With a rapidly growing body of knowledge, it becomes more and more difficult to keep track of the state of the art in a research field. A formal representation of the hypotheses in the field, their relations, the studies that support or question them based on which evidence, would greatly ease this task and help direct future research efforts. We present the design of such a core ontology for one specific field, namely invasion biology. We introduce the design of the Hierarchy of Hypotheses (HoH) core ontology to semantically capture and model the information contained in hierarchies of hypotheses created for invasion biology. The proposed core ontology is based on a number of well structured related ontologies, which provide a solid basis for its main entities.