# BioCreative

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**BioCreAtIvE** (A critical assessment of text mining methods in [molecular biology](/source/Molecular_biology)) consists in a community-wide effort for evaluating [information extraction](/source/Information_extraction) and [text mining](/source/Text_mining) developments in the biological domain.[1]

It was preceded by the Knowledge Discovery and [Data Mining](/source/Data_mining) (KDD) Challenge Cup for detection of [gene](/source/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](/source/Text_mining) tools in real-world [biocuration](/source/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](/source/BioGRID).[12]

## See also

- [Biocuration](/source/Biocuration)

## 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](https://doi.org/10.1186/1471-2105-6-S1-S1). [PMC 1869002](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1869002). [PMID 15960821](https://pubmed.ncbi.nlm.nih.gov/15960821)

1. 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](https://arxiv.org/abs/cs/0308032). [doi:10.1093/bioinformatics/btg1046](https://doi.org/10.1093/bioinformatics/btg1046). [ISSN 1367-4803](https://www.worldcat.org/issn/1367-4803). [PMID 12855478](https://pubmed.ncbi.nlm.nih.gov/12855478)

1. 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](https://doi.org/10.1186/1471-2105-6-S1-S2). [PMC 1869012](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1869012). [PMID 15960832](https://pubmed.ncbi.nlm.nih.gov/15960832)

1. 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](https://doi.org/10.1186/1471-2105-6-S1-S11). [PMC 1869004](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1869004). [PMID 15960823](https://pubmed.ncbi.nlm.nih.gov/15960823)

1. 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](https://doi.org/10.1186/1471-2105-6-S1-S12). [PMC 1869005](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1869005). [PMID 15960824](https://pubmed.ncbi.nlm.nih.gov/15960824)

1. 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](https://doi.org/10.1186/1471-2105-6-S1-S16). [PMC 1869008](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1869008). [PMID 15960828](https://pubmed.ncbi.nlm.nih.gov/15960828)

1. 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](https://doi.org/10.1186/gb-2008-9-s2-s1). [ISSN 1465-6906](https://www.worldcat.org/issn/1465-6906). [PMC 2559980](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2559980). [PMID 18834487](https://pubmed.ncbi.nlm.nih.gov/18834487)

1. 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"](https://www.wikidata.org/wiki/Q34094645). *BMC Bioinformatics*. **12** (Suppl 8): S4. [doi:10.1186/1471-2105-12-S8-S4](https://doi.org/10.1186/1471-2105-12-S8-S4). [PMC 3269939](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3269939). [PMID 22151968](https://pubmed.ncbi.nlm.nih.gov/22151968)

1. 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."](https://www.wikidata.org/wiki/Q36761979). *Database*. **2013**. [doi:10.1093/DATABASE/BAS056](https://doi.org/10.1093/DATABASE/BAS056). [PMC 3625048](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3625048). [PMID 23327936](https://pubmed.ncbi.nlm.nih.gov/23327936)

1. ["BioCreative - Call for Participation"](https://biocreative.bioinformatics.udel.edu/events/biocreative-v/CFP/). *biocreative.bioinformatics.udel.edu*. Retrieved 2021-04-21.

1. 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"](https://www.wikidata.org/wiki/Q30002351). *Database*. **2016**. [doi:10.1093/DATABASE/BAW119](https://doi.org/10.1093/DATABASE/BAW119). [PMC 5009325](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009325). [PMID 27589961](https://pubmed.ncbi.nlm.nih.gov/27589961)

1. 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."](https://www.wikidata.org/wiki/Q36121943). *Database*. **2016**. [doi:10.1093/DATABASE/BAW121](https://doi.org/10.1093/DATABASE/BAW121). [PMC 5009341](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009341). [PMID 27589962](https://pubmed.ncbi.nlm.nih.gov/27589962)

## External links

- [BioCreAtIve, 2007-2015](https://biocreative.bioinformatics.udel.edu/)
- [BioCreAtIve 2, 2006-2007](http://biocreative.sourceforge.net)
- [First BioCreAtIvE workshop, 2004](https://web.archive.org/web/20051220211111/http://www.pdg.cnb.uam.es/BioLink/workshop_BioCreative_04/)
- [BMC Bioinformatics special issue : BioCreAtIvE](https://web.archive.org/web/20060216163236/http://www.biomedcentral.com/1471-2105/6?issue=S1)
- [First BioCreAtIvE data download request](https://web.archive.org/web/20060314001046/http://www.pdg.cnb.uam.es/BioLINK/workshop_BioCreative_04/results/agreetment.html)

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