BioCreAtIvE II Evaluation Series

References

http://biocreative.sourceforge.net/biocreative_2.html
- The Second BioCreAtIvE - Critical Assessment for Information Extraction in Biology challenge (2006-2007 ) is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. The second BioCreAtIvE challenge will focus on:
- (1) Gene mention tagging [GM] http://biocreative.sourceforge.net/biocreative_2_gm.html
- (2) Gene normalization [GN] http://biocreative.sourceforge.net/biocreative_2_gn.html
- (3) Extraction of protein-protein interactions from text [PPI] http://biocreative.sourceforge.net/biocreative_2_ppi.html

(Smith, Tanabe et al., 2008) ⇒ Larry Smith, Lorraine K. Tanabe, Rie J. 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 TH Tsai, Hong-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, and W. John Wilbur. (2008). “Overview of BioCreative II Gene Mention Recognition.” In: Genome Biology, 9(Suppl 2). doi:10.1186/gb-2008-9-s2-s2

(Zweigenbaum et al., 2007) ⇒ Pierre Zweigenbaum, Dina Demner-Fushman, Hong Yu, and Kevin B. Cohen. (2007). “Frontiers of Biomedical Text Mining: current progress.” In: Briefings in Bioinformatics 2007, 8(5). doi:10.1093/bib/bbm045
- The goals of the second BioCreAtIvE evaluation were finding mentions of genes in the text, normalization of gene names and extraction of protein–protein interactions. Morgan et al. [116] analyze issues involved in organizing the evaluation and preparing the text collection on the example of the BioCreAtIvE task of finding EntrezGene identifiers for all human genes and proteins mentioned in a MEDLINE abstract.