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Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports

Harsha Gurulingappa, Abdul Mateen Rajput, Angus Roberts, Juliane Fluck, Martin Hofmann-Apitius, Luca Toldo
2012 Journal of Biomedical Informatics  
A significant amount of information about drug-related safety issues such as adverse effects are published in medical case reports that can only be explored by human readers due to their unstructured nature  ...  The work presented here aims at generating a systematically annotated corpus that can support the development and validation of methods for the automatic extraction of drug-related adverse effects from  ...  We also thank drug safety experts at Merck, Dr. Maren Rohrbacher (MD PhD) and Dr. Yorki Tayrouz (MD PhD) for reviewing a subset of annotations.  ... 
doi:10.1016/j.jbi.2012.04.008 pmid:22554702 fatcat:pbwxdj2tsngbfmtyzbsgqp2chq

Extraction of potential adverse drug events from medical case reports

Harsha Gurulingappa, Abdul Mateen‐Rajput, Luca Toldo
2012 Journal of Biomedical Semantics  
Therefore, this work focusses on the adaptation of a machine learning-based system for the identification and extraction of potential adverse drug event relations from MEDLINE case reports.  ...  The sheer amount of information about potential adverse drug events published in medical case reports pose major challenges for drug safety experts to perform timely monitoring.  ...  Martin Hofmann-Apitius and former colleagues at Fraunhofer Institute SCAI for supporting the foundational aspects of this work.  ... 
doi:10.1186/2041-1480-3-15 pmid:23256479 pmcid:PMC3599676 fatcat:tlxygb4kfve4rclaf7eitp7j5y

Analysis of factors associated with hiccups based on the Japanese Adverse Drug Event Report database

Ryuichiro Hosoya, Yoshihiro Uesawa, Reiko Ishii-Nozawa, Hajime Kagaya, Jinn-Moon Yang
2017 PLoS ONE  
Cases of adverse effects associated with medications were extracted from JADER, and Fisher's exact test was performed to assess the presence or absence of hiccups for each medication.  ...  The present study aimed to investigate the influence of medicines and patient characteristics on hiccups using a large-sized adverse drug event report database and, specifically, the Japanese Adverse Drug  ...  By using large-scale adverse effects report data, we were able to extract medications that induced the rare adverse effect of hiccups.  ... 
doi:10.1371/journal.pone.0172057 pmid:28196104 pmcid:PMC5308855 fatcat:f3oxtb42a5cidana4pe5tgxbb4

Analysis of Factors Associated with Hiccups Using the FAERS Database

Ryuichiro Hosoya, Reiko Ishii-Nozawa, Kota Kurosaki, Yoshihiro Uesawa
2021 Pharmaceuticals  
From 11,810,863 adverse drug reactions reported between the first quarter of 2004 and the first quarter of 2020, we extracted only those in which side effects occurred between the beginning and end of  ...  In this study, we used the large number of cases in the FDA adverse-event reporting system (FAERS) database to investigate risk factors for drug-induced hiccups and to explore the relationship between  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ph15010027 pmid:35056084 pmcid:PMC8780603 fatcat:gzfsa5mitrbtlettucphmt7qtu

A Novel Text Analysis Platform for Pharmacovigilance of Clinical Drugs

Anutosh Maitra, K.M. Annervaz, Tom Geo Jain, Madhura Shivaram, Shubhashis Sengupta
2014 Procedia Computer Science  
Proposed Bio-Medical Text Processing Approach The scope of the proposed text analysis platform spans over a process zone starting from receipt of drug safety reports and ending with the submission of case  ...  Several published drug-safety papers have shown that adverse effects of drugs may be detected too late, when millions of patients have already been exposed to them.  ... 
doi:10.1016/j.procs.2014.09.100 fatcat:zuqgutmh25drxk7nvxqktb6bcu

A knowledge management platform for documentation of case reports in pharmacovigilance

Florence Amardeilh, Cédric Bousquet, Sylvie Guillemin-Lanne, Mathilde Wiss-Thebault, Laetitia Guillot, Denis Delamarre, Agnès Lillo-Le Louet, Anita Burgun
2009 Studies in Health Technology and Informatics  
Most countries have developed information systems to report drug adverse effects.  ...  In order to improve systematic reviews of adverse drug reactions, we developed a prototype that first reproduces and standardizes search strategies, then extracts information from the Medline abstracts  ...  effects and drugs.  ... 
pmid:19745365 fatcat:fxqh2mqwmza45mnqx4jyuf3tb4

A research framework for pharmacovigilance in health social media: Identification and evaluation of patient adverse drug event reports

Xiao Liu, Hsinchun Chen
2015 Journal of Biomedical Informatics  
Patient reports of adverse drug events from social media have great potential to improve current practice of pharmacovigilance.  ...  The framework consists of medical entity extraction for recognizing patient discussions of drug and events, adverse drug event extraction with shortest dependency path kernel based statistical learning  ...  We gratefully acknowledge the contribution of Dr. Randall Brown and Ms. Chanadda Chinthammit for their advices from clinical and pharmaceutical perspectives in this study.  ... 
doi:10.1016/j.jbi.2015.10.011 pmid:26518315 fatcat:53nu3jrxfbdmxe2yqpaaqyrija

Reporting Patterns Indicative of Adverse Drug Interactions

Johanna Strandell, Ola Caster, Andrew Bate, Niklas Norén, I. Ralph Edwards
2011 Drug Safety  
Adverse drug interaction surveillance in collections of Individual Case Safety Reports (ICSRs) remains underdeveloped.  ...  , the assignment of the two drugs as interacting or through an ADR term; co-reporting of effect ORIGINAL RESEARCH ARTICLE  ...  We also thank the Royal Pharmaceutical Society for access to Stockley's Drug Interactions Alerts. Furthermore, the authors are indebted to the national centres that contributed data.  ... 
doi:10.2165/11586990-000000000-00000 pmid:21332249 fatcat:agh37hhdfzgrvpkeiyzm4op2aa

Adverse effects of psychotropic drug interactions with medicinal products and diet supplements containing plant extracts
Niepożądane efekty interakcji leków psychotropowych z produktami leczniczymi i suplementami diety zawierającymi wyciągi roślinne

Jarosław Woroń, Marcin Siwek
2018 Psychiatria Polska  
Analysis of 147 cases of adverse events with clinical picture indicating probability or certainty of resulting from inclusion of HP into the applied pharmacotherapy (mostly psychotropic drugs).  ...  Assessment of adverse drug interactions with herbal preparations (HP), i.e., plant medicines and nutritional supplements which contain plant extracts. Method.  ...  The scope of this issue includes, apart from adverse drug reactions, the need for additional treatment, the use of inadequate medications and their dosage, unnecessary treatment, induction of drug interactions  ... 
doi:10.12740/pp/onlinefirst/80998 fatcat:o3mxzmn7njdn3pp5jq26uu47xa

Oscillococcinum leading to angioedema, a rare adverse event

Y. Azmi, M. Rao, I. Verma, A. Agrawal
2015 BMJ Case Reports  
Clinical evidence exists to support this claim and the product has not previously been reported to cause any serious adverse drug reactions.  ...  Oscillococcinum is an alternative medicine prepared by serial dilution of wild duck heart and liver extracts.  ...  Acknowledgements The authors would like to acknowledge the contributions of the Department of Emergency Medicine and Department of Pulmonary and Critical Care at Monmouth Medical Center.  ... 
doi:10.1136/bcr-2015-210410 pmid:26038386 pmcid:PMC4460524 fatcat:mlycjcutovcsnl62rxjs56tc74

Identification of Adverse Drug Event-Related Articles (Preprint)

Shogo Ujiie, Shuntaro Yada, Shoko Wakamiya, Eiji Aramaki
2020 JMIR Medical Informatics  
Medical articles covering adverse drug events (ADEs) are systematically reported by pharmaceutical companies for drug safety information purposes.  ...  Recall-based reporting, which is implemented in Japan, requires the reporting of any possible ADE.  ...  Its main information source is spontaneous reporting from pharmaceutical companies, and the basis of these reports is medical articles.  ... 
doi:10.2196/22661 pmid:33245290 fatcat:e4aaqxtqwrh73mhrx5zxj3h2pq

Adverse drug reactions in primary care: a scoping review

H. Khalil, C. Huang
2020 BMC Health Services Research  
Medication-related adverse events, or adverse drug reactions (ADRs) are harmful events caused by medication.  ...  Several classes of medications were reported to be associated with adverse events. This scoping review identified that the most causes of ADRs were drug related and due to allergies.  ...  Consequences of ADRs The consequences of the ADRs reported in the included studies ranged from medication cessation to death in some cases.  ... 
doi:10.1186/s12913-019-4651-7 pmid:31902367 pmcid:PMC6943955 fatcat:mu2ognlj7jbixjhllvlj7flzqm

Drug Safety Report Generator

Sudhir Dubey, Pruthviraj Bhamre, Akshay Patil, Rahul Kumar
2021 International Journal of Scientific Research in Science and Technology  
This document provides an overview on identifying ICSR (Individual case safety reports) & Drug Safety Classification of Adverse Drug Events from free Text Electronic Patient Records and Information.  ...  We intend to separate the causes and effects of unfriendly drugs from the records.  ...  NLP and Text Mining are used to extract Adverse Drug Events from safety reports and Bio-medical text without need for a large training set.  ... 
doi:10.32628/cseit21743 fatcat:ws55pdbohrhwfmrsmwmwgiivcy

Mining Adverse Drug Reactions from online healthcare forums using Hidden Markov Model

Hariprasad Sampathkumar, Xue-wen Chen, Bo Luo
2014 BMC Medical Informatics and Decision Making  
The objective of this research is to extract reports of adverse drug side-effects from messages in online healthcare forums and use them as early indicators to assist in post-marketing drug surveillance  ...  can be used to classify a message as containing drug side-effect information and then extract the adverse side-effect mentions from it.  ...  Acknowledgements The authors would like to acknowledge the support from National Science Foundation awards IIS-0644366 and OIA-1028098, and KU General Research Fund GRF-2301677.  ... 
doi:10.1186/1472-6947-14-91 pmid:25341686 pmcid:PMC4283122 fatcat:c7tv5qy6brhlrbazu5lddv3quu

The safety of ritodrine hydrochloride: Adverse effects on fetuses and newborns

Yuriko Yonaga, Akihiko Ito
2021 Drug Discoveries & Therapeutics  
Oral drugs had more adverse effect reports than injectable drugs.  ...  Using the Pharmaceuticals and Medical Devices Agency of Japan's Japanese Adverse Drug Event Report (JADER) database, the AEs on fetuses and newborns caused by oral and injected Rito were extracted and  ...  Conflict of Interest: The authors have no conflicts of interest to disclose.  ... 
doi:10.5582/ddt.2021.01016 pmid:33642492 fatcat:wh5donii2nglzpribwm4qfpjli
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