From: Chris M. <cjm...@lb...> - 2014-07-27 01:46:48
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What about a relation, isotope_of? I'm not sure I fully understand the classification of atoms in CHEBI (but this may just be me). Why isn't 'monoatomic ion' a subtype of atom? On 26 Jul 2014, at 12:53, Emw wrote: > 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 > ------------------------------------------------------------------------------ > Want fast and easy access to all the code in your enterprise? Index > and > search up to 200,000 lines of code with a free copy of Black Duck > Code Sight - the same software that powers the world's largest code > search on Ohloh, the Black Duck Open Hub! Try it now. > http://p.sf.net/sfu/bds_______________________________________________ > Chebi-ontology mailing list > Che...@li... > https://lists.sourceforge.net/lists/listinfo/chebi-ontology |