Ontologies promise more benefits than terminologies in terms of data annotation and computer-assisted reasoning, by defining a hierarchy of terms and their relations within a domain. Here, we present central insights related to the development of an ontology for documenting events during interoperative neuromonitoring (IOM), for which we used the Basic Formal Ontology (BFO) as an upper-level ontology. This work has the following two goals: to describe the development of the IOM ontology and to guide the practice with respect to documenting of biomedical events, as available ontologies pose difficulties on certain issues. We address the following issues: (i) differentiate between the sets documentation, identification, continuant and explanation, understanding, occurrent as we had problems in applying the available ontology of adverse events, (ii) covering diseases and injuries in a consistent way, and (iii) deciding on which level to define relations.