BioCreative explained

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 (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.

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

External links

Notes and References

  1. Hirschman . L. . Yeh . A. . Blaschke . C. . Valencia . A. . Overview of BioCreAtIvE: Critical assessment of information extraction for biology . 10.1186/1471-2105-6-S1-S1 . BMC Bioinformatics . 6 . S1 . 2005 . Suppl 1 . 15960821 . 1869002 . free .
  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. 10.1093/bioinformatics/btg1046. 12855478. 1367-4803. free. cs/0308032.
  3. Yeh. A.. Morgan. A.. Colosimo. M.. Hirschman. L.. 2005. BioCreAtIvE Task 1A: Gene mention finding evaluation. BMC Bioinformatics. 6. Suppl 1 . S2. 10.1186/1471-2105-6-S1-S2. 1869012. 15960832 . free .
  4. Hirschman. L.. Colosimo. M.. Morgan. A.. Yeh. A.. 2005. Overview of BioCreAtIvE task 1B: Normalized gene lists. BMC Bioinformatics. 6. Suppl 1 . S11. 10.1186/1471-2105-6-S1-S11. 1869004. 15960823 . free .
  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. 10.1186/1471-2105-6-S1-S12. 1869005. 15960824 . free .
  6. Blaschke. C.. Leon. E.. Krallinger. M.. Valencia. A.. 2005. Evaluation of BioCreAtIvE assessment of task 2. BMC Bioinformatics. 6. Suppl 1 . S16. 10.1186/1471-2105-6-S1-S16. 1869008. 15960828 . free .
  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. 2559980. 10.1186/gb-2008-9-s2-s1. 18834487. 1465-6906. free.
  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. 3269939 . 10.1186/1471-2105-12-S8-S4. 22151968. free.
  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. 10.1093/DATABASE/BAS056 . 23327936. 3625048. free.
  10. Web site: BioCreative - Call for Participation. 2021-04-21. biocreative.bioinformatics.udel.edu.
  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. English. 2016. baw119. 10.1093/DATABASE/BAW119. 27589961. 5009325. free.
  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. 10.1093/DATABASE/BAW121. 27589962. 5009341. free.

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