ADEpedia: a scalable and standardized knowledge base of Adverse Drug Events using semantic web technology.

Research output: Contribution to journalArticle

Abstract

A source of semantically coded Adverse Drug Event (ADE) data can be useful for identifying common phenotypes related to ADEs. We proposed a comprehensive framework for building a standardized ADE knowledge base (called ADEpedia) through combining ontology-based approach with semantic web technology. The framework comprises four primary modules: 1) an XML2RDF transformation module; 2) a data normalization module based on NCBO Open Biomedical Annotator; 3) a RDF store based persistence module; and 4) a front-end module based on a Semantic Wiki for the review and curation. A prototype is successfully implemented to demonstrate the capability of the system to integrate multiple drug data and ontology resources and open web services for the ADE data standardization. A preliminary evaluation is performed to demonstrate the usefulness of the system, including the performance of the NCBO annotator. In conclusion, the semantic web technology provides a highly scalable framework for ADE data source integration and standard query service.

Original languageEnglish (US)
Pages (from-to)607-616
Number of pages10
JournalAMIA ... Annual Symposium proceedings / AMIA Symposium. AMIA Symposium
Volume2011
StatePublished - 2011
Externally publishedYes

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Knowledge Bases
Drug-Related Side Effects and Adverse Reactions
Semantics
Technology
Information Storage and Retrieval
Phenotype
Pharmaceutical Preparations

ASJC Scopus subject areas

  • Medicine(all)

Cite this

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title = "ADEpedia: a scalable and standardized knowledge base of Adverse Drug Events using semantic web technology.",
abstract = "A source of semantically coded Adverse Drug Event (ADE) data can be useful for identifying common phenotypes related to ADEs. We proposed a comprehensive framework for building a standardized ADE knowledge base (called ADEpedia) through combining ontology-based approach with semantic web technology. The framework comprises four primary modules: 1) an XML2RDF transformation module; 2) a data normalization module based on NCBO Open Biomedical Annotator; 3) a RDF store based persistence module; and 4) a front-end module based on a Semantic Wiki for the review and curation. A prototype is successfully implemented to demonstrate the capability of the system to integrate multiple drug data and ontology resources and open web services for the ADE data standardization. A preliminary evaluation is performed to demonstrate the usefulness of the system, including the performance of the NCBO annotator. In conclusion, the semantic web technology provides a highly scalable framework for ADE data source integration and standard query service.",
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