ADEpedia Project Description
Standardization and Knowledge Base
- FDA SPL-based ADE Knowledge Extraction: 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 the ontology-based approach with the 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.
- Medications - Normalized by RxNorm Codes
- ADEs - Normalized using SNOMED CT and MedDRA codes
- EMR/UMLS-based ADE Knowledge Extraction: A standardized Adverse Drug Events (ADEs) knowledge base that encodes known ADE knowledge can be very useful in improving ADE detection for drug safety surveillance. In the ADEpedia 2.0, the objectives of the study are
- 1) to integrate normalized ADE knowledge from the Unified Medical Language System (UMLS) into the ADEpedia; and
- 2) to enrich the knowledge base with the drug-disorder co-occurrence data from a 51-million-document electronic medical records (EMRs) system. Please see our preliminary results at here.
- FDA AERS-based ADE Knowledge Extraction
- To normalize the AERS reporting data using biomedical ontologies - RxNorm, NDF-RT, MedDRA and UMLS
- To build a severe ADE knowledgebase based on the AERS reporting data and associated outcome codes
- Preliminary results (Cardiac disorders|10007541) - An ADE severity classification based on CTCAE in the Web Ontology Language (OWL) is available at here.
Use Cases and Applications
- Clinical Phenotyping of ADEs -
- Mayo CTSA related project: http://informatics.mayo.edu/adephont/index.php/Main_Page
- SHARPn Project: http://informatics.mayo.edu/sharp/index.php/Main_Page
- Pharmacogenomics target predication of ADEs - a knowledge integration and discovery framework
- PGRN Phont project: http://informatics.mayo.edu/phont/index.php/Main_Page
- Any questions or comments about the ADEpedia, please contact Guoqian Jiang, M.D., Ph.D. by email: jiang.guoqian at mayo.edu.
Publications & Manuscripts in Submission
- Jiang G, Solbrig HR, Chute CG. ADEpedia: a scalable and standardized knowledge base of Adverse Drug Events using semantic web technology. AMIA Annu Symp Proc. 2011; 2011:607-16. Epub 2011 Oct 22. PMID:22195116. PMCID:3243176. See PubMed citation here.
- Jiang G, Duke JD, Pathak J, Chute CG. An ontological representation of adverse drug events. Proceedings of ICBO - International Conference on Biomedical Ontology Representing Adverse Events Workshop. Buffalo NY. July 26, 2011:329-331. See full manuscript in PDF here; And the slides in PDF here.
- Tao C, Jiang G, Clark KK, Sharma DK, Chute CG. Toward Answering Time-Related Questions from Adverse Event Reports Using Ontology-based Approaches. International Conference on Biomedical Ontologies: Representing Adverse. 2011 Jul. See full manuscript in PDF here; And the slides in PDF here.
- Zhu Q, Jiang G, Chute CG. Profiling Structured Product Labeling Using NDF-RT and RxNorm . Proceedings of International Workshop on Vaccine and Drug Ontology in the Study of Mechanism and Effect (VDOSME) in ICBO 2012 - International Conference on Biomedical Ontology. Graz, Austria. July 21-25, 2012. See full manuscript in PDF here. And see the slides in PDF here.
- Zhu Q, Jiang G, Chute CG. A Standardized Drug and Drug Class Universal Network. AMIA Annu Symp Proc. 2012. (In Press)
- Wang L, Jiang G, Wang W, Liu H. A Preliminary Study on Normalizing AERS Drug Names Using RxNorm. AMIA Annu Symp Proc. 2012. (In Press)
- Tao C, Zhang Y, Jiang G, Bouamrane MM, Chute CG. Optimizing Semantic MEDLINE for Translational Science Studies Using Semantic Web Technologies. Proceedings of the Second International Workshop on Managing Interoperability and compleXity in Health Systems (MIXHS 2012). October 29, 2012. Maui, HI. (see here)
- Jiang G, Liu H, Solbrig HR, Chute CG. ADEpedia 2.0: Integration of Normalized Adverse Drug Events (ADEs) Knowledge from the UMLS. AMIA CRI Summit 2013. (Paper)(In Press).
- Jiang G, Wang C, Zhu Q, Chute CG. A Framework of Knowledge Integration and Discovery for Supporting Pharmacogenomics Target Predication of Adverse Drug Events: A Case Study of Drug-Induced Long QT Syndrome. AMIA TBI Summit 2013. (Paper) (In Press).
- Zhang Y, Tao C, Jiang G, Nair AA, Su J. Network-based Analysis Reveals Distinct Association Patterns in a Semantic MEDLINE-based Drug-Gene-Disease Network. AMIA TBI Summit 2013. (Poster) (In Press).
- Jiang G, Wang L, Liu HF, Solbrig HR, Chute CG. Building a knowledge base of severe adverse drug events based on AERS reporting data using semantic web technologies. MedInfo 2013. (Paper) (In Press).
- Zhu Q, Jiang G, Wang L, Chute CG. Standardized drug and pharmacological class network construction. MedInfo 2013. (Abstract) (In Press)
- Wang L, Jiang G, Li DC, Liu HF. Standardizing Drug Adverse Event Reporting Data. MedInfo 2013. (Abstract) (In Press)
- Wang L, Jiang G, Li DC, Liu HF. Standardizing Drug Adverse Event Reporting Data. JAMIA. (In Submission)