ArticleJournal of biomedical semantics2012
Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis.
Article in Journal of biomedical semantics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
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Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Computational Advances in Drug Safety: Systematic and Mapping Review of Knowledge Engineering Based Approaches.Frontiers in pharmacology · 2019Pooled it
- Lessons learned from annotation of VAERS reports on adverse events following influenza vaccination and related to Guillain-Barré syndrome.BMC medical informatics and decision making · 2024Article
- COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning.Briefings in bioinformatics · 2022Article
- Temporal Expression Classification and Normalization From Chinese Narrative Clinical Texts: Pattern Learning Approach.JMIR medical informatics · 2020Article
- Time event ontology (TEO): to support semantic representation and reasoning of complex temporal relations of clinical events.Journal of the American Medical Informatics Association : JAMIA · 2020Article
- A 2018 workshop: vaccine and drug ontology studies (VDOS 2018).BMC bioinformatics · 2019Article
- 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.BMC bioinformatics · 2019Article
- A pattern learning-based method for temporal expression extraction and normalization from multi-lingual heterogeneous clinical texts.BMC medical informatics and decision making · 2018Article
- Use of Biomedical Ontologies for Integration of Biological Knowledge for Learning and Prediction of Adverse Drug Reactions.Gene regulation and systems biology · 2017Review
- Linking MedDRA(®)-Coded Clinical Phenotypes to Biological Mechanisms by the Ontology of Adverse Events: A Pilot Study on Tyrosine Kinase Inhibitors.Drug safety · 2016Article
- OAE: The Ontology of Adverse Events.Journal of biomedical semantics · 2014Article
- A 2012 Workshop: Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME 2012).Journal of biomedical semantics · 2012Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelled
backgroundThe U.S. FDA/CDC Vaccine Adverse Event Reporting System (VAERS) provides a valuable data source for post-vaccination adverse event analyses. The structured data in the system has been widely used, but the information in the write-up narratives is rarely included in these kinds of analyses. In fact, the unstructured nature of the narratives makes the data embedded in them difficult to be used for any further studies.
resultsWe developed an ontology-based approach to represent the data in the narratives in a "machine-understandable" way, so that it can be easily queried and further analyzed. Our focus is the time aspect in the data for time trending analysis. The Time Event Ontology (TEO), Ontology of Adverse Events (OAE), and Vaccine Ontology (VO) are leveraged for the semantic representation of this purpose. A VAERS case report is presented as a use case for the ontological representations. The advantages of using our ontology-based Semantic web representation and data analysis are emphasized.
conclusionsWe believe that representing both the structured data and the data from write-up narratives in an integrated, unified, and "machine-understandable" way can improve research for vaccine safety analyses, causality assessments, and retrospective studies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.