Volume 9 Supplement 2

The BioCreative II - Critical Assessment for Information Extraction in Biology Challenge


Edited by Lynette Hirschman, Martin Krallinger, John Wilbur and Alfonso Valencia

The BioCreative II - Critical Assessment for Information Extraction in Biology Challenge.

Madrid, Spain

23-25 April 2007

  1. Research

    Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge

    Genome sciences have experienced an increasing demand for efficient text-processing tools that can extract biologically relevant information from the growing amount of published literature. In response, a rang...

    Martin Krallinger, Alexander Morgan, Larry Smith, Florian Leitner, Lorraine Tanabe, John Wilbur, Lynette Hirschman and Alfonso Valencia

    Genome Biology 2008 9(Suppl 2):S1

    Published on: 1 September 2008

  2. Research

    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 ...

    Larry Smith, Lorraine K Tanabe, Rie Johnson nee 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…

    Genome Biology 2008 9(Suppl 2):S2

    Published on: 1 September 2008

  3. Research

    Overview of BioCreative II gene normalization

    The goal of the gene normalization task is to link genes or gene products mentioned in the literature to biological databases. This is a key step in an accurate search of the biological literature. It is a cha...

    Alexander A Morgan, Zhiyong Lu, Xinglong Wang, Aaron M Cohen, Juliane Fluck, Patrick Ruch, Anna Divoli, Katrin Fundel, Robert Leaman, Jörg Hakenberg, Chengjie Sun, Heng-hui Liu, Rafael Torres, Michael Krauthammer, William W Lau, Hongfang Liu…

    Genome Biology 2008 9(Suppl 2):S3

    Published on: 1 September 2008

  4. Research

    MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data

    In the absence of consolidated pipelines to archive biological data electronically, information dispersed in the literature must be captured by manual annotation. Unfortunately, manual annotation is time consu...

    Andrew Chatr-aryamontri, Samuel Kerrien, Jyoti Khadake, Sandra Orchard, Arnaud Ceol, Luana Licata, Luisa Castagnoli, Stefano Costa, Cathy Derow, Rachael Huntley, Bruno Aranda, Catherine Leroy, Dave Thorneycroft, Rolf Apweiler, Gianni Cesareni and Henning Hermjakob

    Genome Biology 2008 9(Suppl 2):S5

    Published on: 1 September 2008

  5. Software

    Introducing meta-services for biomedical information extraction

    We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; http://​bcms.​bioinfo.​cnio.​es/​). This pr...

    Florian Leitner, Martin Krallinger, Carlos Rodriguez-Penagos, Jörg Hakenberg, Conrad Plake, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tsai, Hsi-Chuan Hung, William W Lau, Calvin A Johnson, Rune Sætre, Kazuhiro Yoshida, Yan Hua Chen, Sun Kim, Soo-Yong Shin…

    Genome Biology 2008 9(Suppl 2):S6

    Published on: 1 September 2008

  6. Research

    Text mining for biology - the way forward: opinions from leading scientists

    This article collects opinions from leading scientists about how text mining can provide better access to the biological literature, how the scientific community can help with this process, what the next steps...

    Russ B Altman, Casey M Bergman, Judith Blake, Christian Blaschke, Aaron Cohen, Frank Gannon, Les Grivell, Udo Hahn, William Hersh, Lynette Hirschman, Lars Juhl Jensen, Martin Krallinger, Barend Mons, Seán I O'Donoghue, Manuel C Peitsch, Dietrich Rebholz-Schuhmann…

    Genome Biology 2008 9(Suppl 2):S7

    Published on: 1 September 2008

  7. Research

    Concept recognition for extracting protein interaction relations from biomedical text

    Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasin...

    William A Baumgartner Jr, Zhiyong Lu, Helen L Johnson, J Gregory Caporaso, Jesse Paquette, Anna Lindemann, Elizabeth K White, Olga Medvedeva, K Bretonnel Cohen and Lawrence Hunter

    Genome Biology 2008 9(Suppl 2):S9

    Published on: 1 September 2008

  8. Research

    Automating curation using a natural language processing pipeline

    The tasks in BioCreative II were designed to approximate some of the laborious work involved in curating biomedical research papers. The approach to these tasks taken by the University of Edinburgh team was to...

    Beatrice Alex, Claire Grover, Barry Haddow, Mijail Kabadjov, Ewan Klein, Michael Matthews, Richard Tobin and Xinglong Wang

    Genome Biology 2008 9(Suppl 2):S10

    Published on: 1 September 2008

  9. Research

    Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks

    We participated in three of the protein-protein interaction subtasks of the Second BioCreative Challenge: classification of abstracts relevant for protein-protein interaction (interaction article subtask [IAS]...

    Alaa Abi-Haidar, Jasleen Kaur, Ana Maguitman, Predrag Radivojac, Andreas Rechtsteiner, Karin Verspoor, Zhiping Wang and Luis M Rocha

    Genome Biology 2008 9(Suppl 2):S11

    Published on: 1 September 2008

  10. Research

    Mining physical protein-protein interactions from the literature

    Deciphering physical protein-protein interactions is fundamental to elucidating both the functions of proteins and biological processes. The development of high-throughput experimental technologies such as the...

    Minlie Huang, Shilin Ding, Hongning Wang and Xiaoyan Zhu

    Genome Biology 2008 9(Suppl 2):S12

    Published on: 1 September 2008

  11. Research

    OntoGene in BioCreative II

    Research scientists and companies working in the domains of biomedicine and genomics are increasingly faced with the problem of efficiently locating, within the vast body of published scientific findings, the ...

    Fabio Rinaldi, Thomas Kappeler, Kaarel Kaljurand, Gerold Schneider, Manfred Klenner, Simon Clematide, Michael Hess, Jean-Marc von Allmen, Pierre Parisot, Martin Romacker and Therese Vachon

    Genome Biology 2008 9(Suppl 2):S13

    Published on: 1 September 2008