Leveraging MEDLINE indexing for pharmacovigilance - Inherent limitations and mitigation strategies.
Leveraging MEDLINE indexing for pharmacovigilance - Inherent limitations and mitigation strategies.
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DOI：
10.1016/j.jbi.2015.08.022
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发表时间：
2015-10
影响因子：
4.5
通讯作者：
Bodenreider O
中科院分区：
文献类型：
--
作者：
Winnenburg R;Sorbello A;Ripple A;Harpaz R;Tonning J;Szarfman A;Francis H;Bodenreider O
传统的药物警戒方法集中在自发报告的信号检测上，例如，美国食品药品监督管理局（FDA）不良事件报告系统（FAERS）。为了丰富科学证据并加强对可能导致非预期有害结果的新出现的药物不良事件的检测，药物警戒活动需要发展以涵盖新的补充数据流，例如通过MEDLINE获得的生物医学文献。1)审查MEDLINE索引的特征如何影响药物不良事件（ADE）的识别; 2）利用这些知识为从MEDLINE索引中提取ADE的系统设计提供信息; 3）评估MEDLINE索引的某些特征对该系统性能的具体贡献。分析了MEDLINE检索的特点。我们集成了三个具体的特点，从MEDLINE索引提取ADE系统的设计。我们通过实验评估这些特征的具体贡献超过基线系统的基础上，药物描述符之间的共同发生的不良反应和疾病描述符合格的化学诱导。我们的系统从366，120篇MEDLINE文章中提取了405，300个ADE。基线系统占297，093例ADE（73%）。85，318个ADE（21%）只有在整合特定的预协调MeSH描述符和附加限定符后才能提取。仅在考虑目标药物与带有ADE背景的描述符之间的间接联系后，才能提取22，889个ADE（6%）。在本文中，我们证明了从MEDLINE索引中识别ADE的基线方法的显著改进，这减轻了MEDLINE索引用于药物警戒的一些固有局限性。从MEDLINE索引中提取的ADE是对其他来源的补充，而不是替代。
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. 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. 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. 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. 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.