuenca Grau et al. (2008). *OWL 2: The Next Step for OWL*.
http://www.websemanticsjournal.org/index.php/ps/article/viewFile/156/154
6.  Markus Krötzsch (2014). *Foundations of Semantic Web Technologies: OWL
2 - Syntax and Semantics*.
http://www.inf.tu-dresden.de/content/institutes/ki/cl/study/summer14/fswt/slides/FSWT2014-L11-OWL2.pdf
7.  Barry Smith, Cornelius Rosse (2004). *The Role of Foundational
Relations in the Alignment of Biomedical Ontologies*.
http://ontology.buffalo.edu/medo/isa.pdf
 8.  ChEBI OWL export.
ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.owl
9.  Barry Smith, Werner Ceusters (2010). *Ontological Realism as a
Methodology for Coordinated Evolution of Scientific Ontologies.  *
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3104413/
<http://iospress.metapress.com/content/1551884412214u67/fulltext.pdf>