Affiliations: Medical Informatics Research Group, University Medical Center Freiburg, Freiburg, Germany. E-mail: [email protected] | Department of Philosophy, University of Rostock, Rostock, Germany. E-mail: [email protected]
Note:  Corresponding author: Stefan Schulz, Institute of Medical Biometry and Medical Informatics, University Medical Center Freiburg, Stefan-Meier-Str. 26, 79104 Freiburg, Germany. Tel.: +49 761 203 6725; E-mail: [email protected]
Note:  Both authors contributed equally to this work.
Abstract: Statements about the behavior of biochemical entities (e.g., about the interaction between two proteins) abound in the literature on molecular biology and are increasingly becoming the targets of information extraction and text mining techniques. We show that an accurate analysis of the semantics of such statements reveals a number of ambiguities that have to be taken into account in the practice of biomedical ontology engineering: such statements can not only be understood as event reporting statements, but also as ascriptions of dispositions or tendencies that may or may not refer to collectives of interacting molecules or even to collectives of interaction events.