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One ontology schema - heterogeneous instance bases

From: Satya Sahoo <satya30@uga.edu>
Date: Tue, 4 Sep 2007 23:14:49 -0400 (EDT)
To: public-semweb-lifesci@w3.org, public-semweb-lifesci-request@w3.org
Message-Id: <20070904231449.AZU10799@punts5.cc.uga.edu>
Ontology as a common model for enabling semantic integration has significant potential. But, in some cases, reality seems to indicate otherwise.

For example, the BioPAX ontology is a community effort to standardize the representation of pathway data. But, there are serious differences in the way concepts and relationships, defined in the BioPAX ontology schema, are interpreted to create instances. This leads to heterogeneous instance bases for the same ontology!

Specifically, the BioPAX ontology concept 'pathway' is instantiated in the following manner using data from three pathway databases namely KEGG, Reactome and HumanCyc:
1. KEGG: <pathway rdf:ID="BioPAX-30a84dcd-2a16-481d-9337-8185077c4658"> (source: hsa04020.owl, as of July 2007)
2. Reactome: <bp:pathway rdf:ID="Glucose_6_phosphate_is_isomerized_to_form_fructose_6_phosphate"> (source: Homo sapiens.owl, as of July 2007)
3. HumanCyc: <bp:pathway rdf:ID="pathway142286"> (source: biopax.owl, as of July 2007)

The only potential reconciliation approach we see, is by lexical comparison of the textual description, typed as XML schema strings, associated with each ‘pathway’ instance. For example, "Calcium signaling pathway" which would be consistent across all the three instance bases. But, this would constitute a purely syntactic approach to reconcile the three instance bases.

Comments and suggestions would be greatly appreciated.

Thank you.

Satya Sahoo
(Knoesis Center, http://knoesis.wright.edu)
Received on Wednesday, 5 September 2007 03:14:56 UTC

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