BioCreative

BioCreAtIvE (A critical assessment of text mining methods in molecular biology) consists in a community-wide effort for evaluating information extraction and text mining developments in the biological domain [Lynette Hirschman, Alex Yeh, Christian Blaschke, and Alfonso Valencia (2005) Overview of BioCreative: Critical assessment of information extraction for biology. BMC Bioinformatics 6(Suppl. 1)] .

Three main tasks were posed at the first BioCreAtIvE challenge: the entity extraction task [Alex Yeh, Alex Morgan, Marc Colosimo, and Lynette Hirschman (2005) BioCreative task 1A: Gene mention finding evaluation. BMC Bioinformatics 6(Suppl. 1)] , the gene name normalization task [Lynette Hirschman, Mark Colosimo, Alex Morgan, and Alex Yeh (2005) Overview of BioCreative task 1B: Normalized gene lists. BMC Bioinformatics 6(Suppl. 1)] [Marc Colosimo, Alex Morgan, Alex Yeh, J. Colombe, and Lynette Hirschman (2005) Data preparation and interannotator agreement: BioCreative task 1B. BMC Bioinformatics 6(Suppl. 1)] , and the functional annotation of gene products task [Christian Blaschke, E. Leon, Martin Krallinger, and Alfonso Valencia (2005) Evaluation of BioCreative task 2. BMC Bioinformatics 6(Suppl. 1)] . The data sets produced by this contest serve as a Gold Standard training and test set to evaluate and train Bio-NER tools and annotation extraction tools.

The second BioCreAtIvE included three tasks organized by Lynette Hirschman and Alex Morgan of MITRE; Alfonso Valencia and Martin Krallinger of CNIO in Spain; and W. John Wilbur, Lorrie Tanabe and Larry Smith of NIH.

External links

* [http://biocreative.sourceforge.net BioCreAtIve 2, 2006-2007]
* [http://www.pdg.cnb.uam.es/BioLINK/workshop_BioCreative_04/ First BioCreAtIvE workshop, 2004]
* [http://www.biomedcentral.com/1471-2105/6?issue=S1 BMC Bioinformatics special issue : BioCreAtIvE]
* [http://www.pdg.cnb.uam.es/BioLINK/workshop_BioCreative_04/results/agreetment.html First BioCreAtIvE data download request]

References


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