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 Thursday, 13 March 2008 18:15:20 UTC