title: A system for identifying named entities in biomedical text: how results from two evaluations reflect on both the system and the evaluations.
abstract: We present a maximum entropy-based system for identifying named entities (NEs) in biomedical abstracts and present its performance in the only two biomedical named entity recognition (NER) comparative evaluations that have been held to date, namely BioCreative and Coling BioNLP. Our system obtained an exact match F-score of 83.2% in the BioCreative evaluation and 70.1% in the BioNLP evaluation. We discuss our system in detail, including its rich use of local features, attention to correct boundary identification, innovative use of external knowledge resources, including parsing and web searches, and rapid adaptation to new NE sets. We also discuss in depth problems with data annotation in the evaluations which caused the final performance to be lower than optimal.
authors.affiliation: Institute for Communicating and Collaborative Systems, University of Edinburgh, 2 Buccleuch Place, Edinburgh EH8 9LW, UK.
authors.forename: Shipra
authors.initials: S
authors.lastname: Dingare
authors.forename: Malvina
authors.initials: M
authors.lastname: Nissim
authors.forename: Jenny
authors.initials: J
authors.lastname: Finkel
authors.forename: Christopher
authors.initials: C
authors.lastname: Manning
authors.forename: Claire
authors.initials: C
authors.lastname: Grover