Overview of BioCreative II gene mention recognition

Larry Smith, Lorraine K. Tanabe, Rie Ando, Cheng Ju Kuo, I. Fang Chung, Chun Nan Hsu, Yu Shi Lin, Roman Klinger, Christoph M. Friedrich, Kuzman Ganchev, Manabu Torii, Hongfang Liu, Barry Haddow, Craig A. Struble, Richard J. Povinelli, Andreas Vlachos, William A. Baumgartner, Lawrence Hunter, Bob Carpenter, Richard Tzong Han TsaiHong Jie Dai, Feng Liu, Yifei Chen, Chengjie Sun, Sophia Katrenko, Pieter Adriaans, Christian Blaschke, Rafael Torres, Mariana Neves, Preslav Nakov, Anna Divoli, Manuel Maña-López, Jacinto Mata, W. John Wilbur

Research output: Contribution to journalReview articlepeer-review

346 Scopus citations


Nineteen teams presented results for the Gene Mention Task at the BioCreative II Workshop. In this task participants designed systems to identify substrings in sentences corresponding to gene name mentions. A variety of different methods were used and the results varied with a highest achieved F1 score of 0.8721. Here we present brief descriptions of all the methods used and a statistical analysis of the results. We also demonstrate that, by combining the results from all submissions, an F score of 0.9066 is feasible, and furthermore that the best result makes use of the lowest scoring submissions.

Original languageEnglish
Article numberS2
JournalGenome Biology
Issue numberSUPPL. 2
StatePublished - 1 Sep 2008


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