Challenges in Biopathway Extraction from Literature and Ontology Construction for Biology

Recent developments in literature data mining for biology call for the design of a common framework that can be used to assess the performance of the reported systems in a fair and objective way. In this talk, we present an on-going effort to make it possible, in the form of challenges in the extraction of biological pathways and in the ontology construction. We are currently making this effort jointly with Lynette Hirschman (MITRE), Junichi Tsujii (University of Tokyo), Limsoon Wong (KRDL), and Cathy Wu (Georgetown University)