Re: [SO-devel] Question about axioms on OWL version of SO

[Chris M. <cjm...@lb...>]

It is redundant by design. You're looking at the inferred version of SO, which has the inferred subclass axioms asserted. Not all of the inferred axioms are trivial restatements. E.g.

[Term]
id: SO:0000089
name: kinetoplast_gene
def: "A gene located in kinetoplast sequence." [SO:xp]
synonym: "kinetoplast gene" EXACT []
is_a: SO:0000088 ! implied link automatically realized ! mt_gene
intersection_of: SO:0000088 ! mt_gene
intersection_of: has_origin SO:0000741 ! kinetoplast

(the "implied link automatically realized" metadata will make its way into the owl as an axiom annotation at a later date)

Having these inferred links asserted is very useful to most users of the SO who don't want to have to use a complete reasoner to traverse the hierarchy

Some very out of date documentation here:
http://wiki.geneontology.org/index.php/SO:Composite_Terms

On May 3, 2011, at 9:45 AM, Mikel Egaña Aranguren wrote:

> Hi;
> 
> I have been recently exploring the OWL version of SO and I have 
> encountered the following pattern several times:
> 
> B equivalentTo A and (p some C)
> B subClassOf A
> 
> It seems to me that the second axiom is redundant, since it is already 
> entailed by the first one, but I'm sure there is a good reason for it to 
> be there, can anyone help me? Thanks
> 
> An example:
> 
> SO_0001032 equivalentTo SO_0000737 and (has_quality some SO_0000352)
> SO_0001032 subClassOf SO_0000737
> 
> <owl:Class rdf:about="&ns1;SO_0001032">
> <ns1:IAO_0000118 xml:lang="en">mitochondrial DNA</ns1:IAO_0000118>
> <rdfs:label xml:lang="en">mitochondrial_DNA</rdfs:label>
> <rdfs:subClassOf rdf:resource="&ns1;SO_0000737"/>
> <owl:equivalentClass>
> <owl:Class>
> <owl:intersectionOf rdf:parseType="Collection">
> <rdf:Description rdf:about="&ns1;SO_0000737"/>
> <owl:Restriction>
> <owl:onProperty rdf:resource="&ns1;has_quality"/>
> <owl:someValuesFrom rdf:resource="&ns1;SO_0000352"/>
> </owl:Restriction>
> </owl:intersectionOf>
> </owl:Class>
> </owl:equivalentClass>
> </owl:Class>
> 
> 
> 
> Regards
> 
> -- 
> Mikel Egaña Aranguren, PhD
> http://mikeleganaaranguren.com
> 
> Marie Curie post-doc at Ontology Engineering Group, UPM
> http://www.oeg-upm.net/
> 
> 
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