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Overview of BioCreative II gene mention recognition

: Smith, L.; Tanabe, L.K.; Johnson nee Ando, R.; Juo, C.-J.; Chung, I.-F.; Hsu, C.-N.; Lin, Y.-S.; Klinger, R.; Friedrich, C.M.; Ganchev, K.; Torii, M.; Liu, H.; Haddow, B.; Struble, C.A.; Povinelli, R.J.; Vlachos, A.; Baumgartner, W.A.; Hunter, L.; Carpenter, B.; Tsai, R.T.; Dai, H.J.; Liu, F.; Chen, Y.; Sun, C.; Katrenko, S.; Adriaans, P.; Blaschke, C.; Torres Perez, R.; Neves, M.; Nakov, P.; Divoli, A.; Mana, M.; Mata-Vazquez, J.; Wilbur, J.

Fulltext urn:nbn:de:0011-n-941249 (297 KByte PDF)
MD5 Fingerprint: 1a70699f791711fea1f7f4403ab3a5cf
Created on: 12.5.2009

Genome biology 9 (2008), Supplement 2, 19 pp.
ISSN: 1465-6906
ISSN: 1465-6914
Conference "The BioCreative II - Critical Assessment for Information Extraction in Biology Challenge" <2007, Madrid>
Journal Article, Conference Paper, Electronic Publication
Fraunhofer SCAI ()

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.