- From: Tore Eriksson <tore.eriksson@po.rd.taisho.co.jp>
- Date: Thu, 13 Mar 2008 13:06:25 +0900
- To: public-semweb-lifesci@w3.org
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