Re: GO as RDF properties

Hello Tore,

You might consider posing this question to the obo-discuss group,  
where discussion of the use of GO often occurs, or consider joining  
the biopax-obo effort - http://groups.google.com/group/biopax-obo -  
where we are currently working on precisely this sort of problem -  
representing interactions and pathways in a way that maximally reuses  
existing OBO ontologies, and which use OWL and RDF in manner  
consistent with the existing forms of the owl versions of the OBO  
ontologies.

Regards,
Alan

On Mar 13, 2008, at 12:06 AM, Tore Eriksson wrote:

>
> Hi,
>
> I am contemplating how to represent biochemical reactions in RDF,  
> and I
> have some questions about properties and subproperties that I hope
> anyone could shed some light on. What I want to do is to model  
> reactions
> and the involved entities like this:
>
> _:bn1 a :Reaction;
>     :substrate <info:inchi/InChI=1/C4H4O4/c5-3(6)1-2-4(7)8/h1-2H,(H, 
> 5,6)(H,7,8)/b2-1+/f/h5,7H>;
>     :substrate <info:inchi/InChI=1/H2O/h1H2>;
>     :enzyme <http://purl.uniprot.org/uniprot/P07954>;
>     :product <info:inchi/InChI=1/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H, 
> 1H2,(H,6,7)(H,8,9)/t2-/m0/s1/f/h
> 6,8H>.
>
> My idea is to substitute the predicate :enzyme with molecular  
> functions
> that are subclasses of GO:0003824 (catalytic activity), and use the GO
> hiearchy to constrain which type of catalytic activity is:
>
> @prefix GO: <http://purl.org/obo/owl/GO#>
> _:bn1 a :Reaction;
>     :substrate <info:inchi/InChI=1/C4H4O4/c5-3(6)1-2-4(7)8/h1-2H,(H, 
> 5,6)(H,7,8)/b2-1+/f/h5,7H>;
>     :substrate <info:inchi/InChI=1/H2O/h1H2>;
>     GO:GO_0004333 <http://purl.uniprot.org/uniprot/P07954>;
>     :product <info:inchi/InChI=1/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H, 
> 1H2,(H,6,7)(H,8,9)/t2-/m0/s1/f/h
> 6,8H>.
>
> As the GO categories presumably are of type rdfs:Class, my question is
> if I am allowed to do this at all. Also, I suppose I have to remap the
> class hierarchy to a property hierarchy, since the properties will not
> heed the rdfs:subClassOf hierarchy. Perhaps something like this in
> SPARQL:
>
> PREFIX GO: <http://purl.org/obo/owl/GO#>
> CONSTRUCT { ?a a rdfs:Property .
>             ?b a rdfs:Property .
>             ?a rdfs:subPropertyOf ?b }
> WHERE   { GRAPH <http://www.berkeleybop.org/ontologies/obo-all/ 
> molecular_function/molecular_function.owl>
>           {  ?a a GO:GO_000382 .
>              ?b a GO:GO_000382 .
>              ?a rdfs:subClassOf ?b } } .
>
> Another question is how can I write this in RDF schema or OWL? I  
> have a
> nagging feeling that I am over-reaching on this one... Any comments
> welcome.
>
> Regards,
>
> Tore Eriksson
> Taisho Pharmaceutical Co., Ltd.
>
> _______________________________________________________________
> Tore Eriksson [tore.eriksson ad po.rd.taisho.co.jp]
>
>
>
>

Received on Thursday, 13 March 2008 22:44:30 UTC