Bio-event definition in text mining towards event interconnection

Introduction Event extraction is one of the main focuses in bio-text mining (TM). Interconnecting extracted events into reaction networks provides biologists with a wealth of fine-grained information on biochemical reactions [1]. Intuitively, extracted events could be connected into networks based on common entities. However, this approach is limited due to: 1) its dependence on flawless entity normalisation; 2) inability to express the directionality of the various relations/reactions. To enrich the information in extracted events and facilitate their interconnection, we propose a modification to bio-event definition to make it more compatible with the structure of biological reactions and community-supported biological semantic resources. More specifically, we propose alignment of bio-events with the reactions in the Systems Biology Markup Language (SBML), which would make bio-events more biologically meaningful and directly re-usable by domain experts.