Open Access Methodology article

BICEPP: an example-based statistical text mining method for predicting the binary characteristics of drugs

Frank PY Lin1*, Stephen Anthony1, Thomas M Polasek2, Guy Tsafnat1 and Matthew P Doogue23

Author Affiliations

1 Centre for Health Informatics, The University of New South Wales, Sydney, Australia

2 Department of Clinical Pharmacology, Flinders University, Adelaide, Australia

3 Flinders Medical Centre, Adelaide, Australia

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BMC Bioinformatics 2011, 12:112  doi:10.1186/1471-2105-12-112

Published: 21 April 2011



The identification of drug characteristics is a clinically important task, but it requires much expert knowledge and consumes substantial resources. We have developed a statistical text-mining approach (BInary Characteristics Extractor and biomedical Properties Predictor: BICEPP) to help experts screen drugs that may have important clinical characteristics of interest.


BICEPP first retrieves MEDLINE abstracts containing drug names, then selects tokens that best predict the list of drugs which represents the characteristic of interest. Machine learning is then used to classify drugs using a document frequency-based measure. Evaluation experiments were performed to validate BICEPP's performance on 484 characteristics of 857 drugs, identified from the Australian Medicines Handbook (AMH) and the PharmacoKinetic Interaction Screening (PKIS) database. Stratified cross-validations revealed that BICEPP was able to classify drugs into all 20 major therapeutic classes (100%) and 157 (of 197) minor drug classes (80%) with areas under the receiver operating characteristic curve (AUC) > 0.80. Similarly, AUC > 0.80 could be obtained in the classification of 173 (of 238) adverse events (73%), up to 12 (of 15) groups of clinically significant cytochrome P450 enzyme (CYP) inducers or inhibitors (80%), and up to 11 (of 14) groups of narrow therapeutic index drugs (79%). Interestingly, it was observed that the keywords used to describe a drug characteristic were not necessarily the most predictive ones for the classification task.


BICEPP has sufficient classification power to automatically distinguish a wide range of clinical properties of drugs. This may be used in pharmacovigilance applications to assist with rapid screening of large drug databases to identify important characteristics for further evaluation.

data mining; artificial intelligence; drug toxicity; adverse drug reaction reporting systems; cytochromes P450