~hamid

Jump to: How to Cite? | Paper Abstract

This work solves the problem of having to choose between Open Biomedical Ontologies (OBO) language or the Semantic Web's Web Ontology Language (OWL) for building domain ontologies. Our work presents a community effort to create a standard transformation mapping between the two languages. A goal was to reconcile a number of independent efforts. Our mappings provide a lossless roundtrip mapping for OBO ontologies. Our implementation of the mapping tool is a part of the official Gene Ontology project source. Also, a large number of OBO ontologies have been mapped to their OWL versions using this standard mapping.

A basis for reconciling the efforts was an observation that the Semantic Web layer cake itself could serve as a guideline for studying and organizing OBO and creating a transformation system. Compared to other approaches, our method gave us a better organization and enabled effecient identification of matches and mismatches between the two languages.

How to Cite?
Syed Hamid Tirmizi, Stuart Aitken, Dilvan Moreira, Chris Mungall, Juan Sequeda, Nigam H. Shah and Daniel P. Miranker. OBO & OWL: Roundtrip Ontology Transformations. To appear in Proceedings of Semantic Web Applications and Tools for Life Sciences Workshop, 2009.

Paper Abstract
The Open Biomedical Ontology (OBO) format emerged from the Gene Ontology, and now supports many other important ontologies. If we compare OBO to OWL, the ontology language of the Semantic Web, the latter anticipates integral query languages, rule languages and distributed infrastructure for information interchange. A convenient method for leveraging these other features for OBO ontologies is by transforming OBO ontologies to OWL. We have developed a methodology for translating OBO ontologies to OWL using the organization of the Semantic Web layer cake to guide the work. The approach reveals that the constructs of OBO can be grouped together to form a similar layer cake. Thus we were able to identify the constructs of OBO that have easy semantic equivalence to a construct in the OWL stack, and as well as those constructs that entail the challenges to a transformation system. As a result, we have developed a standard common mapping between OBO and OWL for the OBO community. Our mapping produces OWL-DL – a Description Logics based dialect of OWL with desirable computational properties for efficiency and correctness. Our Java implementation of the mapping is part of the official Gene Ontology project source. Our transformation system provides a lossless roundtrip mapping for OBO ontologies, i.e. an OBO ontology may be translated to OWL and back without loss of knowledge.