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]
Three main tasks were posed at the first BioCreAtIvE challenge: the entity extraction task,[ 3] [ 4] [ 5] [ 6]
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] [ 7]
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]
BioCreative V had 5 different tracks,[ 10] [ 11] BioGRID .[ 12]
See also
References
^ 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 . ^ 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 . ^ 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 . ^ 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 . ^ 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 . ^ 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 . ^ a b 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 . ^ 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 . ^ 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 . {{cite journal }}: CS1 maint: article number as page number (link )^ "BioCreative - Call for Participation" . biocreative.bioinformatics.udel.edu . Retrieved 2021-04-21 .^ 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 . {{cite journal }}: CS1 maint: article number as page number (link )^ 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 . {{cite journal }}: CS1 maint: article number as page number (link )
External links
