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[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
- ^ Hirschman, L.; Yeh, A.; Blaschke, C.; Valencia, A. (2005). "Overview of BioCreAtIvE: Critical assessment of information extraction for biology". BMC Bioinformatics 6: S1. doi:10.1186/1471-2105-6-S1-S1. PMC 1869002. PMID 15960821. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1869002.
- ^ Yeh, A.; Morgan, A.; Colosimo, M.; Hirschman, L. (2005). "BioCreAtIvE Task 1A: Gene mention finding evaluation". BMC Bioinformatics 6: S2. doi:10.1186/1471-2105-6-S1-S2. PMC 1869012. PMID 15960832. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1869012.
- ^ Hirschman, L.; Colosimo, M.; Morgan, A.; Yeh, A. (2005). "Overview of BioCreAtIvE task 1B: Normalized gene lists". BMC Bioinformatics 6: S11. doi:10.1186/1471-2105-6-S1-S11. PMC 1869004. PMID 15960823. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1869004.
- ^ Colosimo, M. E.; Morgan, A. A.; Yeh, A. S.; Colombe, J. B.; Hirschman, L. (2005). "Data preparation and interannotator agreement: BioCreAtIvE Task 1B". BMC Bioinformatics 6: S12. doi:10.1186/1471-2105-6-S1-S12. PMC 1869005. PMID 15960824. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1869005.
- ^ Blaschke, C.; Leon, E.; Krallinger, M.; Valencia, A. (2005). "Evaluation of BioCreAtIvE assessment of task 2". BMC Bioinformatics 6: S16. doi:10.1186/1471-2105-6-S1-S16. PMC 1869008. PMID 15960828. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1869008.
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