Re: [Chebi-ontology] "Elements that have no isotopes"

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

I didn't understand Alan to be advocating for inclusion of such a relation,
just arguing that "isotope of" is inherently a relational notion.

So by concurring with Alan, I was not advocating for inclusion of a new
relation in ChEBI, either.

To Alan's point, the following SPARQL query, when run in Ontobee, produces
the following results (CHEBI_25805 is the class oxygen atom):

Query:
prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix owl: <http://www.w3.org/2002/07/owl#>
SELECT distinct ?x ?y
WHERE {
?x rdfs:label ?y .
?x rdfs:subClassOf <http://purl.obolibrary.org/obo/CHEBI_25805>
}

Results:
x
y
http://purl.obolibrary.org/obo/CHEBI_33818
oxygen-16 atom
http://purl.obolibrary.org/obo/CHEBI_33819
oxygen-17 atom
http://purl.obolibrary.org/obo/CHEBI_36933
oxygen-19 atom
http://purl.obolibrary.org/obo/CHEBI_33815
oxygen-18 atom
http://purl.obolibrary.org/obo/CHEBI_36932
oxygen-15 atom


On Thu, Sep 4, 2014 at 11:18 AM, Alan Ruttenberg <ala...@gm...>
wrote:

>
> On Thu, Sep 4, 2014 at 8:54 AM, Colin Batchelor <Bat...@rs...>
> wrote:
>
>> I don't think isotopy expressed as a relation belongs in ChEBI per se. It
>> might belong in some application ontology. I don't think ChEBI should be
>> polluted with that sort of very surfacy application-focussed relation.
>>
>
> I take your point regarding definition of isotope. To me the question
> isn't whether one or the other that is right, but that the overall talk of
> isotope is not clear or consistent.
>
> From my point of view (admittedly I have more physics than chemistry
> background) the natural thing is to query for classes of atom or nuclei
> with a specific number of protons and select the classes that differ either
> by neutron number or atomic mass. *That*, IMO, is something that should be
> possible with ChEBI.
>
> Did you see my note about all the oxygen atom-like entities? I'd be
> curious as to your assessment of that situation - namely that there doesn't
> seem to be enough represented in common across them, in particular that in
> all those cases there is a spectrum of subtypes by atomic mass.
>
> -Alan
>
>
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