IBID is a virtual librarian that processes biology articles and builds semantic annotations based on the contents of an article. It then assists human designers by locating and presenting biology articles related to a design query. IBID’s use of ontologies allows for knowledge extraction and assists users with the identification of key information in an article and comparison of the contents of two articles. In this paper, we describe how the addition of an environment ontology enhances IBID’s capability to understand the habitats of various organisms. In a pilot study, we evaluated IBID’s performance against human subjects who read the same passage and highlighted phrases pertaining to locations and habitats. The preliminary results indicate that the ability to add ontologies to IBID allows it to extract meaning from new documents.