Motivation: Due to different experimental setups and various interpretations of results, the data contained in online bioinformatics resources can be inconsistent, therefore, making it more difficult for users of these resources to assess the suitability and correctness of the answers to their queries. This work investigates the role of argumentation systems to help users evaluate such answers. More specifically, it looks closely at a gene expression case study, creating an appropriate representation of the underlying data and series of rules that are used by a third-party argumentation engine to reason over the query results provided by the mouse gene expression database EMAGE. Results: A prototype using the ASPIC argumentation engine has been implemented and a preliminary evaluation carried out. This evaluation suggested that argumentation can be used to deal with inconsistent data in biological resources. © 2008 The Author(s).