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

[Mikel E. A. <me...@fi...>]

I see. All clear now

thx

On ar., 2011.eko mairen 03a 19:46, Chris Mungall wrote:
> 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 Some very out of date documentation here: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/
>>
>>
>> ------------------------------------------------------------------------------
>> WhatsUp Gold - Download Free Network Management Software
>> The most intuitive, comprehensive, and cost-effective network
>> management toolset available today.  Delivers lowest initial
>> acquisition cost and overall TCO of any competing solution.
>> http://p.sf.net/sfu/whatsupgold-sd
>> _______________________________________________
>> SOng-devel mailing list
>> SOn...@li...
>> https://lists.sourceforge.net/lists/listinfo/song-devel
> ------------------------------------------------------------------------------
> WhatsUp Gold - Download Free Network Management Software
> The most intuitive, comprehensive, and cost-effective network
> management toolset available today.  Delivers lowest initial
> acquisition cost and overall TCO of any competing solution.
> http://p.sf.net/sfu/whatsupgold-sd
> _______________________________________________
> SOng-devel mailing list
> SOn...@li...
> https://lists.sourceforge.net/lists/listinfo/song-devel


-- 
Mikel Egaña Aranguren, PhD
http://mikeleganaaranguren.com

Marie Curie post-doc at Ontology Engineering Group, UPM
http://www.oeg-upm.net/