Ontology Mapping in rule-based mediation

Our rule-based mediation method uses ontology mapping to link a source entity or entities to a target entity or entities from different ontologies. In general, ontology mapping does not require either class to be described using the same language. Mapping rewrites the required features of syntactic ontologies as a function of a core ontology, such as in [10]. Querying over those mappings can be performed either over a core ontology directly or over the syntactic ontologies via their core ontology using views.

Mapping data sources to biologically-relevant, ontologically-rigorous core ontologies must be considered carefully. There are two broad mapping strategies: GAV and LAV. GAV is when the core ontology is defined as a function of the syntactic ontologies. With LAV, the core ontology is independent of the syntactic ontologies and the syntactic ontologies themselves are described as views of the core ontology. The advantages and disadvantages of both approaches are discussed in [11,10]. In general, both of these approaches do not materialize data in the core ontology, but retain the data in the syntactic ontologies and use query reformulation to get the data out of the syntactic ontologies.

The rule-based mediation methodology uses a modified version of these approaches. It is similar to the BGLaV approach described by [11], where mappings are generated between syntactic ontologies and the core ontology based on a core ontology which is independent of any of the syntactic ontologies. This approach allows both the straightforward addition of new syntactic ontologies as well as the maintenance of the core ontology as an independent entity. Our rule-based mediation methodology uses an materialized BGLaV approach which populates the core ontology with the integrated data from the syntactic ontologies. This allows reasoning and inference to be performed over the integrated data. Detailed information on the descriptions of each data source are available in Section 3.

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