BioCreative

From Wikipedia, the free encyclopedia

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^[1].

Three main tasks were posed at the first BioCreAtIvE challenge: the entity extraction task^[2], the gene name normalization task^[3][4], and the functional annotation of gene products task^[5]. 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.

[edit] External links

• BioCreAtIve 2, 2006-2007

• First BioCreAtIvE workshop, 2004

• BMC Bioinformatics special issue : BioCreAtIvE

• First BioCreAtIvE data download request

[edit] References

1. ^ 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)
2. ^ Alex Yeh, Alex Morgan, Marc Colosimo, and Lynette Hirschman (2005) BioCreative task 1A: Gene mention finding evaluation. BMC Bioinformatics 6(Suppl. 1)
3. ^ Lynette Hirschman, Mark Colosimo, Alex Morgan, and Alex Yeh (2005) Overview of BioCreative task 1B: Normalized gene lists. BMC Bioinformatics 6(Suppl. 1)
4. ^ 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)
5. ^ Christian Blaschke, E. Leon, Martin Krallinger, and Alfonso Valencia (2005) Evaluation of BioCreative task 2. BMC Bioinformatics 6(Suppl. 1)