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

Journal of Biomedical Informatics
Harsha GurulingappaLuca Toldo

Abstract

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 medical case reports. The documents are systematically double annotated in various rounds to ensure consistent annotations. The annotated documents are finally harmonized to generate representative consensus annotations. In order to demonstrate an example use case scenario, the corpus was employed to train and validate models for the classification of informative against the non-informative sentences. A Maximum Entropy classifier trained with simple features and evaluated by 10-fold cross-validation resulted in the F₁ score of 0.70 indicating a potential useful application of the corpus.

References

Oct 1, 1995·International Journal of Bio-medical Computing·G C Miller, H Britt
Mar 19, 1999·Drug Safety : an International Journal of Medical Toxicology and Drug Experience·E G BrownS Wood
Jan 22, 2003·Journal of General Internal Medicine·Syed Rizwanuddin Ahmad
Jun 18, 2005·BMC Bioinformatics·Daniel HanischJuliane Fluck
Dec 31, 2005·Nucleic Acids Research·David S WishartJennifer Woolsey
Apr 4, 2006·Drug Discovery Today·Ramón A-A ErhardtChristian Blaschke
Oct 8, 2008·International Journal of Medical Informatics·V JagannathanPavani Bandaru
Oct 17, 2008·Bioinformatics·Nigel CollierKiyosu Taniguchi
Jun 19, 2009·Journal of Biomedical Informatics·Angus RobertsAndrea Setzer
Jul 4, 2009·Computers, Informatics, Nursing : CIN·Sookyung HyunSuzanne Bakken
Sep 8, 2010·Journal of the American Medical Informatics Association : JAMIA·Ozlem UzunerEithon Cadag

❮ Previous
Next ❯

Citations

Dec 22, 2012·Journal of Biomedical Semantics·Harsha GurulingappaLuca Toldo
Mar 7, 2014·BMC Bioinformatics·Ning KangJan A Kors
Feb 25, 2014·BMC Medical Informatics and Decision Making·Srijyothsna YeleswarapuRajgopal Srinivasan
Aug 26, 2014·Drug Safety : an International Journal of Medical Toxicology and Drug Experience·Rave HarpazNigam H Shah
Aug 13, 2013·Pharmacoepidemiology and Drug Safety·Harsha GurulingappaYorki Tayrouz
Jul 5, 2015·Journal of Biomedical Informatics·Maite OronozArantza Casillas
Apr 16, 2016·Database : the Journal of Biological Databases and Curation·Ewoud PonsJan A Kors
Jun 24, 2015·BMC Medical Informatics and Decision Making·Isabel Segura-BedmarJulián Moreno-Schneider
Mar 31, 2015·Journal of Biomedical Informatics·Sarvnaz KarimiChen Wang
Feb 18, 2015·Journal of Biomedical Informatics·Ming YangWei Shang
Aug 3, 2013·Journal of Biomedical Informatics·María Herrero-ZazoThierry Declerck
Dec 3, 2014·Journal of Biomedical Informatics·Abeed Sarker, Graciela Gonzalez
Feb 3, 2015·Methods : a Companion to Methods in Enzymology·Wilco W M Fleuren, Wynand Alkema
May 11, 2016·Database : the Journal of Biological Databases and Curation·Jiao LiZhiyong Lu
May 8, 2015·Journal of the American Medical Informatics Association : JAMIA·Jan A KorsDietrich Rebholz-Schuhmann
Mar 11, 2015·Journal of the American Medical Informatics Association : JAMIA·Azadeh NikfarjamGraciela Gonzalez
Jun 19, 2017·Journal of Biomedical Informatics·Isabel MorenoM Teresa Romá-Ferri
Aug 18, 2017·Methods of Information in Medicine·Xingyu ZhangJustin D Schrager
Apr 7, 2018·Expert Opinion on Drug Safety·Chen Zou
Mar 21, 2016·Database : the Journal of Biological Databases and Curation·Chih-Hsuan WeiZhiyong Lu
Jan 17, 2019·Drug Safety : an International Journal of Medical Toxicology and Drug Experience·Abhyuday JagannathaHong Yu
Aug 8, 2019·Journal of the American Medical Informatics Association : JAMIA·Fenia ChristopoulouSophia Ananiadou
Sep 20, 2019·BMC Bioinformatics·Tongxuan ZhangYijia Zhang
Jun 21, 2018·International Journal of Environmental Research and Public Health·Donghua ChenLei Hou
Aug 15, 2018·Journal of Cheminformatics·Paul ThompsonSophia Ananiadou
Jan 4, 2020·Scientific Data·Joël LegrandAdrien Coulet
Mar 21, 2017·Journal of Cheminformatics·Yifan PengZhiyong Lu
May 5, 2017·JMIR Public Health and Surveillance·Nestor AlvaroNigel Collier
Feb 19, 2020·Journal of Biomedical Informatics·Cong SunJian Wang
May 4, 2020·Journal of Biomedical Informatics·Ying ZhangHuiying Gao
Aug 21, 2021·Artificial Intelligence in Medicine·Andrey KormilitzinAlejo Nevado-Holgado
May 6, 2017·Chemical Reviews·Martin KrallingerAlfonso Valencia
Aug 24, 2021·Computational and Mathematical Methods in Medicine·Sajid HussainMir Yasir Umair
Sep 7, 2021·Journal of Biomedical Informatics·Tongxuan ZhangXiaodong Duan

❮ Previous
Next ❯

Related Concepts

Related Feeds

Blood And Marrow Transplantation

The use of hematopoietic stem cell transplantation or blood and marrow transplantation (bmt) is on the increase worldwide. BMT is used to replace damaged or destroyed bone marrow with healthy bone marrow stem cells. Here is the latest research on bone and marrow transplantation.

Bioinformatics in Biomedicine

Bioinformatics in biomedicine incorporates computer science, biology, chemistry, medicine, mathematics and statistics. Discover the latest research on bioinformatics in biomedicine here.

Related Papers

Journal of Biomedical Informatics
Erik M van MulligenLaura I Furlong
Journal of Biomedical Informatics
Son DoanNigel Collier
Journal of Biomedical Informatics
Angus RobertsAndrea Setzer
© 2021 Meta ULC. All rights reserved