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This article is part of the supplement: Proceedings of the BioNLP 08 ACL Workshop: Themes in biomedical language processing

Open Access Research

Cascaded classifiers for confidence-based chemical named entity recognition

Peter Corbett1* and Ann Copestake2

Author Affiliations

1 Unilever Centre For Molecular Science Informatics, Chemical Laboratory, University Of Cambridge, CB2 1EW, UK

2 Computer Laboratory, University Of Cambridge, CB3 0FD, UK

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BMC Bioinformatics 2008, 9(Suppl 11):S4  doi:10.1186/1471-2105-9-S11-S4

Published: 19 November 2008



Chemical named entities represent an important facet of biomedical text.


We have developed a system to use character-based n-grams, Maximum Entropy Markov Models and rescoring to recognise chemical names and other such entities, and to make confidence estimates for the extracted entities. An adjustable threshold allows the system to be tuned to high precision or high recall. At a threshold set for balanced precision and recall, we were able to extract named entities at an F score of 80.7% from chemistry papers and 83.2% from PubMed abstracts. Furthermore, we were able to achieve 57.6% and 60.3% recall at 95% precision, and 58.9% and 49.1% precision at 90% recall.


These results show that chemical named entities can be extracted with good performance, and that the properties of the extraction can be tuned to suit the demands of the task.