Ontology Views, An Update

Jim Brinkley

Structural Informatics Group, University of Washington

The purpose of our collaborative RO1 is to develop methods for deriving application ontologies from one or more reference ontologies so that they become practical for use in real-world applications. Our general approach is based on the database notion of a “view”, where for an ontology the view is defined by a query over the underlying reference ontology(s), in this case using extensions that we designed for the SparQL semantic web query language.

In this talk I will describe some of our progress since my last presentation to this group in May 2008, including 1) vSparQL, an implemented extension to SparQL that permits regular path expressions, sub-queries and recursive queries, 2) a demonstration of the expressiveness of vSparQL in deriving a complex neuroanatomy view from the Foundational Model of Anatomy, 3) creation of a view from two source ontologies, 4) incorporation of materialized views into Bioportal, 5) use of views in two driving use cases: RadLex, and biosimulation model integration, and 6) ongoing and planned work in additional use cases, intermediate languages, graphical view generation, and a portal for generating and saving vSparQL querie.s