Our emphasis is on highlighting the key events in the field and pointing at promising research areas for the future. Ross, E. G., Jung, K., Dudley, J. T., Li, L., Leeper, N. J., Shah, N. H. Predicting Need for Advanced Illness or Palliative Care In A Primary Care Population Using Electronic Health Record Data. Most OBO constructs have easy and obvious equivalence to a construct in OWL. Agarwal, V., Zhang, L., Zhu, J., Fang, S., Cheng, T., Hong, C., Shah, N. H. Reply to R.L. HyQue hypotheses and data are available at http://semanticscience.org/projects/hyque. Promoting the use of simple, dictionary-based methods for population level analyses can advance adoption of NLP in practice. Dr. Shah graduated with distinction in biomedical engineering from Duke University, received his medical doctorate from Stanford University, and Masters in Public Health from Harvard University. After pre-filtering the associations by removing those found in public databases, we devised a ranking for associations based on the support from the remaining sources, and evaluated the results of this rank-based prioritization.We collected information for 5983 putative EHR-derived drug-drug-event associations involving 345 drugs and ten adverse events from four data sources and four prediction methods. Dr. Maulik Shah is a cardiologist practicing in Stanford, CA. View details for Web of Science ID 000251864600008. Of those, more than 73% lack supporting scientific evidence. This dataset can be leveraged to quantitatively assess comorbidity, drug-drug, and drug-disease patterns for a range of clinical, epidemiological, and financial applications. The association with allergy drugs when adjusted for known associations remained significant (OR 2.54, 95% CI 1.22-5.4).This study shows the potential of using a validated text analytics pipeline on clinical data warehouses to examine practice-based evidence for evaluating hypotheses formed during patient care. Propensity score-matched analysis (hazard ratio, 1.88; 95% CI, 1.10 to 3.20; P = .021) and traditional multivariable-adjusted Cox regression analysis (hazard ratio, 1.66; 95% CI, 1.05 to 2.64; P = .031) both supported a statistically significant association between ADT use and Alzheimer's disease risk. The Stanford Tissue Microarray Database (TMAD; http://tma.stanford.edu) is a public resource for disseminating annotated tissue images and associated expression data. StressDB provides small user groups with a locally installable web-based relational microarray database. In this paper, we quantify this trade-off among text processing systems that make different trade-offs between speed and linguistic understanding. Recent pre-clinical results suggest that this risk might extend to subjects without any prior history of cardiovascular disease. Bio Dr. Nirao Shah is a Professor of Psychiatry and Behavioral Sciences and of Neurobiology at Stanford University. Ling, A. Y., Kurian, A. W., Caswell-Jin, J. L., Sledge, G. W., Shah, N. H., Tamang, S. R. Finding missed cases of familial hypercholesterolemia in health systems using machine learning. More than two-thirds of the genes in the stress cDNA collection have not been identified in previous studies as stress/defense response genes. Lee, W., Raschid, L., Srinivasan, P., Shah, N., Rubin, D., Noy, N. Searching Ontologies Based on Content: Experiments in the Biomedical Domain. Dr. Shah is affiliated with Stanford … Prognostic models were developed on training data available in the first week of care to predict delayed healing wounds. View details for PubMedCentralID PMC6457095. Shah, N. H., King, D. C., Shah, P. N., Fedoroff, N. V. A contradiction-based framework for testing gene regulation hypotheses, Characterizing the stress/defense transcriptome of Arabidopsis. Our approach provides the basis for ontology-driven data integration for translational research on gene and protein expression data. Excellent physician and clinic staff. LIMIT represents a fast and inexpensive solution for calculating reference intervals, and shows that it is possible to use laboratory results and coded diagnoses to learn laboratory test reference intervals from clinical data warehouses. Shah, Manan P MD 300 Pasteur Dr Stanford CA 94304. Shah, N. H., Rubin, D. L., Supekar, K. S., Musen, M. A. Temporal evolution of the Arabidopsis oxidative stress response. We evaluate our approach using two different types of reference standards consisting of known adverse drug events (ADEs) and negative controls. The Lexicon Builder promotes collaboration, sharing and standardization of lexicons amongst researchers by automating the creation, maintainence and cross referencing of custom lexicons. Although countless highly penetrant variants have been associated with Mendelian disorders, the genetic etiologies underlying complex diseases remain largely unresolved. Ross, E., Jung, K., Dudley, J. T., Li, L., Leeper, N. J., Shah, N. H. Predicting Future Cardiovascular Events in Patients With Peripheral Artery Disease Using Electronic Health Record Data. Demonstrated empathy. A significant section of UMLS users use a MySQL installation of the metathesaurus and Perl programming language as their access mechanism. The collection of multiple genome-scale datasets is now routine, and the frontier of research in systems biology has shifted accordingly. In this work we generalize our methods to map text annotations of gene expression datasets to concepts in the UMLS. We demonstrate the use of the resulting high-throughput data for detecting drug-adverse event associations and adverse events associated with drug-drug interactions. Detecting skin adverse reactions by analyzing content in a health social network.Finding drug adverse events, and drug-drug interactions by analyzing using clinical notes; and developing weakly supervised methods for medical device surveillance. Gombar, S., Chang, M., Hogan, C. A., Zehnder, J., Boyd, S., Pinsky, B. We are interested in understanding the biological basis of physiological and behavioral differences between men and women. Dr. Shah received his undergraduate degrees from Stanford University, where he graduated with distinction with degrees in Economics and Biological Sciences. Soldatova, L. N., Lord, P., Sansone, S., Stephens, S. M., Shah, N. H. Optimize First, Buy Later: Analyzing Metrics to Ramp-Up Very Large Knowledge Bases. These conditions include heart attacks, heart murmurs, coronary heart disease, and hypertension. In our opinion the NCI thesaurus can facilitate integration of this resource with other biological data. Dr. Nirao Shah is a Professor of Psychiatry and Behavioral Sciences and of Neurobiology at Stanford University. Datamining methods that can transform data into meaningful knowledge to inform patient safety have proven essential for this purpose. View details for DOI 10.1136/amiajnl-2011-000631, View details for Web of Science ID 000314151400029, View details for PubMedCentralID PMC3392849. Undetected adverse drug reactions (ADRs) pose a major burden on the health system. In conclusion, in this open-label, cross-over pilot study conducted among healthy subjects and coronary disease patients, PPI use did not significantly influence vascular endothelial function. We demonstrate how this mapping enables ontology driven integration and querying of tissue microarray data. The results suggest that leveraging nontraditional sources such as online search logs could supplement existing pharmacovigilance approaches. While progress has recently been made in developing such benchmarks, our understanding of the performance characteristics of the data mining methodologies is limited because existing benchmarks do not support prospective performance evaluations. Such a method implies to specify an initial set of seed concepts, which are based on concept unique identifiers. However, this annotation process cannot be easily automated and often requires expert curators. Response to "Logistic regression in signal detection: another piece added to the puzzle". Choice of training ground for evidence-based pharmacovigilance". Wiley, L. K., Tarczy-Hornoch, P., Denny, J. C., Freimuth, R. R., Overby, C. L., Shah, N., Martin, R. D., Sarkar, I. N. Predicting hospital visits from geo-tagged Internet search logs. Oellrich, A., Collier, N., Groza, T., Rebholz-Schuhmann, D., Shah, N., Bodenreider, O., Boland, M. R., Georgiev, I., Liu, H., Livingston, K., Luna, A., Mallon, A., Manda, P., Robinson, P. N., Rustici, G., Simon, M., Wang, L., Winnenburg, R., Dumontier, M. Impact of Predicting Health Care Utilization Via Web Search Behavior: A Data-Driven Analysis. We describe, RANSUM - Rich Annotation Summarizer - which performs enrichment analysis using any ontology in the National Center for Biomedical Ontology's (NCBO) BioPortal. Liu, Y., LePendu, P., Iyer, S., Shah, N. H. Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting. Such a comparison can offer insight on the validity of different approaches. The biomedical community can use the annotator service to tag datasets automatically with ontology terms (from UMLS and NCBO BioPortal ontologies). View details for DOI 10.1161/CIRCULATIONAHA.113.003602. Dr. Hema Shah, M.D., is an Internal Medicine Doctor practicing in San Mateo, CA. Using a de-identified dataset of geo-tagged mobile Internet search logs, we mined text and location patterns that are predictors of healthcare resource utilization and built statistical models that predict the probability of a user's future visit to a medical facility. View details for DOI 10.1136/amiajnl-2011-000744, View details for Web of Science ID 000314151400025, View details for PubMedCentralID PMC3392861. Get directions, reviews and information for Shah, Manan P MD in Stanford, CA. The Unstructured Information Management Architecture (UIMA) framework and web services are emerging as useful tools for integrating biomedical text mining tools. Influence of age on androgen deprivation therapy-associated Alzheimer's disease. These data provide an example of how a combination of experimental studies and data-mining approaches can be applied to prioritize drug safety signals for further investigation. The Annotator also leverages the hierarchical structure of the ontologies and their mappings to expand annotations. Vashisht, R., Jung, K., Schuler, A., Banda, J. M., Park, R. W., Jin, S., Li, L., Dudley, J. T., Johnson, K. W., Shervey, M. M., Xu, H., Wu, Y., Natrajan, K., Hripcsak, G., Jin, P., Van Zandt, M., Reckard, A., Reich, C. G., Weaver, J., Schuemie, M. J., Ryan, P. B., Callahan, A., Shah, N. H. Association of Hemoglobin A1c Levels With Use of Sulfonylureas, Dipeptidyl Peptidase 4 Inhibitors, and Thiazolidinediones in Patients With Type 2 Diabetes Treated With MetforminAnalysis From the Observational Health Data Sciences and Informatics Initiative. Over the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. BioPortal also enables integrated search of biomedical data resources such as the Gene Expression Omnibus (GEO), ClinicalTrials.gov, and ArrayExpress, through the annotation and indexing of these resources with ontologies in BioPortal. For example, by annotating known protein mutations with disease terms from the ontologies in BioPortal, Mort et al. The models use commonly available data on diagnosis, medication, and clinical progress notes, making them easily portable. After MEDLINE frequency-based filtering, the augmented UMLS Metathesaurus contains 518,835 terms and is roughly 13% of its original size. Androgen Deprivation Therapy and Future Alzheimer's Disease Risk. Hernandez-Boussard, T., Tamang, S., Blayney, D., Brooks, J., Shah, N. Harnessing next-generation informatics for personalizing medicine: a report from AMIA's 2014 Health Policy Invitational Meeting. Bowen et al, M. Froehner et al, J.L. Patterns in general consumer online search logs have been used to monitor health conditions and to predict health-related activities, but the multiple contexts within which consumers perform online searches make significant associations difficult to interpret. Finlayson, S. G., LePendu, P., Shah, N. H. Building the graph of medicine from millions of clinical narratives. View details for DOI 10.1007/s11103-005-2860-4, View details for Web of Science ID 000231220400007, Experimental design, hypothesis-testing and model-building in the current data-rich environment require the biologists' to collect, evaluate and integrate large amounts of information of many disparate kinds. Disease status is often summarized by repeated recordings of one or more physiological measures. The files in ways that can produce accurate signals of novel methods to compile a database statistically! Schuler, A., Steinberg, E., Fries, J adjusted disproportionality to! 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