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Open Access Highly Accessed Research article

A pipeline to extract drug-adverse event pairs from multiple data sources

SriJyothsna Yeleswarapu, Aditya Rao*, Thomas Joseph, Vangala Govindakrishnan Saipradeep and Rajgopal Srinivasan

Author Affiliations

TCS Innovation Labs, Tata Consultancy Services Ltd, Deccan Park, 1, Software Units Layout, Madhapur, Hyderabad 500081, Andhra Pradesh, India

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BMC Medical Informatics and Decision Making 2014, 14:13  doi:10.1186/1472-6947-14-13

Published: 24 February 2014

Abstract

Background

Pharmacovigilance aims to uncover and understand harmful side-effects of drugs, termed adverse events (AEs). Although the current process of pharmacovigilance is very systematic, the increasing amount of information available in specialized health-related websites as well as the exponential growth in medical literature presents a unique opportunity to supplement traditional adverse event gathering mechanisms with new-age ones.

Method

We present a semi-automated pipeline to extract associations between drugs and side effects from traditional structured adverse event databases, enhanced by potential drug-adverse event pairs mined from user-comments from health-related websites and MEDLINE abstracts. The pipeline was tested using a set of 12 drugs representative of two previous studies of adverse event extraction from health-related websites and MEDLINE abstracts.

Results

Testing the pipeline shows that mining non-traditional sources helps substantiate the adverse event databases. The non-traditional sources not only contain the known AEs, but also suggest some unreported AEs for drugs which can then be analyzed further.

Conclusion

A semi-automated pipeline to extract the AE pairs from adverse event databases as well as potential AE pairs from non-traditional sources such as text from MEDLINE abstracts and user-comments from health-related websites is presented.

Keywords:
Pharmacovigilance; NLP; Text mining; Social media; Adverse event; Biomedical literature; Unstructured text; BCPNN