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.