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

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Eric,

> major innovation in OWL 2 DL,
> however, is that things can be both
> an instance and a class [6].

"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.

At least regarding material entities, there are clear-cut criteria for the
distinction between classes and individuals.

> (This construct is already used in
> some major biological taxonomy
> ontologies, e.g. UniProt [7].)

This 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.

>
> Janna, finally, you mention that
> "Option B [modeling oxygen-18 as a
> class and instance] would be less
> compatible as we model all atom
> types as classes rather than
> as instances.

OWL DL only distinguishes between classes and individuals. If one wants to
represent types differently from classes it has been proposed to represent
them as OWL individuals. Then:

    X equivalentTo instanceOf value X_Type

This say: an entity is a member of the class X iff it instantiates X_Type.

This representation is somewhat redundant but it would allow to create
links between types without the need of punning, such as the triple

Deuterium_Type isIsotopeOf Hydrogen_Type

with isIsotopeOf being a relation between types.

In a simpler OWL DL model, which does not introduce types as ABox entities,
the following axiom seems acceptable:

Deuterium subClassOf isIsotopeOf only (Hydrogen and not Deuterium)

which means that for every given Deuterium atom an isotope relation only
holds for another atom which is of the type Hydrogen, but not of the type
Deuterium.

The statement is still weak because it accepts a case in which there is a
Deuterium atom and Tritium atom that do not stand in an isIsotopeOf
relation.

Deuterium and not (isIsotopeOf some (Hydrogen and not Deuterium)) subclass
Of Nothing

could be an additional constraining axiom (not yet tested).

-
Stefan

>
> Thanks for any further insight here!
>
> Eric
>
> 1.  See statements such as "A has_subclass B = [definition] B is_a A" in
Smith et al. 2005 [8], and the mapping of is_a to rdfs:subClassOf
throughout OWL exports of ChEBI and other OBO ontologies.
> 2.  "IRIs with prefixes rdf:, rdfs:, xsd:, and owl: constitute the
reserved vocabulary of OWL 2."  http://www.w3.org/TR/owl2-syntax/#IRIs
> 3.  "IRIs from the reserved vocabulary other than owl:topObjectProperty
and owl:bottomObjectProperty MUST NOT be used to identify object properties
in an OWL 2 DL ontology."
http://www.w3.org/TR/owl2-syntax/#Object_Properties
> 4.  Definition of rdfs:domain.  http://www.w3.org/TR/rdf-schema/#ch_domain
> 5.  Barry Smith, Cornelius Rosse (2004). The Role of Foundational
Relations in the Alignment of Biomedical Ontologies.
http://ontology.buffalo.edu/medo/isa.pdf
> 6.  http://www.w3.org/TR/owl2-new-features/#F12:_Punning
> 7.  UniProt models "human" as an instance of taxon and subclass of Homo;
see rdf:type and rdfs:subClassOf statements in
http://www.uniprot.org/taxonomy/9606.rdf.
> 8.  Barry Smith et al. (2005).  Relations in Biomedical Ontologies.
http://genomebiology.com/2005/6/5/r46
>
>
>
> On Mon, Jul 28, 2014 at 6:44 AM, Janna Hastings <has...@eb...>
wrote:
>>
>> Dear Eric,
>>
>>
>>
>> We have no specific representation of ‘isotope’ in ChEBI because all
elements have isotopes, so it would not really add any information to have
this extra class.
>>
>>
>>
>> In our atom classification, the specific isotopes tend to be the leaves
(i.e. they have no is_a children). We believe that your Option A would not
be incompatible with what ChEBI is doing, though. Option B would be less
compatible as we model all atom types as classes rather than instances.
>>
>>
>>
>> In fact, it seems to us that the most correct way to model isotopes
would be to have a relation such as ‘is_isotope_of’ which was a subproperty
of is_a, just for that last level of classification in the atom hierarchy.
However, ChEBI is somewhat constrained by old legacy architecture and thus
does not have the flexibility to add a relation such as this.
>>
>>
>>
>> Thank you for your interest in ChEBI,
>>
>>
>>
>> Best wishes,
>>
>> Janna and the ChEBI team.
>>
>>
>>
>> From: Emw [mailto:emw...@gm...]
>> Sent: 26 July 2014 20:53
>> To: che...@li...
>> Subject: [Chebi-ontology] Oxygen-18 to isotope: instance or subclass?
>>
>>
>>
>> Hello,
>>
>> While reviewing the ChEBI ontology, it struck me that there is no entity
for the subject "isotope".  Classes like oxygen-18 are subclasses of oxygen
[1], but while they are clearly isotopes and described as such in the
free-text definition, that fact is not stated in the ontology's structured
data.
>>
>>
>>
>> This lack of an "isotope" concept presents a practical issue.  How would
one retrieve all entities like oxygen-18, oxygen-16, carbon-12, hydrogen-1
(protium), hydrogen-3 (tritium), etc. using a SPARQL query?  By convention,
ChEBI seems to set isotopes as the direct subclasses of chemical elements
like oxygen, carbon, hydrogen etc.   But perhaps in the future things that
are not "an isotope" could be set as a direct subclasses of elements.
>>
>> One solution (Option A) might be to model oxygen-18 as a direct subclass
of isotope, i.e.:
>>
>>     oxygen-18:
>>         subclass of oxygen
>>
>>         subclass of isotope
>>
>> Users could then get only things like oxygen-16, oxygen-17 and oxygen-18
with a query like:
>>
>>     SELECT ?subject WHERE { ?subject rdfs:subClassOf oxygen . ?subject
rdfs:subClassOf isotope . }
>>
>> This query avoids retrieving any potential subclasses of oxygen-18 by
not using inference, i.e. using rdfs:subClassOf instead of
rdfs:subClassOf*.
>>
>> Another solution (Option B) might be to model oxygen-18 as an instance
of (i.e., rdf:type) isotope as follows:
>>
>>     oxygen-18
>>
>>         subclass of oxygen
>>
>>         instance of isotope
>>
>> This approach explicitly metamodels isotope via punning, a feature in
OWL 2 DL [2], and might allow queries to retrieve things like oxygen-16,
oxygen-17 and oxygen-18 without disabling inference.  It may also be
applicable for other types of nuclides; perhaps as metamodeling is used in
biological taxonomy to say "human instance of taxon; human subclass of
primate".  On the other hand, this approach seems to conflict with the
interpretation of an "instance" as a particular thing in space and time as
used for other material entities, e.g. "Dmitri Mendeleev instance of human".
>>
>> Would an ontology that modeled oxygen-18 and other isotopes as in Option
B be interoperable with ChEBI?  Is Option A or Option B preferable?
>>
>>
>>
>> Also, is there a reason ChEBI does not contain an entry on the generic
subject "isotope"?  At a glance, tying "isotope" into the wider ontology
with a statement like "isotope subclass of atom" seems reasonable.
However, the statement "atom subclass of isotope" also seems valid.  This
entails "atom owl:equivalentClass isotope" [3], which stands to human
reason as there are no instances of atom that are not also instances of
isotope, and vice versa.  Nevertheless, most textbooks separate their
explanation of "atom" and "isotope", and for many humans they do seem like
separate concepts.  How would ChEBI address this?
>>
>> These questions arise from discussion among contributors on Wikidata,
the free knowledge base used by Wikipedia [4, 5].  We are trying to find
the best way to classify subjects like isotope and oxygen-18 [6, 7] among
over 15 million other subjects from the rest of human knowledge.  We use
properties with semantics in OWL 2 DL like rdf:type (instance of) and
rdfs:subClassOf (subclass of, i.e. is_a in ChEBI) [8, 9].
>>
>> Ideally we would like Wikidata's classification of chemical entities to
be interoperable with ChEBI and other ontologies in the Semantic Web.
Thanks in advance for any help!
>>
>>
>>
>> Regards,
>>
>> Eric
>> https://www.wikidata.org/wiki/User:Emw
>>
>>
>>
>> 1.
http://www.ebi.ac.uk/chebi/chebiOntology.do?treeView=true&chebiId=CHEBI:33815
>> 2.  http://www.w3.org/TR/owl2-new-features/#F12:_Punning
>> 3.  http://www.w3.org/TR/owl-ref/#equivalentClass-def
>> 4.  https://www.wikidata.org
>> 5.  Introducing Wikidata to the Linked Data Web. Erxleben et al.  2014.
http://korrekt.org/papers/Wikidata-RDF-export-2014.pdf
>> 6.  "oxygen-18" on Wikidata. https://www.wikidata.org/wiki/Q662269
>> 7.  "isotope" on Wikidata. https://www.wikidata.org/wiki/Q25276
>> 8.  instance of. https://www.wikidata.org/wiki/Property:P31
>>
>> 9.  subclass of. https://www.wikidata.org/wiki/Property:P279
>
>
>
>
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Re: [Chebi-ontology] Oxygen-18 to isotope: instance or subclass?

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