CLASSES INSTRUCTED (100 series represents upper division, 200 series represents graduate We explain how the integration and validation steps spring from a Bayesian description of network uncertainty, and conclude by describing an important near-term milestone for systems biology: the construction of a set of rich reference networks for key model organisms. Finally, four temporal trends are identified among research topics.This work utilizes disease ontology (DO)-based annotation to profile effectively the landscape of biomedical research activity. Laurence Baker. These methods have broad application for quality improvement efforts in which events of interest occur outside of a network that allows for patient data sharing. Pannu, J., Poole, S., Shah, N., Shah, N. H. Enhanced Quality Measurement Event Detection: An Application to Physician Reporting. Recently, advances in clinical text processing and the increasing availability of clinical data have enabled analogous analyses on data from electronic medical records. Gallego, B., Walter, S. R., Day, R. O., Dunn, A. G., Sivaraman, V., Shah, N., Longhurst, C. A., Coiera, E. Proton Pump Inhibitor Usage and the Risk of Myocardial Infarction in the General Population. Off-label drug use, defined as use of a drug in a manner that deviates from its approved use defined by the drug's FDA label, is problematic because such uses have not been evaluated for safety and efficacy. Second, we analyze a small (N=1746), local dataset documenting the clinical progression of autism spectrum disorder patients using granular features from the electronic health record, including text from physician notes. O. FFICE ADDRESS: Stanford Center for Biomedical Informatics Research . The ability to automatically determine severity can facilitate assembly of large patient cohorts with similar severity from multiple sites, which may enable elucidation of the moderators of treatment response in the future. Recent pre-clinical results suggest that this risk might extend to subjects without any prior history of cardiovascular disease. endstream endobj startxref A., Sunshine, J. Profiling risk factors for chronic uveitis in juvenile idiopathic arthritis: a new model for EHR-based research. HyQue features a knowledge model to accommodate diverse hypotheses structured as events and represented using Semantic Web languages (RDF/OWL). A small subset of OBO constructs requires deeper consideration. The result is an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality. However, the number of putative associations produced by such computational approaches is typically large, making experimental validation difficult. The papers span a wide range of topics including practical solutions for data and knowledge integration for translational medicine, hypothesis based querying , understanding kidney and urinary pathways, mining the pharmacogenomics literature; theoretical research into the orthogonality of biomedical ontologies, the representation of diseases, the representation of research hypotheses, the combination of ontologies and natural language processing for an annotation framework, the generation of textual definitions, and the discovery of gene interaction networks. View details for DOI 10.1186/2041-1480-1-S1-S1, View details for PubMedCentralID PMC2903720. Our extracted relationships have a 70-87.7% precision and involve not only key PGx entities such as genes, drugs, and phenotypes (e.g., VKORC1, warfarin, clotting disorder), but also critical entities that are frequently modified by these key entities (e.g., VKORC1 polymorphism, warfarin response, clotting disorder treatment). Only seven drug-drug-event associations (<0.5 %) had support from the majority of evidence sources, and about one third (1777) had support from at least one of the evidence sources.Our proof-of-concept method for scoring putative drug-drug-event associations from EHRs offers a systematic and reproducible way of prioritizing associations for further study. More information about Neil Shah. While GO has been the principal target for enrichment analysis, the methods of enrichment analysis are generalizable. We can aggregate the annotating GO concepts for each gene in this list, and arrive at a profile of the biological processes or mechanisms affected by the condition under study. Kannan, A., Fries, J. We consider that this approach can be extended to support other domains such as cohort building tools.
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