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NaCTeM success at BioCreative IV

2013-10-10

BioCreative: Critical Assessment of Information Extraction in Biology is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. NaCTeM participated in the 4th of these challenges, which took place from October 7th-9th 2013 in Bethesda, Maryland, USA. BioCreative IV consists of several tasks (or tracks), and NaCTeM's systems outperformed other participating systems in a number of these tracks. The Comparative Toxicogenomics Database (CTD) track involved recognising 4 concept types: chemicals, genes, diseases and action terms. The NaCTeM team achieved the best results among 12 participating teams in both the recognition of chemicals and genes. In terms of combined performance of the recognition of all 4 concept types, NaCTeM also ranked highest. In another track, Chemical and Drug Named Entity Recognition (CHEMDNER), NaCTeM was ranked 1st out of 23 teams participating in the Chemical Document Indexing (CDI) subtask.

Details of NaCTeM's contributions to BioCreative IV can be found in the following papers:

Batista-Navarro, R. T. B., Rak, R. and Ananiadou, S.. (2013). NaCTeM CTD Web Services. In: Fourth BioCreative Challenge Evaluation Workshop, Bethesda, Maryland, USA, pp. 85-89

Batista-Navarro, R. T. B., Rak, R. and Ananiadou, S.. (2013). Chemistry-specific Features and Heuristics for Developing a CRF-based Chemical Named Entity Recogniser. In: Fourth BioCreative Challenge Evaluation Workshop, Bethesda, Maryland, USA, pp. 55-59

Rak, R., Batista-Navarro, R. T. B., Rowley, A., Carter, J. and Ananiadou, S.. (2013). Customisable Curation Workflows in Argo. In: Fourth BioCreative Challenge Evaluation Workshop, Bethesda, Maryland, USA, pp. 270-278

Rak, R., Batista-Navarro, R. T. B., Rowley, A., Miwa, M., Carter, J. and Ananiadou, S.. (2013). NaCTeM's BioC Modules and Resources for BioCreative IV. In: Fourth BioCreative Challenge Evaluation Workshop, Bethesda, Maryland, USA, pp. 61-67