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BioCreative

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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.

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

Community Challenges

First edition (2004-2005)

Three main tasks were posed at the first BioCreAtIvE challenge: the entity extraction task, the gene name normalization task, and the functional annotation of gene products task. 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 (2006-2007)

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

Third edition (2011-2012)

The third edition of BioCreative included for the first time the InterActive Task (IAT), designed to evaluate the practical usability of text mining tools in real-world biocuration tasks.

Fifth edition (2016)

BioCreative V had 5 different tracks, including an interactive task (IAT) for usability of text mining systems and a track using the BioC format for curating information for BioGRID.

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 (Suppl 1): 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. arXiv:cs/0308032. doi:10.1093/bioinformatics/btg1046. ISSN 1367-4803. PMID 12855478.
  3. Yeh, A.; Morgan, A.; Colosimo, M.; Hirschman, L. (2005). "BioCreAtIvE Task 1A: Gene mention finding evaluation". BMC Bioinformatics. 6 (Suppl 1): 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 (Suppl 1): 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 (Suppl 1): 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 (Suppl 1): 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. PMC 2559980. PMID 18834487.
  8. Arighi, Cecilia; Roberts, Phoebe M.; Agarwal, Shashank; Bhattacharya, Sanmitra; Cesareni, Gianni; Chatr-Aryamontri, Andrew; Clematide, Simon; Gaudet, Pascale; Giglio, Michelle; Harrow, Ian; Huala, Eva (2011-10-03). "BioCreative III interactive task: an overview". BMC Bioinformatics. 12 (Suppl 8): S4. doi:10.1186/1471-2105-12-S8-S4. PMC 3269939. PMID 22151968.
  9. Carterette, Ben; Cohen, Kevin Bretonnel; Cooper, Laurel; Li, Donghui; Jimenez, Silvia; Roberts, Phoebe; Drabkin, Harold; Bello, Susan; Schaeffer, Mary L.; Park, Julie; Li, Yuling (2013-01-17). "An overview of the BioCreative 2012 Workshop Track III: interactive text mining task". Database. 2013: bas056. doi:10.1093/DATABASE/BAS056. PMC 3625048. PMID 23327936.
  10. "BioCreative - Call for Participation". biocreative.bioinformatics.udel.edu. Retrieved 2021-04-21.
  11. Wang, Qinghua; Abdul, Shabbir S.; Almeida, Lara; Ananiadou, Sofia; Balderas-Martínez, Yalbi I.; Batista-Navarro, Riza; Campos, David; Chilton, Lucy; Chou, Hui-Jou; Contreras, Gabriela; Cooper, Laurel (2016-01-01). "Overview of the interactive task in BioCreative V". Database. 2016: baw119. doi:10.1093/DATABASE/BAW119. PMC 5009325. PMID 27589961.
  12. Kim, Sun; Doğan, Rezarta Islamaj; Chatr-Aryamontri, Andrew; Chang, Christie S.; Oughtred, Rose; Rust, Jennifer; Batista-Navarro, Riza; Carter, Jacob; Ananiadou, Sofia; Matos, Sérgio; Santos, André (2016-09-01). "BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID". Database. 2016: baw121. doi:10.1093/DATABASE/BAW121. PMC 5009341. PMID 27589962.

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