Overview of BioCreative II gene mention recognition.
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.
Smith
Larry
L
National Center for Biotechnology Information, Bethesda, Maryland, USA. lsmith@ncbi.nlm.nih.gov
Tanabe
Lorraine K
LK
Ando
Rie Johnson nee
RJ
Kuo
Cheng-Ju
CJ
Chung
I-Fang
IF
Hsu
Chun-Nan
CN
Lin
Yu-Shi
YS
Klinger
Roman
R
Friedrich
Christoph M
CM
Ganchev
Kuzman
K
Torii
Manabu
M
Liu
Hongfang
H
Haddow
Barry
B
Struble
Craig A
CA
Povinelli
Richard J
RJ
Vlachos
Andreas
A
Baumgartner
William A
WA
Hunter
Lawrence
L
Carpenter
Bob
B
Tsai
Richard Tzong-Han
RT
Dai
Hong-Jie
HJ
Liu
Feng
F
Chen
Yifei
Y
Sun
Chengjie
C
Katrenko
Sophia
S
Adriaans
Pieter
P
Blaschke
Christian
C
Torres
Rafael
R
Neves
Mariana
M
Nakov
Preslav
P
Divoli
Anna
A
Maña-López
Manuel
M
Mata
Jacinto
J
Wilbur
W John
WJ
D019295:Computational Biology / Q000379:methods*; D003226:Congresses as Topic; D005796:Genes; D012958:Societies, Scientific