Development of an ontology for biofilms

Microorganisms make up most of the earth’s biomass, and most microbes exist in the form of biofilms, complex communities of microorganisms growing attached to surfaces. Biofilms are directly relevant to a large number of scientific disciplines, and are the subjects of growing multidisciplinary research. As such, there is a pressing requirement for information systems that specialize in biofilm knowledge. Realization of such systems will require a coherent approach to understanding and curating the language used to study biofilms; an ontology of biofilms-related terms offers a foundation for such systems. Here we present an ontology for the study of biofilms (BIFO), a tool that will provide precisely defined terms describing all aspects involved in the biofilms domain. We describe semi-automated methods for the identification of relevant terms from a body of literature, the selection of a set of important terms by domain experts, and the construction of the ontology. A generic approach for BIFO is presented, in which foundational biofilm-related entities and relationships are represented. This ontology reuses terms from other ontologies that provide biofilm knowledge from the Open Biological and Biomedical Ontologies (OBO) foundry.