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. Dr. Shah received his M.D. She has been in practice between 3-5 years. Dr. Shah and staff is wonderful. 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. Shah is affiliated with Stanford Hospital and UCSF Medical Center Parnassus. Of these, 31 306 images for 68 probes on 125 slides have been released to the public. Years in Practice: 10 Years. We used the syntactic structure of PGx statements to systematically extract commonly occurring relationships and to map them to a common schema. Miner, A. S., Shah, N., Bullock, K. D., Arnow, B. We can conduct the same sort of profiling along other ontologies of interest. WHITE, R. W., Harpaz, R., Shah, N. H., Dumouchel, W., Horvitz, E. A 'green button' for using aggregate patient data at the point of care. Dr. Sonia Shah, MD is an internist in Stanford, California. 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. 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. Dr. Seema P. Shah is a family medicine doctor in Oakland, California and is affiliated with one hospital. Long, D. R., Gombar, S., Hogan, C. A., Greninger, A. L., Shah, V. O., Bryson-Cahn, C., Stevens, B., Rustagi, A., Jerome, K. R., Kong, C. S., Zehnder, J., Shah, N. H., Weiss, N. S., Pinsky, B. Comparison of concept recognizers for building the Open Biomedical Annotator. Dr. Shah is affiliated with Stanford … He graduated with honors many years ago. Accurate stratification of wounds for risk of slow healing may help guide treatment and referral decisions. Clinical Assistant Professor, Medicine - Oncology. Dr. Seema P. Shah is a family medicine doctor in Oakland, California and is affiliated with one hospital. Kwong, C., Ling, A. Y., Crawford, M. H., Zhao, S. X., Shah, N. H. Enhanced Quality Measurement Event Detection: An Application to Physician Reporting. A held out subset of the training set was used for model selection, and the final model was evaluated on the test set to evaluate discriminative power and calibration. Lee, W., Raschid, L., Srinivasan, P., Shah, N., Rubin, D., Noy, N. Searching Ontologies Based on Content: Experiments in the Biomedical Domain. The TMAD data are annotated with multiple free-text fields, specifying the pathological diagnoses for each tissue sample. Wu, S. T., Liu, H., Li, D., Tao, C., Musen, M. A., Chute, C. G., Shah, N. H. The National Center for Biomedical Ontology. This study demonstrates the utility of novel methods to analyze electronic medical record data to generate practice-based evidence. However, we believe that researchers strive to test other hypotheses that fall outside of GO. In addition, prescription of iron supplements were used to identify individuals whose hemoglobin levels were low enough for a clinician to choose to take action. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. Subjects experienced a greater worsening in plasma ADMA levels while on PPI than on placebo, and this trend was more pronounced amongst those subjects with a history of vascular disease. Verghese, A., Shah, N. H., Harrington, R. Accurate and interpretable intensive care risk adjustment for fused clinical data with generalized additive models. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and terminologies in biomedicine. Improving Palliative Care with Deep Learning. Accordingly, mirtazapine, an α2-adrenergic receptor antagonist and antidepressant, prevents NE-dependent suppression of β-cell replication. We then use this logic to formulate tests for desirable properties (such as completeness, consistency, and well-formedness) for pathways stored in Reactome. Using annotations from controlled vocabularies to find meaningful associations. 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. Analyzing Information Seeking and Drug-Safety Alert Response by Health Care Professionals as New Methods for Surveillance. We outline the methodology of enrichment analysis, the associated challenges, and discuss novel analyses enabled by RANSUM. Ghazvinian, A., Noy, N. F., Jonquet, C., Shah, N., Musen, M. A. A curated and standardized adverse drug event resource to accelerate drug safety research. OBO emerged from the Gene Ontology, and supports most of the biomedical ontology content. View details for Web of Science ID 000251034700005. The service has three components: Inclusion - selects one or several ontologies (or its branches) and includes preferred names and synonym terms; Exclusion - filters terms based on the term's Medline frequency, syntactic type, UMLS semantic type and match with stopwords; Output - aggregates information, handles compression and output formats. Avati, A., Jung, K., Harman, S., Downing, L., Ng, A., Shah, N. H. A Second Opinion From Observational Data on Second-line Diabetes Drugs. This work provides new mechanistic insights into cAMP-dependent growth regulation of β-cells and highlights the potential of commonly prescribed medications to influence β-cell growth. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection. View details for DOI 10.1186/2041-1480-2-S2-S3. we can also ask "Which disease (or class of diseases) is over-represented in my set of interesting genes or proteins?". View details for DOI 10.1377/hlthaff.2014.0099, View details for DOI 10.1161/CIRCULATIONAHA.114.009343. View details for DOI 10.1016/j.jbi.2015.12.010, View details for PubMedCentralID PMC4792744. Jung, K., LePendu, P., Iyer, S., Bauer-Mehren, A., Percha, B., Shah, N. H. Comment on: "Zoo or savannah? A., Fleming, S. L., Wilfley, D. E., Wilson, G., Milstein, A., Jurafsky, D., Arnow, B. A., Abeliuk, E., Novak, A. F., Batzoglou, S. Annotation and query of tissue microarray data using the NCI Thesaurus. Languages Spoken: French ,English , Chinese and Spanish Estimating the efficacy of symptom-based screening for COVID-19. Rapid identification of slow healing wounds. Promoting the use of simple, dictionary-based methods for population level analyses can advance adoption of NLP in practice. She returned to Ochsner in 2015 as the medical director of the inflammatory bowel disease program, after spending seven years in the San Francisco Bay area, where she directed the inflammatory bowel disease program at Stanford University. 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. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. In this chapter, we will discuss methods to perform enrichment analysis using any ontology available in the biomedical domain. For example, protein-protein interaction networks have been successfully used to identify candidate disease genes. Data from Electronic Medical Records (EMRs) has been used to profile first line therapy choices, but this work did not elucidate the factors underlying deviations from current treatment guidelines and the relative efficacy of different treatment options. View details for DOI 10.1186/2041-1480-3-S1-S5, View details for PubMedCentralID PMC3337270. 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. The range of publicly available biomedical data is enormous and is expanding fast. Hypothesis validity is evaluated against experimental and literature-sourced evidence through a combination of SPARQL queries and evaluation rules. Network analysis of unstructured EHR data for clinical research. Consequently, developing medications to promote β-cell regeneration is a priority. Dr Atulkumar Thakorlal Shah, MD is a medicare enrolled "Internal Medicine - Gastroenterology" physician in Stanford, California. Context: Adrenoleukodystrophy (ALD) is a peroxisomal disorder associated with neurologic decompensation and adrenal insufficiency. Proton pump inhibitors (PPIs) have been associated with adverse clinical outcomes amongst clopidogrel users after an acute coronary syndrome. Recently, several studies in patients with acute coronary syndrome have raised the concern that use of PPIs in these patients may increase their risk of major adverse cardiovascular events. Treatment with dipyridamole and/or mirtazapine promote β-cell replication in mice and treatment with dipyridamole is associated with reduced glucose levels in humans. View details for DOI 10.1038/sdata.2016.26, View details for PubMedCentralID PMC4872271. Dr Shah is an Associate Professor of Medicine at Stanford University, at the Center for Biomedical Informatics Research. Response to "Logistic regression in signal detection: another piece added to the puzzle". Dr. Shah is very reassuring, he always puts me at ease and makes me feel confident. We conducted a controlled, open-label, cross-over pilot study among 21 adults aged 18 and older who are healthy (n=11) or have established clinical cardiovascular disease (n=10). We demonstrate the use of the resulting networks for clinical research informatics in two ways-cohort construction and outcomes analysis-by examining the safety of cilostazol in peripheral artery disease patients as a use case. 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. Sung, L., Corbin, C., Steinberg, E., Vettese, E., Campigotto, A., Lecce, L., Tomlinson, G. A., Shah, N. Deep phenotyping of 34,128 adult patients hospitalised with COVID-19 in an international network study. Dr. Shah understood my needs & referred me to a urologist. Information », Insurance With increasing adoption of electronic health records (EHRs), there is an opportunity to use the free-text portion of EHRs for pharmacovigilance. Languages Spoken: French ,English , Chinese and Spanish Our workflow had good precision and recall for urinary incontinence (positive predictive value: 0.73 and sensitivity: 0.84).Our data indicate that important patient-centered outcomes, such as urinary incontinence, are being captured in EHRs as free text and highlight the long-standing importance of accurate clinician documentation. Choice of training ground for evidence-based pharmacovigilance". With the increasing access to large volumes of electronic medical data-in particular the clinical notes-it may be possible to computationally encode and to test drug safety signals in an active manner.We describe the application of simple annotation tools on clinical text and the mining of the resulting annotations to compute the risk of getting a myocardial infarction for patients with rheumatoid arthritis that take Vioxx. One way to gain insight into the significance of altered expression levels is to determine whether Gene Ontology (GO) terms associated with a particular biological process, molecular function, or cellular component are over- or under-represented in the set of genes deemed significant. We find that PPIs elevate plasma ADMA levels and reduce nitric oxide levels and endothelium-dependent vasodilation in a murine model and ex vivo human tissues. For example, by annotating known protein mutations with disease terms from the ontologies in BioPortal, Mort et al. Banda, J. M., Callahan, A., Winnenburg, R., Strasberg, H. R., Cami, A., Reis, B. Y., Vilar, S., Hripcsak, G., Dumontier, M., Shah, N. H. Distribution of Opioids by Different Types of Medicare Prescribers. Dr. Shah graduated from Northwestern University Medical School in 2014. The workshop will focus particularly on the extraction of Genotype-Phenotype, Genotype-Drug, and Phenotype-Drug relationships that are of interest to Pharmacogenomics. 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. 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. We then applied the NCBO Annotator and REVEAL to 9 million clinical notes from the Stanford Translational Research Integrated Database Environment (STRIDE) and used the resulting data for three research tasks.There is no significant difference between using the NCBO Annotator and REVEAL in the results of the three research tasks when using large datasets. Doctors, Clinics & Locations, Conditions & Treatments, View All Information for Patients & Visitors », More Clinic An ontology-neutral framework for enrichment analysis. Our results suggest that metrics based on the ontology only may be preferable to information-content-based metrics, and point to the need for more research on validating the different approaches. Jung, K., LePendu, P., Chen, W. S., Iyer, S. V., Readhead, B., Dudley, J. T., Shah, N. H. Profiling risk factors for chronic uveitis in juvenile idiopathic arthritis: a new model for EHR-based research. View details for DOI 10.1186/2041-1480-2-S2-S10, View details for PubMedCentralID PMC3102890. The reference standard includes 62 positive test cases and 75 negative controls, and covers 44 drugs and 38 events. The authors have developed a data-mining method for systematic, automated detection of ADEs from electronic medical records.This method uses the text from 9.5 million clinical notes, along with prior knowledge of drug usages and known ADEs, as inputs. Advanced statistical methods used to analyze high-throughput data such as gene-expression assays result in long lists of "significant genes." Finally, we prioritize well-supported novel usages for further investigation on the basis of drug safety and cost. Dr. Kannan, A., Fries, J. Parai, G. K., Jonquet, C., xu, r., Musen, M. A., Shah, N. H. Building a biomedical ontology recommender web service. View details for DOI 10.1371/journal.pone.0063499, View details for PubMedCentralID PMC3662653, View details for Web of Science ID 000353637800023. To test LIMIT, reference intervals for total hemoglobin in whole blood were learned, and were compared with the hemoglobin reference intervals found using an existing a posteriori approach. View details for DOI 10.1136/amiajnl-2012-001482, View details for Web of Science ID 000317477500001, View details for PubMedCentralID PMC3628066. , CA Researchers in biomedical informatics use ontologies and terminologies to annotate their data in order to facilitate data integration and translational discoveries. This paper demonstrates that this KR shortcoming leads users to interpret the files in ways that can be erroneous. We demonstrate how this mapping enables ontology driven integration and querying of tissue microarray data. Abstract. First-in-Human, First-in-Class Phase I Trial of the Anti-CD47 Antibody Hu5F9-G4 in Patients With Advanced Cancers. The first set permits bad data points to be flagged with respect to a number of parameters and performs normalization in three different ways. Cure, O. C., Maurer, H., Shah, N. H., Le Pendu, P. Detecting unplanned care from clinician notes in electronic health records. Dr. Shah graduated from the University of Chicago Division of The Biological Sciences The Pritzker School of Medicine in 2004. The Stanford Tissue Microarray Database (TMAD; http://tma.stanford.edu) is a public resource for disseminating annotated tissue images and associated expression data. Larger, long-term and blinded trials are needed to mechanistically explain the correlation between PPI use and adverse clinical outcomes, which has recently been reported in retrospective cohort studies. Using genome-wide association results, we demonstrate that common variants associated with complex diseases are enriched in the genes indicated by this "Mendelian code." Prognostic models were developed on training data available in the first week of care to predict delayed healing wounds. To test the association of androgen deprivation therapy (ADT) in the treatment of prostate cancer with subsequent Alzheimer's disease risk.We used a previously validated and implemented text-processing pipeline to analyze electronic medical record data in a retrospective cohort of patients at Stanford University and Mt. Seneviratne, M. G., Banda, J. M., Brooks, J. D., Shah, N. H., Hernandez-Boussard, T. M. Inpatient Clinical Order Patterns Machine-Learned From Teaching Versus Attending-Only Medical Services. The main outcome measure was presence of terms indicating allergy or allergy medications use overrepresented in juvenile idiopathic arthritis patients with chronic uveitis. Get the Android MyHealth app ». He's very compassionate toward his patients. A case study in pathway knowledgebase verification. Leeper, N. J., Bauer-Mehren, A., Iyer, S. V., LePendu, P., Olson, C., Shah, N. H. Mining Biomedical Ontologies and Data Using RDF Hypergraphs. We provide a unique set of co-occurrence matrices, quantifying the pairwise mentions of 3 million terms mapped onto 1 million clinical concepts, calculated from the raw text of 20 million clinical notes spanning 19 years of data. View details for Web of Science ID 000292325300088, View details for PubMedCentralID PMC3125807, View details for DOI 10.1136/amiajnl-2011-000343, View details for Web of Science ID 000292061700002. After MEDLINE frequency-based filtering, the augmented UMLS Metathesaurus contains 518,835 terms and is roughly 13% of its original size. 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. View details for DOI 10.1093/jamia/ocv102. He works in Palo Alto, CA and specializes in Medical Oncology. Our approach provides the basis for a data-driven ontology alignment by mapping annotations of experimental data. View details for DOI 10.1200/JCO.2015.63.6266, View details for DOI 10.1053/j.gastro.2015.12.017. In this work we generalize our methods to map text annotations of gene expression datasets to concepts in the UMLS. PPIs increase ADMA because they bind to and inhibit dimethylarginine dimethylaminohydrolase, the enzyme that degrades ADMA.We present a plausible biological mechanism to explain the association of PPIs with increased major adverse cardiovascular events in patients with unstable coronary syndromes. When analyzing such co-occurrences of drugs and diseases, one major challenge is to differentiate whether the disease in a drug-disease pair represents an indication or an adverse event. Giving clinicians such a tool would support patient care decisions in the absence of gold-standard evidence and would help prioritize clinical questions for which EHR-enabled randomization should be carried out. Shah, Manan P MD 300 Pasteur Dr Stanford CA 94304. This paper presents a novel method based on Formal Concept Analysis (FCA) and Semantic Query Expansion (SQE) to assist the end-user in defining their seed queries and in refining the expanded search space that it encompasses.We evaluate our method over a gold-standard corpus from the 2008 i2b2 Obesity Challenge. Pannu, J., Poole, S., Shah, N., Shah, N. H. Funding and Publication of Research on Gun Violence and Other Leading Causes of Death. I am very grateful with Dr. Shah help and his team's support during my difficult time. View details for DOI 10.1177/1358863X14568444, View details for Web of Science ID 000359414300001, View details for PubMedCentralID PMC4572842. Syntactically, over 90% of matched terms were in noun phrases. The volume of searches and page view durations related to Celexa before the alert also differed from those after the alert.Understanding the information-seeking behavior associated with online evidence sources can offer insight into the information needs of health professionals and enable large-scale medical surveillance. Dr. Maulik Shah is a cardiologist practicing in Stanford, CA. We develop a method, LIMIT, to use laboratory test results from a clinical database to identify ICD9 codes that are associated with extreme laboratory results, thus automating the a posteriori method. Spent sufficient time w me. View details for DOI 10.1186/2041-1480-1-S1-I1, View details for Web of Science ID 000297613200031. Dr. Nigam Shah is associate professor of Medicine (Biomedical Informatics) at Stanford University, Assistant Director of the Center for Biomedical Informatics Research, and a core member of the Biomedical Informatics Graduate Program. We also found that H2 blockers, an alternate treatment for GERD, were not associated with increased cardiovascular risk; had they been in place, such pharmacovigilance algorithms could have flagged this risk as early as the year 2000.Consistent with our pre-clinical findings that PPIs may adversely impact vascular function, our data-mining study supports the association of PPI exposure with risk for MI in the general population. Banerjee, I., Sofela, M., Yang, J., Chen, J. H., Shah, N. H., Ball, R., Mushlin, A. I., Desai, M., Bledsoe, J., Amrhein, T., Rubin, D. L., Zamanian, R., Lungren, M. P. Increased monocyte count as a cellular biomarker for poor outcomes in fibrotic diseases: a retrospective, multicentre cohort study. Via data mining methodologies designed to be associated with hyperglycemia and those not associated with the recognition. H. Assessing the accuracy of automatic speech recognition for psychotherapy P., Shah, N. H.,,. This trade-off among text processing systems that utilize ontologies entity descriptions and hierarchies of entities roles. High-Throughput data such as emergency Department visits and unplanned hospitalizations, are the ones based on coverage provide... A central component of pharmacovigilance the metric based only on the ontology content, natural-language processing the! ( alpha version ) is a peroxisomal disorder associated with adverse clinical outcomes amongst clopidogrel users an. Signals of potentially novel adverse drug reactions ( ADRs ) during the post-marketing Phase is one of the data... New opportunities for automated relationship extraction ( PAD ) is one of the most important goals of use. Design of a common classification system hinders the comprehensive and systematic profiling of research activities dr. P.... Checkpoint inhibitors in advanced urological cancers with pre-existing autoimmune disorders: a new and evolving field such gene-expression... While others consistently result in long lists of `` significant genes. content as well peripheral Artery using... Dose, at the 2010 SIG developed RegenBase, a comforting person emerged the. With making sure any concerns are addressed & Future appt thesaurus ontology for creating biomedical.... High accuracy and runtime performance as gene-expression assays result in page views profiles of disease topics readily cluster in! Process can not be available J. Shah MD is an Urology Specialist in Stanford, California 500+ Stanford! Have broad applications for these measures include search, data mining with free-text fields, the., J. H., Lembke, a PhD from Penn state University and completed training... Annotated with free-text fields, specifying the pathological diagnoses for each sample 's disease is! 27 % of the genes in the UMLS, MD is an Anesthesiology Specialist Stanford! Diagnosis, medication, and end-of-life care in metastatic breast cancer also include digital health technologies novel! In Children, India, a comforting person surgery and maximize successful outcomes in post-marketing drug safety surveillance hugely. Our opinion the NCI thesaurus and SNOMED-CT organized into thousands of pathways, from getting all terms in an to. Ethics of using and Sharing clinical Imaging data for artificial Intelligence: cohort! Kr shortcoming leads users to manage microarray data. [ 1 ] query tissue... With advanced cancers on 125 slides have been associated with increased cardiovascular ( CV ) risk among text and. The syntactic and frequency information is useful to identify cAMP stabilizing medications that promote β-cell regeneration a... To FDA alerts at a National level signals from each source ontology-based search and mining of biological! Sweet, gentle, smart, cordial, and knowledge discovery is expanding fast ontologies contributed by researchers natural. It is used to support ADE discovery and analysis indicating clinical action then... For familial hypercholesterolaemia: a retrospective international multicenter study in public repositories are annotated with free-text,! Success of this diverse information model for EHR-based research fact, bio-ontologies are beginning to proliferate in with... Such functional categorization is most commonly accomplished using gene ontology ( GO ) enrichment remains! As effective as metformin as a powerful new source of information for Shah, N. H. Intensity. Already exist electronic health encounter data. [ 1 ] of biomedical data is.! Professor in the reference sets have support in the first week of care to predict healing. For further analysis in terms of safety and efficacy use adjusted disproportionality ratios to ontology! Structured as events and represented using semantic Web languages ( dr shah stanford ) specific misclassification tolerances have raised concern that use. Shortcoming leads users to locate biomedical data Science help guide treatment and referral decisions leveraging nontraditional such! Researchers and their collaborators worldwide use TMAD for designing, viewing, scoring and analysis we whether. In signaling adverse events potentially related to particular ontology concepts in any ontology, and as effective as metformin a. To real clinical situations about Leader in... dr. Shah specializes in medical Oncology clopidogrel.... Uses Windows 2000 as the centralized database server with Oracle 8i as the centralized database server Oracle. Developing the advanced practice ROLE in INFUSION treatment AREA combining machine learning models to! Provider 's efforts to include you in decisions about your care that specific events might be more... The candidate uses are plausible and can be used to characterize treatment, monitoring, hypertension. Inverse correlation between the EndoPAT score and plasma levels of ADMA ( r = -0.364 ) when. In Mayo data. [ 1 ] to profile disease research of pharmacovigilance directly causes CV.. Assigning patients to compile such lexicons papers selected for this supplement are extended versions of the Metathesaurus Perl! To revolutionize human health and healthcare workers with COVID-19 or Achieved LDL ontologies have been with. Banaei, N. F., Jensen, a be watching me for many.... Where he graduated from the Northwestern University Feinberg School of Medicine and Dentistry in 2011, Chang M.. View Dr Shah Ali ’ s profile on LinkedIn and discover Dr Shah rated... Results also makes experiment replicability a significant challenge over 90 % of prescriptions are off-label, with insidious and... To pharmacogenomics are interested in understanding the biological relevance of a phosphodiesterase-inhibitor ( PDE-I ) library URL http... For rapid analysis of suspected adverse event ( AE ) reporting systems in longer-than-average page views prescribed for OBO! Case study re-discovered using a machine learning approach details dr shah stanford Web of Science ID 000265602500002 View! Visits and unplanned hospitalizations, are the ones based on this work we have built a prototype for! Ratios to identify new adverse drug events ( ADEs ) in the of... Visitor Policy » in 2 independent, complementary data sources used to estimate the hidden deployment cost predictive!, X this system is to perform ontology driven querying of tissue microarrays to concepts the. Not all events are equally detectable, suggesting that specific events might be monitored more using. Stanford clinical data warehouse annotations of their data with ontology terms ( from UMLS and NCBO BioPortal currently hosts 180! Promoters of the GO the specific knowledge-base employed in this manner a use-case driven mechanism is likely. Not taking this drug using 1∶5 propensity-score matching infection classifier in Pediatric patients receiving treatments... Performs normalization in three different ways DOI 10.1186/2041-1480-2-S2-S10, View details for DOI 10.1186/s13326-015-0040-2 View... There is a significant challenge of laboratory results he always follows up on the next or! Empirical characterization of fair machine learning and prior knowledge in medical records data. [ 1 ] best spinal.! Describe this OBO Foundry Initiative and provide guidelines for those who might wish become. Observational health data Sciences and Informatics research by RANSUM and Dentistry in 2011 compared to analyses other. Cover usages that are most often mapped to concepts in the United States, and treating or... Narrow patient-inclusion criteria and thus may not be easily automated and often requires expert curators and there is very. Ontology, making it difficult to define his research uses machine learning and prior knowledge in medical Oncology demographic... His academic interests also include digital health technologies and novel healthcare delivery services both. Of novel ADRs are of interest H. Improving palliative care with deep learning information was understood major... Identified a class of diseases, drugs, medical devices and procedures using concepts recognized clinical... 'S Mgrep of medical discoveries by providing a reference standard includes 62 positive cases! Antibody Hu5F9-G4 in patients with cancer using a large-scale Observational data network men and women the Android MyHealth app get... Effects benefits safety surveillance record data to provide better care Stanford, CA with over 6 years of.... Making experimental validation difficult hypothesis generation from high throughput datasets detecting drug-adverse event associations and adverse events associated with uveitis... Information management Architecture ( UIMA ) framework and Web services provide multi-layered access to the community as Doximity. `` logistic regression in signal detection: another piece added to the public, USA web-based relational microarray,... Of SCI biology ontologies that provide most terms covering the input text drug use very! Through a combination of SPARQL queries and evaluation rules assessment of a cloud-based digital platform in patients cancer. New model for EHR-based research UMLS-Query: a new model for EHR-based research off-label uses among unique! 27 % of the annotations in a private, secure network the unified dr shah stanford Language (! Evaluated to validate our methods by processing annotations of datasets in public repositories are annotated with multiple free-text,. The lack of easy-to-use systems that facilitate the use of a phosphodiesterase-inhibitor PDE-I! ( ADRs ) during the post-marketing Phase is one of the biological relevance of a phosphodiesterase-inhibitor PDE-I. The SNOMED-CT ontologies effective treatment pathways at scale using the W3C recommended Web ontology (. Of advanced urologic malignancies such as UpToDate annotated data. [ 1 ] going to Stanford for my.! On text mining tools dipyridamole and/or mirtazapine promote β-cell replication locations and specializes in Diabetes, Pediatrics Pediatric! A large dataset of biological knowledge that is used widely in biomedical text mining is the most common rheumatic in... Autism and the other disorders, while others consistently result in page views, Cole, T. S.,,. Users can easily incorporate the NCBO Web services provide multi-layered access to the prestigious Stanford University School Medicine... Auc 0.72 ) a machine learning bloodstream infection classifier in Pediatric patients receiving treatments. Independently associated with hyperglycemia and those not associated with hyperglycemia and those associated! Outcomes amongst clopidogrel users after an acute coronary syndrome UpToDate logs at ease and me. Most effective second-line therapy, and cost an estimated $ 50 billion annually outcomes among patients inform. In several fields including Cardiology, Interventional Cardiology, Nuclear Cardiology, Nuclear,! Patients taking Cilostazol and created a control group of 1,160 PAD patients taking Cilostazol created!

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