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OAE: The Ontology of Adverse Events

Yongqun He, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao, Barry Smith
2014 Journal of Biomedical Semantics  
After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention.  ...  The representation and analysis of AEs are critical to the improvement of public health.  ...  We appreciate Darrell Abernethy and Keith Burkhart for their consultation in the domain of clinical adverse event reporting.  ... 
doi:10.1186/2041-1480-5-29 pmid:25093068 pmcid:PMC4120740 fatcat:fjkxotcponejphoy6u5s26xsmi

The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines

Erica Marcos, Bin Zhao, Yongqun He
2013 Journal of Biomedical Semantics  
To better represent and analyze VAEs, we developed the Ontology of Vaccine Adverse Events (OVAE) as an extension of the Ontology of Adverse Events (OAE) and the Vaccine Ontology (VO).  ...  Results: Like OAE and VO, OVAE is aligned with the Basic Formal Ontology (BFO). The commercial vaccines and adverse events in OVAE are imported from VO and OAE, respectively.  ...  Two existing ontologies are closely related to the VAE studies. The Ontology of Adverse Events (OAE) is a community-based biomedical ontology in the area of adverse events [2, 3] .  ... 
doi:10.1186/2041-1480-4-40 pmid:24279920 pmcid:PMC4177204 fatcat:nqsapfl7mzdqfay2zsrc7uwfee

Ontology-Based Classification and Analysis of Adverse Events Associated With the Usage of Chloroquine and Hydroxychloroquine

Jamie Ngai, Madison Kalter, James Brian Byrd, Rebecca Racz, Yongqun He
2022 Frontiers in Pharmacology  
or package inserts), the FDA Adverse Event Reporting System (FAERS), and peer-reviewed literature from PubMed/EMBASE, followed by AE classification and modeling using the Ontology of Adverse Events (OAE  ...  Multiple methodologies have been developed to identify and predict adverse events (AEs); however, many of these methods do not consider how patient population characteristics, such as diseases, age, and  ...  The Ontology of Adverse Events (OAE) is a community-based formal AE ontology designed to standardize and classify different types of AEs arising subsequent to medical interventions.  ... 
doi:10.3389/fphar.2022.812338 pmid:35401219 pmcid:PMC8983871 fatcat:m2fsg33rqngm5fq5oj64q3amra

Linking MedDRA®-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors

Sirarat Sarntivijai, Shelley Zhang, Desikan G. Jagannathan, Shadia Zaman, Keith K. Burkhart, Gilbert S. Omenn, Yongqun He, Brian D. Athey, Darrell R. Abernethy
2016 Drug Safety  
The ontology of adverse events (OAE) was extended with 884 additional clinical adverse event (AE) terms and correspondingly mapped to Medical Dictionary for Regulatory Activities (MedDRA Ò ) terms to classify  ...  The combination of MedDRA Ò and OAE in the TKI study provided the first use case of a semantic framework for linking clinical drug-AE phenotypes to biological processes and mechanisms.  ...  Acknowledgments The authors thank Zuoshuang Xiang for his programming assistance in building OAE. Compliance with Ethical Standards  ... 
doi:10.1007/s40264-016-0414-0 pmid:27003817 pmcid:PMC4933310 fatcat:5jpz5hhcdnhvzk3ndgq2etipdy

The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events

Yu Lin, Yongqun He
2014 Journal of Biomedical Semantics  
The OGSF framework was then applied in the area of vaccine adverse events (VAEs). Results: OGSF aligns with the Basic Formal Ontology (BFO).  ...  Due to human variations in genetic susceptibility, vaccination often triggers adverse events in a small population of vaccinees.  ...  The publication fee was paid by a discretionary fund from Dr. Robert Dysko, the director of the Unit  ... 
doi:10.1186/2041-1480-5-19 pmid:24963371 pmcid:PMC4068904 fatcat:bglnw4bebrhlrp6ervabhhjc2a

Towards precision informatics of pharmacovigilance: OAE-CTCAE mapping and OAE-based representation and analysis of adverse events in patients treated with cancer drugs

Mei U Wong, Rebecca Racz, Edison Ong, Yongqun He
2018 AMIA Annual Symposium Proceedings  
The Ontology of Adverse Events (OAE) is a community-based ontology in the domain of AEs. In this study, OAE was first updated by including AE severity grading and OAE-CTCAE mapping.  ...  A critical issue in the usage of cancer drugs is its association with various adverse events (AEs) in some, but not all, patients.  ...  Disclaimer This article reflects the views of the authors and should not be construed to represent FDA's views or policies.  ... 
pmid:29854250 pmcid:PMC5977606 fatcat:uxzaqxq4fvgtzgb25yi5pm5aeq

Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis

Cui Tao, Yongqun He, Hannah Yang, Gregory A Poland, Christopher G Chute
2012 Journal of Biomedical Semantics  
The Time Event Ontology (TEO), Ontology of Adverse Events (OAE), and Vaccine Ontology (VO) are leveraged for the semantic representation of this purpose.  ...  The U.S. FDA/CDC Vaccine Adverse Event Reporting System (VAERS) provides a valuable data source for post-vaccination adverse event analyses.  ...  Acknowledgements This project was supported by the National Science Foundation under Grant #0937060 and the National Center for Biomedical Ontologies (NCBO) to C.T. and the NIH-NIAID grant R01AI081062  ... 
doi:10.1186/2041-1480-3-13 pmid:23256916 pmcid:PMC3554604 fatcat:n5ae3wcnlnejfosmtdedctewki

Use of Biomedical Ontologies for Integration of Biological Knowledge for Learning and Prediction of Adverse Drug Reactions

Shadia Zaman, Sirarat Sarntivijai, Darrell R Abernethy
2017 Gene Regulation and Systems Biology  
The integration process is accommodated by biomedical ontologies, a set of standardized vocabularies that define terms and logical relationships between them in each vocabulary.  ...  adverse drug reactions will improve the capacity to understand drug-induced clinical adverse drug reactions.  ...  The Ontology of Adverse Events (OAE) was developed to represent adverse event data in an ontological format.  ... 
doi:10.1177/1177625017696075 pmid:28469412 pmcid:PMC5398297 fatcat:tioq5cn4rjaxzm22nf5s3246om

ODAE: Ontology-based systematic representation and analysis of drug adverse events and its usage in study of adverse events given different patient age and disease conditions

Hong Yu, Solomiya Nysak, Noemi Garg, Edison Ong, Xianwei Ye, Xiangyan Zhang, Yongqun He
2019 BMC Bioinformatics  
The Ontology of Adverse Events (OAE) has been widely used for adverse event AE representation, standardization, and analysis.  ...  Drug adverse events (AEs), or called adverse drug events (ADEs), are ranked one of the leading causes of mortality.  ...  The Ontology of Adverse Events (OAE) is a community-based biomedical ontology in the area of adverse events [22, 23] .  ... 
doi:10.1186/s12859-019-2729-1 fatcat:omdyll52e5e5xapauyirmax55q

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

Integrative representations and analyses of vaccine-induced intended protective immunity and unintended adverse events using ontology-based and theory-guided approaches

Yongqun He, Edison Ong, Jiangan Xie
2016 Global Vaccines and Immunology  
He Y (2016) Integrative representations and analyses of vaccine-induced intended protective immunity and unintended adverse events using ontology-based and theory-guided approaches  ...  Acknowledgements The development of VO, OAE, and OVAE was supported by an NIH NIAID grant 1R01AI081062. The development of VICO was supported by a MCubed fund at the University of Michigan.  ...  By extending VO and the Ontology of Adverse Events (OAE) [15] , OVAE effectively imports the information of vaccines and adverse events.  ... 
doi:10.15761/gvi.1000110 pmid:27868103 pmcid:PMC5111632 fatcat:46tigqbzpfcgdosrjiuo2hcfa4

Developing an Ontology for Documenting Adverse Events While Avoiding Pitfalls [chapter]

Stefanie Neuenschwander, Patricia Romao, Jürgen Holm, Murat Sariyar
2022 Studies in Health Technology and Informatics  
This work has the following two goals: to describe the development of the IOM ontology and to guide the practice with respect to documenting of biomedical events, as available ontologies pose difficulties  ...  of adverse events, (ii) covering diseases and injuries in a consistent way, and (iii) deciding on which level to define relations.  ...  With respect to the handling of events in our ontology, we initially relied on the OAE.  ... 
doi:10.3233/shti210885 pmid:35062118 fatcat:ckqkwngdabettdto4awfcnttse

A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012)

Yongqun He, Luca Toldo, Gully Burns, Cui Tao, Darrell R Abernethy
2012 Journal of Biomedical Semantics  
events), vaccine and drug adverse event text mining, and ontology-based Semantic Web applications.  ...  The workshop covered two main areas: (i) ontologies of vaccines, of drugs, and of studies thereof; and (ii) analysis of administration, mechanism and effect in terms of representations based on such ontologies  ...  We also appreciate the discussions, suggestions, and support from the co-organizers of another ICBO 2012 workshop titled "Methods for adverse events representation Ontology and Information Model", including  ... 
doi:10.1186/2041-1480-3-12 pmid:23249650 pmcid:PMC3554582 fatcat:zzkqbjxgavhszp4ku6m6ug2u3q

Ontology-based collection, representation and analysis of drug-associated neuropathy adverse events

Abra Guo, Rebecca Racz, Junguk Hur, Yu Lin, Zuoshuang Xiang, Lili Zhao, Jordan Rinder, Guoqian Jiang, Qian Zhu, Yongqun He
2016 Journal of Biomedical Semantics  
ODNAE extends the Ontology of Adverse Events (OAE). Our combinatorial approach identified 215 US FDA-licensed small molecule drugs that induce signs and symptoms of various types of neuropathy.  ...  Results: To support data representation and analysis of drug-associated neuropathy adverse events (AEs), we developed the Ontology of Drug Neuropathy Adverse Events (ODNAE).  ...  Jane Bai's help in discussion and data interpretation in the domain of neuropathy adverse events.  ... 
doi:10.1186/s13326-016-0069-x pmid:27213033 pmcid:PMC4875649 fatcat:pvg7ocuntffmhfpvk54nltdgqq

Ontology-Based Combinatorial Comparative Analysis of Adverse Events Associated with Killed and Live Influenza Vaccines

Sirarat Sarntivijai, Zuoshuang Xiang, Kerby A. Shedden, Howard Markel, Gilbert S. Omenn, Brian D. Athey, Yongqun He, Gary P. Kobinger
2012 PLoS ONE  
These AE terms were classified using the Ontology of Adverse Events (OAE), MedDRA, and SNOMED-CT. The OAE method provided better classification results than the two other methods.  ...  Different adverse event profiles induced by these two groups of seasonal influenza vaccines were studied based on the data drawn from the CDC Vaccine Adverse Event Report System (VAERS).  ...  Comparison of concept reorganization based on semantic similarity of the Ontology of Adverse Events (OAE) The OAE ( was previously named the Adverse Event Ontology (AEO) [  ... 
doi:10.1371/journal.pone.0049941 pmid:23209624 pmcid:PMC3509157 fatcat:vo2262aemndzpgb6nxjrryhiqe
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