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.

BioCreative V will have 5 different tracks, described at: http://www.biocreative.org/events/biocreative-v/CFP/

References

  1. ↑ 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.
  2. ↑ 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.
  3. ↑ 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.
  4. ↑ 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.
  5. ↑ 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.


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