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. [1]

Contents

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

Community Challenges

First edition (2004-2005)

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 (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. [7] It counted with participation of 44 teams from 13 countries. [7]

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. [8] [9]

Fifth edition (2016)

BioCreative V had 5 different tracks, [10] including an interactive task (IAT) for usability of text mining systems [11] and a track using the BioC format for curating information for BioGRID. [12]

See also

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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. 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. 1 2 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 (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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