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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: [1]
       SHARPn Project: [2]
   Pharmacogenomics target predication of ADEs - a knowledge integration and discovery framework
       PGRN Phont project: [3]