A semantic web framework for the life sciences based on foundational ontologies and metadata standards

This article describes an ontology framework called bio-zen, which can be used for the representation of information from biomedical research on the Semantic Web. The ontology framework adheres to the OWL DL format and is based on existing foundational ontologies and metadata standards like DOLCE, SKOS and Dublin Core. It is optimised for the usage in distributed environments like the Internet. Novel ontological design patterns in bio-zen allow the unification of good ontological consistency with a flexible, clean and intuitive structure. A unique feature of the bio-zen ontology is that it allows the seamless integration of mathematical descriptions and simulation parameters into qualitative information, making a quick transition from plain data to model simulations possible. A growing number of extension packages are available for the ontology, including concepts from taxonomies such as the Gene Ontology, Medical Subject Headings or the NCBI Taxonomy. -- Semantic web ; life sciences ; ontology ; simulation ; data integration