Leveraging MEDLINE indexing for pharmacovigilance - Inherent limitations and mitigation strategies

Rainer Winnenburg; Alfred Sorbello; Anna Ripple; Rave Harpaz; Joseph Tonning; Ana Szarfman; Henry Francis; Olivier Bodenreider

doi:10.1016/j.jbi.2015.08.022

Leveraging MEDLINE indexing for pharmacovigilance - Inherent limitations and mitigation strategies

J Biomed Inform. 2015 Oct:57:425-35. doi: 10.1016/j.jbi.2015.08.022. Epub 2015 Sep 2.

Authors

Rainer Winnenburg¹, Alfred Sorbello², Anna Ripple¹, Rave Harpaz³, Joseph Tonning², Ana Szarfman², Henry Francis², Olivier Bodenreider⁴

Affiliations

¹ Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA.
² US Food and Drug Administration, Center for Drug Evaluation and Research, Office of Translational Sciences, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA.
³ Oracle Health Sciences GBU, 100 Crosby Drive, Bedford, MA 01730, USA.
⁴ Lister Hill National Center for Biomedical Communications, U.S. National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA. Electronic address: olivier.bodenreider@nih.gov.

Abstract

Background: Traditional approaches to pharmacovigilance center on the signal detection from spontaneous reports, e.g., the U.S. Food and Drug Administration (FDA) adverse event reporting system (FAERS). In order to enrich the scientific evidence and enhance the detection of emerging adverse drug events that can lead to unintended harmful outcomes, pharmacovigilance activities need to evolve to encompass novel complementary data streams, for example the biomedical literature available through MEDLINE.

Objectives: (1) To review how the characteristics of MEDLINE indexing influence the identification of adverse drug events (ADEs); (2) to leverage this knowledge to inform the design of a system for extracting ADEs from MEDLINE indexing; and (3) to assess the specific contribution of some characteristics of MEDLINE indexing to the performance of this system.

Methods: We analyze the characteristics of MEDLINE indexing. We integrate three specific characteristics into the design of a system for extracting ADEs from MEDLINE indexing. We experimentally assess the specific contribution of these characteristics over a baseline system based on co-occurrence between drug descriptors qualified by adverse effects and disease descriptors qualified by chemically induced.

Results: Our system extracted 405,300 ADEs from 366,120 MEDLINE articles. The baseline system accounts for 297,093 ADEs (73%). 85,318 ADEs (21%) can be extracted only after integrating specific pre-coordinated MeSH descriptors and additional qualifiers. 22,889 ADEs (6%) can be extracted only after considering indirect links between the drug of interest and the descriptor that bears the ADE context.

Conclusions: In this paper, we demonstrate significant improvement over a baseline approach to identifying ADEs from MEDLINE indexing, which mitigates some of the inherent limitations of MEDLINE indexing for pharmacovigilance. ADEs extracted from MEDLINE indexing are complementary to, not a replacement for, other sources.

Keywords: Adverse drug events; MEDLINE indexing; Pharmacovigilance.

Published by Elsevier Inc.

MeSH terms

Adverse Drug Reaction Reporting Systems
Data Mining
Drug-Related Side Effects and Adverse Reactions*
Humans
Information Storage and Retrieval
MEDLINE*
Medical Subject Headings*
Pharmacovigilance*
United States
United States Food and Drug Administration

Abstract

MeSH terms

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