Literature DB >> 25151493

Text mining for adverse drug events: the promise, challenges, and state of the art.

Rave Harpaz1, Alison Callahan, Suzanne Tamang, Yen Low, David Odgers, Sam Finlayson, Kenneth Jung, Paea LePendu, Nigam H Shah.   

Abstract

Text mining is the computational process of extracting meaningful information from large amounts of unstructured text. It is emerging as a tool to leverage underutilized data sources that can improve pharmacovigilance, including the objective of adverse drug event (ADE) detection and assessment. This article provides an overview of recent advances in pharmacovigilance driven by the application of text mining, and discusses several data sources-such as biomedical literature, clinical narratives, product labeling, social media, and Web search logs-that are amenable to text mining for pharmacovigilance. Given the state of the art, it appears text mining can be applied to extract useful ADE-related information from multiple textual sources. Nonetheless, further research is required to address remaining technical challenges associated with the text mining methodologies, and to conclusively determine the relative contribution of each textual source to improving pharmacovigilance.

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Mesh:

Year:  2014        PMID: 25151493      PMCID: PMC4217510          DOI: 10.1007/s40264-014-0218-z

Source DB:  PubMed          Journal:  Drug Saf        ISSN: 0114-5916            Impact factor:   5.606


  63 in total

1.  Automated encoding of clinical documents based on natural language processing.

Authors:  Carol Friedman; Lyudmila Shagina; Yves Lussier; George Hripcsak
Journal:  J Am Med Inform Assoc       Date:  2004-06-07       Impact factor: 4.497

2.  A drug-adverse event extraction algorithm to support pharmacovigilance knowledge mining from PubMed citations.

Authors:  Wei Wang; Krystl Haerian; Hojjat Salmasian; Rave Harpaz; Herbert Chase; Carol Friedman
Journal:  AMIA Annu Symp Proc       Date:  2011-10-22

3.  Predicting adverse drug events from personal health messages.

Authors:  Brant W Chee; Richard Berlin; Bruce Schatz
Journal:  AMIA Annu Symp Proc       Date:  2011-10-22

4.  Using information mining of the medical literature to improve drug safety.

Authors:  Kanaka D Shetty; Siddhartha R Dalal
Journal:  J Am Med Inform Assoc       Date:  2011-05-05       Impact factor: 4.497

5.  Design and validation of an automated method to detect known adverse drug reactions in MEDLINE: a contribution from the EU-ADR project.

Authors:  Paul Avillach; Jean-Charles Dufour; Gayo Diallo; Francesco Salvo; Michel Joubert; Frantz Thiessard; Fleur Mougin; Gianluca Trifirò; Annie Fourrier-Réglat; Antoine Pariente; Marius Fieschi
Journal:  J Am Med Inform Assoc       Date:  2012-11-29       Impact factor: 4.497

6.  Identifying potential adverse effects using the web: a new approach to medical hypothesis generation.

Authors:  Adrian Benton; Lyle Ungar; Shawndra Hill; Sean Hennessy; Jun Mao; Annie Chung; Charles E Leonard; John H Holmes
Journal:  J Biomed Inform       Date:  2011-07-26       Impact factor: 6.317

7.  Mining clinical text for signals of adverse drug-drug interactions.

Authors:  Srinivasan V Iyer; Rave Harpaz; Paea LePendu; Anna Bauer-Mehren; Nigam H Shah
Journal:  J Am Med Inform Assoc       Date:  2013-10-24       Impact factor: 4.497

8.  A reference standard for evaluation of methods for drug safety signal detection using electronic healthcare record databases.

Authors:  Preciosa M Coloma; Paul Avillach; Francesco Salvo; Martijn J Schuemie; Carmen Ferrajolo; Antoine Pariente; Annie Fourrier-Réglat; Mariam Molokhia; Vaishali Patadia; Johan van der Lei; Miriam Sturkenboom; Gianluca Trifirò
Journal:  Drug Saf       Date:  2013-01       Impact factor: 5.606

9.  Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis.

Authors:  Stephen T Wu; Hongfang Liu; Dingcheng Li; Cui Tao; Mark A Musen; Christopher G Chute; Nigam H Shah
Journal:  J Am Med Inform Assoc       Date:  2012-04-04       Impact factor: 4.497

10.  A side effect resource to capture phenotypic effects of drugs.

Authors:  Michael Kuhn; Monica Campillos; Ivica Letunic; Lars Juhl Jensen; Peer Bork
Journal:  Mol Syst Biol       Date:  2010-01-19       Impact factor: 11.429

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  58 in total

1.  A method for systematic discovery of adverse drug events from clinical notes.

Authors:  Guan Wang; Kenneth Jung; Rainer Winnenburg; Nigam H Shah
Journal:  J Am Med Inform Assoc       Date:  2015-07-31       Impact factor: 4.497

Review 2.  Medication-indication knowledge bases: a systematic review and critical appraisal.

Authors:  Hojjat Salmasian; Tran H Tran; Herbert S Chase; Carol Friedman
Journal:  J Am Med Inform Assoc       Date:  2015-09-02       Impact factor: 4.497

3.  A Multiagent System for Integrated Detection of Pharmacovigilance Signals.

Authors:  Vassilis Koutkias; Marie-Christine Jaulent
Journal:  J Med Syst       Date:  2015-11-21       Impact factor: 4.460

Review 4.  Utilizing social media data for pharmacovigilance: A review.

Authors:  Abeed Sarker; Rachel Ginn; Azadeh Nikfarjam; Karen O'Connor; Karen Smith; Swetha Jayaraman; Tejaswi Upadhaya; Graciela Gonzalez
Journal:  J Biomed Inform       Date:  2015-02-23       Impact factor: 6.317

5.  deepBioWSD: effective deep neural word sense disambiguation of biomedical text data.

Authors:  Ahmad Pesaranghader; Stan Matwin; Marina Sokolova; Ali Pesaranghader
Journal:  J Am Med Inform Assoc       Date:  2019-05-01       Impact factor: 4.497

6.  Adverse drug event and medication extraction in electronic health records via a cascading architecture with different sequence labeling models and word embeddings.

Authors:  Hong-Jie Dai; Chu-Hsien Su; Chi-Shin Wu
Journal:  J Am Med Inform Assoc       Date:  2020-01-01       Impact factor: 4.497

7.  A study of deep learning approaches for medication and adverse drug event extraction from clinical text.

Authors:  Qiang Wei; Zongcheng Ji; Zhiheng Li; Jingcheng Du; Jingqi Wang; Jun Xu; Yang Xiang; Firat Tiryaki; Stephen Wu; Yaoyun Zhang; Cui Tao; Hua Xu
Journal:  J Am Med Inform Assoc       Date:  2020-01-01       Impact factor: 4.497

8.  Comparative assessment of manual chart review and ICD claims data in evaluating immunotherapy-related adverse events.

Authors:  Andrew Nashed; Shijun Zhang; Chien-Wei Chiang; M Zitu; Gregory A Otterson; Carolyn J Presley; Kari Kendra; Sandip H Patel; Andrew Johns; Mingjia Li; Madison Grogan; Gabrielle Lopez; Dwight H Owen; Lang Li
Journal:  Cancer Immunol Immunother       Date:  2021-02-24       Impact factor: 6.968

Review 9.  Natural Language Processing for EHR-Based Pharmacovigilance: A Structured Review.

Authors:  Yuan Luo; William K Thompson; Timothy M Herr; Zexian Zeng; Mark A Berendsen; Siddhartha R Jonnalagadda; Matthew B Carson; Justin Starren
Journal:  Drug Saf       Date:  2017-11       Impact factor: 5.606

10.  Accuracy of an automated knowledge base for identifying drug adverse reactions.

Authors:  E A Voss; R D Boyce; P B Ryan; J van der Lei; P R Rijnbeek; M J Schuemie
Journal:  J Biomed Inform       Date:  2016-12-16       Impact factor: 6.317

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