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Re: GO as RDF properties

From: Talapady Bhat <talapady.bhat@nist.gov>
Date: Thu, 13 Mar 2008 15:37:35 -0400
Message-ID: <001801c88541$b03a0520$83c20681@campus.nist.gov>
To: <public-semweb-lifesci@w3.org>, "Tore Eriksson" <tore.eriksson@po.rd.taisho.co.jp>
Cc: <goldber@nist.gov>, "Talapady N Bhat" <bhat@nist.gov>

Hi,

Why not use EC number to denote enzyme and use GO as an alias? EC numbers 
are far more popular and more universily known to other databases for 
exchange of information.
Also why not use thermodynamics data as well ?

Thanks
T N Bhat





----- Original Message ----- 
From: "Tore Eriksson" <tore.eriksson@po.rd.taisho.co.jp>
To: <public-semweb-lifesci@w3.org>
Sent: Thursday, March 13, 2008 12:06 AM
Subject: GO as RDF properties


>
> 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 Friday, 14 March 2008 00:13:39 UTC

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