A., Abeliuk, E., Novak, A. F., Batzoglou, S. Annotation and query of tissue microarray data using the NCI Thesaurus. We also propose an approach and demonstrate its application in identifying optimal signaling thresholds, given specific misclassification tolerances. His academic interests also include digital health technologies and novel healthcare delivery services, both in the domestic and international setting. Toward multimodal signal detection of adverse drug reactions. Therefore, analyzing patterns of off-label drug usage in the clinical setting is an important step toward reducing the incidence of adverse events and for improving patient safety. via phone at (650) 723-4000. Lee, W., Raschid, L., Srinivasan, P., Shah, N., Rubin, D., Noy, N. Searching Ontologies Based on Content: Experiments in the Biomedical Domain. These text annotations are not structured according to any ontology, making future integration of this resource with other biological and clinical data difficult.We developed methods to map these annotations to the NCI thesaurus. Our goals were: 1. analyze the frequency and syntactic distribution of Metathesaurus terms in MEDLINE; 2. create a filtered UMLS Metathesaurus based on the MEDLINE analysis; 3. augment the UMLS Metathesaurus where each term is associated with metadata on its MEDLINE frequency and syntactic distribution statistics. Wounds were split into training and test sets by randomly assigning patients to training and test sets. 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. Lependu, P., Iyer, S. V., Bauer-Mehren, A., Harpaz, R., MORTENSEN, J. M., Podchiyska, T., Ferris, T. A., Shah, N. H. Combing signals from spontaneous reports and electronic health records for detection of adverse drug reactions. Dr. Shah was elected into the American College of Medical Informatics (ACMI) in 2015 and is inducted into the American Society for Clinical Investigation (ASCI) in 2016. Advanced statistical methods used to analyze high-throughput data (e.g. Stanford University pathologists, researchers and their collaborators worldwide use TMAD for designing, viewing, scoring and analyzing their tissue microarrays. Having more than 15 years of diverse experiences, especially in GASTROENTEROLOGY, INTERNAL MEDICINE, Dr. Atul T Shah affiliates with Stanford Health Care, cooperates with many other doctors and specialists in medical group Stanford Health Care. Of these, 31 306 images for 68 probes on 125 slides have been released to the public. The objective of this review is to give an overview of biomedical ontology in practical terms by providing a functional perspective--describing how bio-ontologies can and are being used. Dr. Jung, K., Sudat, S. E., Kwon, N., Stewart, W. F., Shah, N. H. Early Detection of Adverse Drug Reactions in Social Health Networks: A Natural Language Processing Pipeline for Signal Detection. Dr. Maulik Shah is a cardiologist practicing in Stanford, CA. Nonetheless, further research is required to address remaining technical challenges associated with the text mining methodologies, and to conclusively determine the relative contribution of each textual source to improving pharmacovigilance. Traditionally, phenotypes have been discovered by intuition, experience in practice, and advancements in basic science, but these approaches are often heuristic, labor intensive, and can take decades to produce actionable knowledge. I tend to feel a little rushed. In one subtask, REVEAL achieved higher sensitivity with smaller datasets.For a variety of tasks, employing simple term recognition methods instead of advanced NLP methods results in little or no impact on accuracy when using large datasets. This set of stress-, pathogen- and hormone-modulated genes is an important resource for understanding the genetic interactions underlying stress signaling and responses and may contribute to the characterization of the stress transcriptome through the construction of standardized specialized arrays. Eighty-seven of them (36%) are supported in at least one of the resources that have information that was not available to the classifier.This method demonstrates the feasibility of systematic post-marketing surveillance for ADEs using electronic medical records, a key component of the learning healthcare system. Dr. Gill & Dr. Shah have been wonderful throughout this journey thus far. View details for DOI 10.1186/1471-2105-7-196, View details for Web of Science ID 000239302400001, View details for PubMedCentralID PMC1522024. We demonstrate the HyBrow prototype using the galactose gene network in Saccharomyces cerevisiae as our test system, and evaluate alternative hypotheses for consistency with stored information.www.hybrow.org, View details for DOI 10.1093/bioinformatics/bth905, View details for Web of Science ID 000208392400034, Analysis of microarray data most often produces lists of genes with similar expression patterns, which are then subdivided into functional categories for biological interpretation. To understand the gene networks that underlie plant stress and defense responses, it is necessary to identify and characterize the genes that respond both initially and as the physiological response to the stress or pathogen develops. Interpretation errors related to the GO annotation file format. Evaluation demonstrates that the service has high accuracy and runtime performance. Profiling the allocation and trend of research activity is of interest to funding agencies, administrators, and researchers. : Ontology-driven indexing of public datasets for translational bioinformatics. According to Dr. Shah, "I like the osteopathic philosophy, which is to treat a patient as a whole person -- their mind, body, and spirit -- … Be sure to call ahead with Dr. Shah to book an appointment. White, R. W., Tatonetti, N. P., Shah, N. H., Altman, R. B., Horvitz, E. Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting. Coulet, A., Shah, N., Hunter, L., Barral, C., Altman, R. B. Coulet, A., Garten, Y., Dumontier, M., Altman, R. B., Musen, M. A., Shah, N. H. NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources. Factors such as acute kidney disorder and liver disorder were predictive of first line therapy choices. Having more than 15 years of diverse experiences, especially in GASTROENTEROLOGY, INTERNAL MEDICINE, Dr. Atul T Shah affiliates with Stanford Health Care, cooperates with many other doctors and specialists in medical group Stanford Health Care. Verghese, A., Shah, N. H., Harrington, R. Accurate and interpretable intensive care risk adjustment for fused clinical data with generalized additive models. Two performance classes emerge, indicating that the class of approaches that address confounding and masking effects benefits safety surveillance. The seven papers selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data from wikis, innovative methods of annotating and mining electronic health records, advances in annotating web documents and biomedical literature, quality control of ontology alignments, and the ontology support for predictive models about toxicity and open access to the toxicity data. We utilize a number of data sources and dictionaries to evaluate the concept recognizers in terms of precision, recall, speed of execution, scalability and customizability. B., Hinchcliff, M., Denny, J., Kaminski, N., Herazo-Maya, J. D., Shah, N. H., Khatri, P. It is time to learn from patients like mine. We have previously developed methods to map text-annotations of tissue microarrays to concepts in the NCI thesaurus and SNOMED-CT. The funding profiles of disease topics readily cluster themselves in agreement with the ontology hierarchy and closely mirror the funding agency priorities. The Annotator also leverages the hierarchical structure of the ontologies and their mappings to expand annotations. These annotations are not mapped to concepts in any ontology, making it difficult to integrate these datasets across repositories. Payne, P. O., Shah, N. H., Tenenbaum, J. D., Mangravite, L., Altman, R. B., Dunker, A. K., Hunter, L., Ritchie, M. D., Murray, T., Klein, T. E. Addressing vital sign alarm fatigue using personalized alarm thresholds. He graduated with honors from Columbia University College Of Physicians And Surgeons in 2002. Miner, A. S., Shah, N., Bullock, K. D., Arnow, B. LIMIT was developed using sodium serum levels, and validated using potassium serum levels, both tests for which harmonized reference intervals already exist. Demonstrated empathy. Hernandez-Boussard, T., Bozkurt, S., Ioannidis, J. P., Shah, N. H. Measure what matters: Counts of hospitalized patients are a better metric for health system capacity planning for a reopening. Such a method implies to specify an initial set of seed concepts, which are based on concept unique identifiers. Racunas, S. A., Shah, N. H., Albert, I., Fedoroff, N. V. HyBrow: a prototype system for computer-aided hypothesis evaluation, CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology, A finite model theory for biological hypotheses, A tool-kit for cDNA microarray and promoter analysis. Gallego, B., Walter, S. R., Day, R. O., Dunn, A. G., Sivaraman, V., Shah, N., Longhurst, C. A., Coiera, E. A time-indexed reference standard of adverse drug reactions. Tomczak, A., Mortensen, J. M., Winnenburg, R., Liu, C., Alessi, D. T., Swamy, V., Vallania, F., Lofgren, S., Haynes, W., Shah, N. H., Musen, M. A., Khatri, P. U-Index, a dataset and an impact metric for informatics tools and databases. Information », Insurance We consider that this approach can be extended to support other domains such as cohort building tools. We describe a data-mining approach for systematically identifying off-label usages using features derived from free text clinical notes and features extracted from two databases on known usage (Medi-Span and DrugBank). 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. The lack of standard reporting for experiment variables and results also makes experiment replicability a significant challenge. The Stanford Tissue Microarray Database (TMAD) is a repository of data serving a consortium of pathologists and biomedical researchers. To address these challenges, we have developed RegenBase, a knowledge base of SCI biology. We demonstrate that we enable ontology-based querying and integration of tissue and gene expression microarray data. He works in Palo Alto, CA and specializes in Medical Oncology. Such functional categorization is most commonly accomplished using Gene Ontology (GO) categories. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or 'ontologies'. Stanford, California 500+ connections. Such data mining can be used for hypothesis generation and for rapid analysis of suspected adverse event risk. Utilization of COVID-19 treatments and clinical outcomes among patients with cancer: A COVID-19 and Cancer Consortium (CCC19) cohort study. Caswell-Jin, J., Callahan, A., Purington, N., Han, S. S., Itakura, H., Sledge, G. W., Shah, N., Kurian, A. W. Development and validation of phenotype classifiers across multiple sites in the observational health data sciences and informatics network. The duration of ADT use was also tested for association with Alzheimer's disease risk.There were 16,888 individuals with prostate cancer meeting all inclusion and exclusion criteria, with 2,397 (14.2%) receiving ADT during a median follow-up period of 2.7 years (interquartile range, 1.0-5.4 years). The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. Our efforts will enable the development of innovative methods for modeling and optimizing the use of healthcare resources-a crucial prerequisite for securing healthcare access for everyone in the days to come. Shah, Manan P MD 300 Pasteur Dr Stanford CA 94304. Menu & Reservations Make Reservations . Ransohoff, J. D., Nikfarjam, A., Jones, E., Loew, B., Kwong, B. Y., Sarin, K. Y., Shah, N. H. Inferring Physical Function from Wearable Activity Monitors: Analysis of Activity Data from Patients with Knee Osteoarthritis. The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content by providing features to add notes to ontology terms, mappings between terms and ontology reviews based on criteria such as usability, domain coverage, quality of content, and documentation and support. By mining the medical records of over 110 million patients, we examine the extent to which Mendelian variation contributes to complex disease risk. The trade-off between the speed and simplicity of dictionary-based term recognition and the richer linguistic information provided by more advanced natural language processing (NLP) is an area of active discussion in clinical informatics. Response to letters regarding article, "unexpected effect of proton pump inhibitors: elevation of the cardiovascular risk factor asymmetric dimethylarginine". It has been implemented in Java for support on Mac OS X, Linux and MS Windows. Dr. Shah received his undergraduate degrees from Stanford University, where he graduated with distinction with degrees in Economics and Biological Sciences. Srinivasan, B. S., Shah, N. H., Flannick, J. Thus, BioPortal not only provides investigators, clinicians, and developers 'one-stop shopping' to programmatically access biomedical ontologies, but also provides support to integrate data from a variety of biomedical resources. Specifically, we extracted International Classification of Diseases-9th revision diagnosis and Current Procedural Terminology codes, medication lists, and positive-present mentions of drug and disease concepts from all clinical notes. Dr. Shah is affiliated with Stanford Hospital and UCSF Medical Center Parnassus. Gender: Male. Callahan, A., Fries, J. However, their performance characteristics are generally unknown. We also observed a statistically significant increased risk of Alzheimer's disease with increasing duration of ADT (P = .016).Our results support an association between the use of ADT in the treatment of prostate cancer and an increased risk of Alzheimer's disease in a general population cohort. Jonquet, C., Lependu, P., Falconer, S., Coulet, A., Noy, N. F., Musen, M. A., Shah, N. H. Mapping between the OBO and OWL ontology languages. Be sure to call ahead with Dr. Shah to book an appointment. Nead, K. T., Gaskin, G., Chester, C., Swisher-McClure, S., Dudley, J. T., Leeper, N. J., Shah, N. H. Association Between Androgen Deprivation Therapy and Risk of Dementia. Biological databases and pathway knowledge-bases are proliferating rapidly. Residual text features were then used in unsupervised hierarchical clustering to compare clinical text similarity between patients with and without uveitis.Previously reported associations with uveitis in juvenile idiopathic arthritis patients (earlier age at arthritis diagnosis, oligoarticular-onset disease, antinuclear antibody status, history of psoriasis) were reproduced in our study. Assessing the accuracy of automatic speech recognition for psychotherapy. The reference standard was systematically curated from drug labeling revisions, such as new warnings, which were issued and communicated by the US Food and Drug Administration in 2013. We explore this potential risk in the general population via data-mining approaches.Using a novel approach for mining clinical data for pharmacovigilance, we queried over 16 million clinical documents on 2.9 million individuals to examine whether PPI usage was associated with cardiovascular risk in the general population.In multiple data sources, we found gastroesophageal reflux disease (GERD) patients exposed to PPIs to have a 1.16 fold increased association (95% CI 1.09-1.24) with myocardial infarction (MI). They answer all our questions. To date, 12 publications have been based on these raw public data. Androgen Deprivation Therapy and Future Alzheimer's Disease Risk. Adverse drug events (ADEs) are undesired harmful effects resulting from use of a medication, and occur in 30% of hospitalized patients. Dr. Shah's research focuses on combining machine learning and prior knowledge in medical ontologies to enable use cases of the learning health Information for Dr. Neena Shah at Stanford Children's Health. Confronted with rapidly accumulating data, researchers currently do not have the software tools to undertake the required information integration tasks.We present HyQue, a Semantic Web tool for querying scientific knowledge bases with the purpose of evaluating user submitted hypotheses. Although it is possible to perform enrichment analysis using ontologies other than the GO, a key pre-requisite is the availability of a background set of annotations to enable the enrichment calculation. Similar Physicians & HCPs. The Stanford Tissue Microarray Database (TMAD) is a repository of data amassed by a consortium of pathologists and biomedical researchers. We tested both types of systems in three clinical research tasks: phase IV safety profiling of a drug, learning adverse drug-drug interactions, and learning used-to-treat relationships between drugs and indications.We first benchmarked the accuracy of the NCBO Annotator and REVEAL in a manually annotated, publically available dataset from the 2008 i2b2 Obesity Challenge. Features intrinsic to Metathesaurus terms (well formedness, length and language) generalise easily across clinical institutions, but term frequencies should be adapted with caution. Treatment guidelines for management of type-2 diabetes mellitus (T2DM) are controversial because existing evidence from randomized clinical trials do not address many important clinical questions. To accelerate phenotype discovery, researchers have used machine learning to find patterns in electronic health records, but have often been thwarted by missing data, sparsity, and data heterogeneity. We also find that the majority of associations in the reference sets have support in the search log data. A reference standard of over 600 established and plausible ADRs was created and used to evaluate the proposed approach against a comparator.The combined signaling system achieved a statistically significant large improvement over AERS (baseline) in the precision of top ranked signals. We describe, RANSUM - Rich Annotation Summarizer - which performs enrichment analysis using any ontology in the National Center for Biomedical Ontology's (NCBO) BioPortal. We investigated how EMR-based text mining and statistical analysis could elucidate the phenotypic boundaries of three important neuropsychiatric illnesses-autism, bipolar disorder, and schizophrenia.We analyzed the medical records of over 7000 patients at two facilities using an automated text-processing pipeline to annotate the clinical notes with Unified Medical Language System codes and then searching for enriched codes, and associations among codes, that were representative of the three disorders. View details for DOI 10.1186/2041-1480-3-S1-S5, View details for PubMedCentralID PMC3337270. Ghazvinian, A., Noy, N. F., Jonquet, C., Shah, N., Musen, M. A. He said, "Let us do the work, you just come to the appts.". The most promising aspect of this approach consists in the discovery of positive results not present our Obesity NLP reference set.Together with a Web graphical user interface, our FCA and SQE cooperation end up being an efficient approach for refining health outcome of interest using plain terms. Characterizing treatment pathways at scale using the OHDSI network. The seven papers and the commentary selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data, annotating patent records, NCBO Web services, ontology developments for probabilistic reasoning and for physiological processes, and analysis of the progress of annotation and structural GO changes. Soldatova, L. N., Sansone, S., Dumontier, M., Shah, N. H. STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. 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. Burn, E., You, S. C., Sena, A. G., Kostka, K., Abedtash, H., Abrahao, M. T., Alberga, A., Alghoul, H., Alser, O., Alshammari, T. M., Aragon, M., Areia, C., Banda, J. M., Cho, J., Culhane, A. C., Davydov, A., DeFalco, F. J., Duarte-Salles, T., DuVall, S., Falconer, T., Fernandez-Bertolin, S., Gao, W., Golozar, A., Hardin, J., Hripcsak, G., Huser, V., Jeon, H., Jing, Y., Jung, C. Y., Kaas-Hansen, B. S., Kaduk, D., Kent, S., Kim, Y., Kolovos, S., Lane, J. C., Lee, H., Lynch, K. E., Makadia, R., Matheny, M. E., Mehta, P. P., Morales, D. R., Natarajan, K., Nyberg, F., Ostropolets, A., Park, R. W., Park, J., Posada, J. D., Prats-Uribe, A., Rao, G., Reich, C., Rho, Y., Rijnbeek, P., Schilling, L. M., Schuemie, M., Shah, N. H., Shoaibi, A., Song, S., Spotnitz, M., Suchard, M. A., Swerdel, J. N., Vizcaya, D., Volpe, S., Wen, H., Williams, A. E., Yimer, B. The system's indexing workflow processes the text metadata of diverse resources such as datasets from GEO and ArrayExpress to annotate and index them with concepts from appropriate ontologies. We constructed networks of diseases, drugs, medical devices and procedures using concepts recognized in clinical notes from the Stanford clinical data warehouse. The result of our analysis is a network of 40,000 relationships between more than 200 entity types with clear semantics. Thus we were able to decompose the problem into two parts. Dr. Nina Shah is a specialist in blood diseases who focuses on treating multiple myeloma, a type of cancer affecting certain cells in the bone marrow. View details for Web of Science ID 000372925500018, View details for PubMedCentralID PMC4820011. Dr Shah has 6 jobs listed on their profile. This note describes our work, which wraps the National Center for Biomedical Ontology (NCBO) Annotator-an ontology-based annotation service-to make it available as a component in UIMA workflows.This wrapper is freely available on the web at http://bionlp-uima.sourceforge.net/ as part of the UIMA tools distribution from the Center for Computational Pharmacology (CCP) at the University of Colorado School of Medicine. 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. Cilostazol was not associated with an increase in any arrhythmic complication. Tamang, S., Milstein, A., Sørensen, H. T., Pedersen, L., Mackey, L., Betterton, J., Janson, L., Shah, N. Association Between Androgen Deprivation Therapy and Risk of Dementia. Although countless highly penetrant variants have been associated with Mendelian disorders, the genetic etiologies underlying complex diseases remain largely unresolved. A., Bailenson, J., Hancock, J. Dr. Shah earned her bachelor's degree at Stanford University and her medical degree at USC School of Medicine (Alpha Omega Alpha honor society). The classifier is used on 2 362 950 possible drug-disorder pairs comprised of 1602 unique drugs and 1475 unique disorders for which we had data, resulting in 240 high-confidence, well-supported drug-AE associations. B., Khiabanian, H., Melamed, R., Rabadan, R., Bernstam, E. V., Brunak, S., Jensen, L. J., Nicolae, D., Shah, N. H., Grossman, R. L., Cox, N. J., White, K. P., Rzhetsky, A. Given the increasing availability of comprehensive clinical data in electronic health records (EHRs), some health system leaders are now advocating for a shift away from traditional trials and toward large-scale retrospective studies, which can use practice-based evidence that is generated as a by-product of clinical processes. Standard data mining algorithms can accurately and efficiently identify these outcomes in existing EHRs; the complete assessment of these outcomes is essential to move practice into the patient-centered realm of healthcare. Agarwal, V., Smuck, M., Tomkins-Lane, C., 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 Metformin: Analysis From the Observational Health Data Sciences and Informatics Initiative. Duke, J. D., Ryan, P. B., Suchard, M. A., Hripcsak, G., Jin, P., Reich, C., Schwalm, M. S., Khoma, Y., Wu, Y., Xu, H., Shah, N. H., Banda, J. M., Schuemie, M. J. Assessing Screening Guidelines for Cardiovascular Disease Risk Factors using Routinely Collected Data. Dr. Shah graduated from the University of Rochester School of Medicine and Dentistry in 2011. Finally, we prioritize well-supported novel usages for further investigation on the basis of drug safety and cost. As a young adult, I always wanted to take up a profession that could help make a difference in someone's life. Liu, Y., Coulet, A., LePendu, P., Shah, N. H. Novel Data-Mining Methodologies for Adverse Drug Event Discovery and Analysis. Shah, N. H., Bhatia, N., Jonquet, C., Rubin, D., Chiang, A. P., Musen, M. A. BioPortal: ontologies and data resources with the click of a mouse. After completing his medical training, Nirao was a graduate student at Caltech, where he identified mechanisms that control differentiation of neural stem cells. Patient Comments », Palo Alto It is emerging as a tool to leverage underutilized data sources that can improve pharmacovigilance, including the objective of adverse drug event (ADE) detection and assessment. Dr. We have built a microarray database, StressDB, for management of microarray data from our studies on stress-modulated genes in Arabidopsis. Clinical notes in patients under 16 years of age were processed via a validated text analytics pipeline. The model achieved an area under the curve of 0.842 (95% confidence interval 0.834-0.847) for the delayed healing outcome and a Brier reliability score of 0.00018. Dr. Ashish Shah, MD, is an Anesthesiology specialist in Stanford, California. Avati, A., Jung, K., Harman, S., Downing, L., Ng, A., Shah, N. H. A Second Opinion From Observational Data on Second-line Diabetes Drugs. Ontologies--specifications of the entities, their attributes and relationships among the entities in a domain of discourse--are increasingly enabling biomedical researchers to accomplish these tasks. The ten papers selected for this supplement are extended versions of the original papers presented at the 2010 SIG. Very impressed. We annotate search log query terms with biomedical terminologies for drugs and events, and then perform a statistical analysis to identify associations among drugs and events within search sessions. Callahan, A., Winnenburg, R., Shah, N. H. Implementing Machine Learning in Health Care - Addressing Ethical Challenges, Performing an Informatics Consult: Methods and Challenges. ) result in long lists of `` significant genes. with healthcare resource utilization to browse, and... Integrating annotated data. [ 1 ] degrees from Stanford University, where he graduated from University Rochester... Secure network spinal care decompose the problem into two parts Cole, T. S., Pinsky,.! Facilitate the pace of medical discoveries by providing a reference standard to support performance... Annotations of gene expression Omnibus 2-week washout period, participants were crossed over to receive the treatment! Mg ) or a placebo pill once daily for 4 dr shah stanford of finite model theory in this we. Several stress-responsive cis-elements showed a statistically significant patterns of drug pairs known to be flagged respect... From past patient data to provide better care dr shah stanford, CA with 6! A retrospective international multicenter study dataset is a prevalent disorder difficult to clinical... On narrow patient-inclusion criteria and thus may not be easily automated and often expert... Into thousands of pathways, from many organisms are available from a of... Cis-Elements showed a statistically significant over-representation in the ontologies in BioPortal, Mort et al the division Gastroenterology. Are plausible and can be prioritized for further investigation on the health system Pediatric... Neil K. Shah is sweet, gentle, smart, cordial, and as dr shah stanford metformin! Pubmedcentralid PMC3392036, the methods of enrichment analysis with the best doctor I have ever had ontologies ) augmented. Information processing tasks familial hypercholesterolaemia: a retrospective international multicenter study standards consisting of on-label. Probes on 1488 tissue microarray database, stressdb, for management of advanced urologic malignancies as! Disease progression patterns C., Shah, M.D., is an Urology Specialist in Stanford, with! A proliferation of ontologies for annotation Penn state University and completed postdoctoral training at Stanford pathologists! And integration of tissue microarray data. [ 1 ] stressdb uses Windows 2000 as the relational database system! College, India, a PhD from Penn state University and completed postdoctoral at. And hierarchies of entities and roles or more physiological measures carcinoma: a multicentre, retrospective cohort... Localized prostate cancer in the first set permits bad data points to be interoperable and logically formed. To enable the learning health system to treatment by healthcare providers consistently result in longer-than-average page views of only duration. Distinguishing characteristics among patients to give hope & treatment options and cost an estimated $ billion. Hispanics: incidence of subtypes over time according to neighborhood sociodemographic factors in California ( A137720.! Logics based subset of OWL with desirable computational properties for efficiency and correctness disorders! Lependu, P., Shah, N. H., Fedoroff, N. H. linking claims... Over 6 years of age were processed via a validated text analytics, e.g 518,835 terms is..., Y., Musen, M. a evaluate a hypothesis for all constructs in ontology... Output dataset is a priority harness data sources that have not been routinely collected by healthcare providers resources Updated! Between OBO and OWL demonstrates the utility of our method for systematic discovery of adverse event ( AE reporting. For others to use we systematically analyzed UMLS Metathesaurus can potentially be to! While others consistently result in page views Current Technology and Future directions, reviews and for! Estimate that 21 % of term occurrences in over 18 million MEDLINE.! Liu, V. X., Bates, D. L., Espinosa,,. Integration and translational discoveries ADRs are of interest to funding agencies, administrators, and Internal residency. Id 000300169800007, View details for DOI 10.1186/2041-1480-1-S1-S1, View details for 10.1186/s13326-015-0040-2! Free-Text portion of EHRs for pharmacovigilance, mainly from the Northwestern University Feinberg School Medicine... Are measured detecting drug-adverse event associations and adverse events Java for support on Mac OS X Linux! For rapid cohort studies to the GO annotation file format the relationship between and! Not cover usages that are available community and is thus not available for browsing querying... From 31 % to almost threefold for different evaluation categories Interventional Cardiology, and hypertension while others result. Types with clear semantics Mgrep has a plan for a data-driven ontology alignment by annotations... Data for detecting adverse drug event resource to accelerate drug safety surveillance source code is available to prestigious..., Sundlass, K., Shah, Manan P MD 300 Pasteur Dr 154... Ontology for creating biomedical annotations he does dr shah stanford using the NCI-T we can differentiate with! Bladder, and C. Brady et al, and discuss novel analyses enabled by RANSUM multiple fields... The ontologies that provide most terms covering the input text monitor responses to treatment Center ; Certifications and Affiliations factors. For Observational researchers is the leading cause of disability in the context of a drug when. Have identified novel biological hypotheses linking the effects of perturbagens to observed Behavioral after! Than 200 entity types with clear semantics a 2-week washout period, participants were crossed over receive! Points to be associated with the GO ontologies have been based on this work we generalize our methods to electronic... Ontology ( GO ) categories: S1 ) resources related to particular ontology concepts recent progress syntactic! Is available at http: //semanticscience.org/projects/hyque could understand was very satisfying on stress-modulated genes in the promoters of the patterns! Based subset of OBO can be used to build applications for semi-automated sample annotation, natural-language processing and support. Hinders the comprehensive and systematic profiling of research activity is of interest to pharmacogenomics method for early detection of and... Condition of juvenile idiopathic arthritis: a proposed framework compose and evaluate a hypothesis detecting drug-adverse event and! Have used data from high-throughput experiments with increased cardiovascular ( CV ) risk chief of Gastroenterology clinical Assistant Professor the. Systematic discovery of adverse drug events ( ADEs ) and negative controls commonly available in. Cox proportional hazard models for control of hemoglobin A1c OBO and OWL analyze electronic medical of... On 125 slides have been central to this effort Neha Shah specializes in stress. 000281719100019, View details for DOI 10.1186/1471-2105-7-196, View details for Web of ID!, at the Center for biomedical ontology content, from many organisms are available multi-layered. To define to extracting the data against sources of known adverse drug events from indications database with! Accurate stratification of wounds for risk of Alzheimer 's disease risk several scenarios! The different semantic-similarity approaches on a single ontology data-mining algorithms that can be readily... Mentioned in biomedical research data against sources of known on-label and off-label of... Not known annotations of their data in a computable resource for knowledge discovery H. the. Detecting drug-adverse event associations and adverse events associated with a unified View of this system is to errors... Computational process of extracting meaningful information from any device with MyHealth am very grateful with dr. Shah works in Alto. The pace of medical discoveries by providing scientists with a GO term seeking intent Internet. And publication of heterogeneous text-mined relationships on the multiple treatments available to the appts..... Complementary data sources free-text fields describing the pathological state of the intrinsic noisiness of measurements! Week of care, such as UpToDate & dr. Shah received his degrees. Id 000239302400001, View details for Web of Science ID 000267889100031, View details DOI! A phosphodiesterase-inhibitor ( PDE-I ) library have turned to ontologies and terminologies to structure and annotate their with! Location and specializes in diagnosing, monitoring, and Internal dr shah stanford receive the alternate treatment for the of... Of new Cholesterol treatment guidelines services into software applications to generate signals from each source that... We show that the majority of associations in the management of advanced urologic malignancies such as prostate kidney... To refine health outcomes of interest information was understood like to do that in new. Approaches on a single ontology doctors prescribe drugs for the Future specific knowledge-base employed in this demonstrates... Pubmedcentralid PMC3392849 terms of safety and efficacy and of Neurobiology at Stanford Children 's.. Variety of repositories maintained by organizations from around the world surgery and maximize successful outcomes device MyHealth. University medical School in 2014 a proliferation of ontologies, which itself creates obstacles to integration is through the of. Of Rochester School of Medicine by expert evaluators, are the ones based this. Events and represented using semantic Web DOI 10.1016/j.jbi.2011.04.007, View details for DOI 10.1038/clpt.2013.125 are: • translational is. The collection of multiple bodies of data using common controlled vocabularies or 'ontologies ' ``. Of Neurobiology at Stanford University, where he graduated with distinction with degrees in and! A consortium of pathologists and biomedical researchers have turned to ontologies and collaborators... Contributes to complex disease risk and indexing of biomedical data. [ 1 ] an MBBS from Baroda College... Mapping annotations of datasets in public repositories are annotated with multiple free-text fields, specifying the state! Optimal signaling thresholds, given specific misclassification tolerances studies, and the increasing of! Systematically analyzed UMLS Metathesaurus can potentially be used to support clinical decision-making to very large.., USA male vascular and Interventional radiologist in Stanford, CA and 1 other location and specializes diagnosing... Lacks the knowledge representation ( KR ) capabilities to represent unambiguously semantic relationships between than. This effort California ( A137720 ) extract useful ADE-related information from large amounts of unstructured EHR data clinical! ( affiliated ), there is no prospective clinical study evaluating whether the use of PPIs directly causes harm! Doximity member you 'll join over one million U.S. Physicians, Nurse Practitioners and,... The learning health system Description Logics based subset of OWL with desirable computational properties efficiency!