James Brinkley, Structural Informatics Group, University of Washington

Presently, most ontologies are application ontologies designed for specific applications. However, these ontologies do not scale up, often overlap, and are difficult to link together because of incompatible knowledge models.

Reference ontologies, such as our Foundational Model of Anatomy (FMA) and others being developed as part of the OBO Foundry Project, are an emerging ontology type that have the potential to provide a conceptual foundation for linking these diverse application ontologies together into the semantic web. However, their large scope and high level of complexity make reference ontologies difficult for application developers to use.

The purpose of this collababorative project is to make reference ontologies easy to use while maintaining their potential to link application ontologies. We are developing methods for deriving application ontologies from reference ontologies, so that they may fullfull their potential as a foundation for the semantic web.

Our approach is to adapt and extend research from the database community to create application ontologies as views over reference ontologies, and then embed these views as queryable web services. In developing these methods we are pursuing the following specific aims:

1. Investigate view-based approaches for mapping between reference and application ontologies
2. Design and develop software tools that implement these approaches, like the FMA and NCI-Thesaurus
3. Develop graphical interfaces that allow end-users to view these mappings, an example of which can be seen in this screenshot (best seen in a full-screen view) - a graphical interface for deriving a view from an input ontology.

The tools we develop will be integrated as one component of the NCBO BioPortal framework for accessing interlinked ontologies and data. Their development and evaluation are being driven by an increasing number of use cases, particularly the need to integrate data and computational models describing cardiac function. Currently, the FMA ontology is implemented in Protégé. To view the FMA, either Protégé or the FM Explorer (Structural Informatics Group, UW) can be used.

A few publications related to this project:

• Custom views of reference Ontologies
• Aligning Multiple Anatomical Ontologies through a Reference (PDF)
• A framework for using reference ontologies as a foundation for the semantic web

This program was developed by Gary Yngve for his PhD thesis in computer science at the UW.