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]

It was preceded by the Knowledge Discovery and Data Mining (KDD) Challenge Cup for detection of gene mentions. [2]

Community Challenges

First edition

Three main tasks were posed at the first BioCreAtIvE challenge: the entity extraction task,[3] the gene name normalization task,[4][5] and the functional annotation of gene products task.[6] 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.

Second edition

The second BioCreAtIvE challenge (2006-2007) had also 3 tasks: detection of gene mentions, extrction of unique idenfiers for genes and extraction information related to physical protein-protein interactions. [7] It counted with participation of 44 teams from 13 countries. [7]

Fifth edition

BioCreative V will have 5 different tracks, described at: https://biocreative.bioinformatics.udel.edu/events/biocreative-v/CFP/

See also

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. S.; Hirschman, L.; Morgan, A. A. (2003-07-03). "Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup". Bioinformatics. 19 (Suppl 1): i331–i339. doi:10.1093/bioinformatics/btg1046. ISSN 1367-4803.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. Krallinger, Martin; Morgan, Alexander; Smith, Larry; Leitner, Florian; Tanabe, Lorraine; Wilbur, John; Hirschman, Lynette; Valencia, Alfonso (2008). "Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge". Genome Biology. 9 (Suppl 2): S1. doi:10.1186/gb-2008-9-s2-s1. ISSN 1465-6906.


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