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Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis
BACKGROUND: The 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 analyse...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3554604/ https://www.ncbi.nlm.nih.gov/pubmed/23256916 http://dx.doi.org/10.1186/2041-1480-3-13 |
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author | Tao, Cui He, Yongqun Yang, Hannah Poland, Gregory A Chute, Christopher G |
author_facet | Tao, Cui He, Yongqun Yang, Hannah Poland, Gregory A Chute, Christopher G |
author_sort | Tao, Cui |
collection | PubMed |
description | BACKGROUND: The 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. RESULTS: We 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. CONCLUSIONS: We 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. |
format | Online Article Text |
id | pubmed-3554604 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-35546042013-01-29 Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis Tao, Cui He, Yongqun Yang, Hannah Poland, Gregory A Chute, Christopher G J Biomed Semantics Research BACKGROUND: The 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. RESULTS: We 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. CONCLUSIONS: We 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. BioMed Central 2012-12-20 /pmc/articles/PMC3554604/ /pubmed/23256916 http://dx.doi.org/10.1186/2041-1480-3-13 Text en Copyright ©2012 Tao et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Tao, Cui He, Yongqun Yang, Hannah Poland, Gregory A Chute, Christopher G Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis |
title | Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis |
title_full | Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis |
title_fullStr | Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis |
title_full_unstemmed | Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis |
title_short | Ontology-based time information representation of vaccine adverse events in VAERS for temporal analysis |
title_sort | ontology-based time information representation of vaccine adverse events in vaers for temporal analysis |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3554604/ https://www.ncbi.nlm.nih.gov/pubmed/23256916 http://dx.doi.org/10.1186/2041-1480-3-13 |
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