Integrating Hierarchical Controlled Vocabularies With OWL Ontology: A Case Study from the Domain of Molecular Interactions

Many efforts at standardising terminologies within the biological domain have resulted in the construction of hierarchical controlled vocabularies that capture domain knowledge. Vocabularies, such as the PSI-MI vocabulary, capture both deep and extensive domain knowledge, in the OBO (Open Biomedical Ontologies) format. However hierarchical vocabularies, such as PSI-MI which are represented in OBO, only represent simple parent-child relationships between terms. By contrast, ontologies constructed using the Web Ontology Language (OWL), such as BioPax, define many richer types of relationships between terms. OWL provides a semantically rich structured language for expressing classes and sub-classes of entities and properties, relationships between them and domain-specific rules or axioms that can be applied to extract new information through semantic inferencing. In order to fully exploit the domain knowledge inherent in domain-specific controlled vocabularies, they need to be represented as OWL-DL ontologies, rather than in formats such as OBO. In this paper, we describe a method for converting OBO vocabularies into OWL and class instances represented as OWL-RDF triples. This approach preserves the hierarchical arrangement of the domain knowledge whilst also making the underlying parent-child relationships available to inferencing engines. This approach also has clear advantages over existing methods which incorporate terms from external controlled vocabularies as literals stripped of the context associated with their place in the hierarchy. By preserving this context, we enable machine inferencing over the ordered domain knowledge captured in OBO controlled vocabularies