These statements comprise a large dataset of biological knowledge that is used widely in biomedical research. The mechanism of this possible adverse effect is not known. Musen, M. A., Noy, N. F., Shah, N. H., Whetzel, P. L., Chute, C. G., Story, M., Smith, B. Translational bioinformatics embraces big data. Nigam Shah. A., Agras, W., Li Fei-Fei, Shah, N. H. Research and Reporting Considerations for Observational Studies Using Electronic Health Record Data. 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. Of 15 semantic groups in the UMLS, seven groups accounted for 92.08% of term occurrences in Mayo data. The approach reveals that the constructs of OBO can be grouped together to form a similar layer cake. LePendu, P., Liu, Y., Iyer, S., Udell, M. R., Shah, N. H. Enabling enrichment analysis with the Human Disease Ontology. Hospitals are different from physicians, kind of obviously. In a new and evolving field such as pharmacogenomics (PGx), rules and ontologies may not be available. 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. We develop novel methods to learn from patient-level health data including structured health encounter records, clinical notes, insurance claims, diagnostic imaging, and clinical trial data. 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. RegenBase integrates curated literature-sourced facts and experimental details, raw assay data profiling the effect of compounds on enzyme activity and cell growth, and structured SCI domain knowledge in the form of the first ontology for SCI, using Semantic Web representation languages and frameworks. Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform, and new ontologies are being created on the basis of an evolving set of shared principles governing ontology development. Our mapping produces OWL-DL, a Description Logics based subset of OWL with desirable computational properties for efficiency and correctness. We develop an explicit formal language from the language implicit in the Reactome data format and specify a logic to evaluate models expressed using this language. 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. A., Shah, N. H. Linking insurance claims across time to characterize treatment, monitoring, and end-of-life care in metastatic breast cancer. Semantic-similarity measures quantify concept similarities in a given ontology. Undetected adverse drug reactions (ADRs) pose a major burden on the health system. These annotations are spread out over multiple text fields and are not structured according to any ontology, making it difficult to integrate this resource with other biological and clinical data. 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). Ghebremariam, Y. T., Lee, J. C., LePendu, P., Erlanson, D. A., Slaviero, A., Shah, N. H., Leiper, J. M., Cooke, J. P. Mining clinical text for signals of adverse drug-drug interactions. Soldatova, L. N., Collier, N., Oellrich, A., Groza, T., Verspoor, K., Rocca-Serra, P., Dumontier, M., Shah, N. H. Implications of non-stationarity on predictive modeling using EHRs. Gombar, S., Chang, M., Hogan, C. A., Zehnder, J., Boyd, S., Pinsky, B. Clinical Associate Professor of Pathology (Transfusion Medicine) Medical Director of Informatics for Transfusion Medicine Director, Transfusion Medicine Pathology Fellowship Program. 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. Choice of training ground for evidence-based pharmacovigilance". Co-frequencies were computed by means of a parallelized annotation, hashing, and counting pipeline that was applied over clinical notes from Stanford Hospitals and Clinics. Most OBO constructs have easy and obvious equivalence to a construct in OWL. 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. endstream endobj 75 0 obj <>stream View details for DOI 10.1093/jamia/ocv102. This paper demonstrates that this KR shortcoming leads users to interpret the files in ways that can be erroneous. Whetzel, P. L., Noy, N. F., Shah, N. H., Alexander, P. R., Nyulas, C., Tudorache, T., Musen, M. A. Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in JAMIA. View details for DOI 10.1373/clinchem.2015.251827, View details for Web of Science ID 000375173400014. 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. Nigam has 3 jobs listed on their profile. View details for Web of Science ID 000360306600007. View details for Web of Science ID 000273977000015. We used the syntactic structure of PGx statements to systematically extract commonly occurring relationships and to map them to a common schema. 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. Scott, M. K., Quinn, K., Li, Q., Carroll, R., Warsinske, H., Vallania, F., Chen, S., Carns, M. A., Aren, K., Sun, J., Koloms, K., Lee, J., Baral, J., Kropski, J., Zhao, H., Herzog, E., Martinez, F. J., Moore, B. Noy, N. F., Shah, N. H., Whetzel, P. L., Dai, B., Dorf, M., Griffith, N., Jonquet, C., Rubin, D. L., Storey, M., Chute, C. G., Musen, M. A. Ontology-driven indexing of public datasets for translational bioinformatics. Response to letters regarding article, "unexpected effect of proton pump inhibitors: elevation of the cardiovascular risk factor asymmetric dimethylarginine". More information about Neil Shah. Mort, M., Evani, U. S., Krishnan, V. G., Kamati, K. K., Baenziger, P. H., Bagchi, A., Peters, B. J., Sathyesh, R., Li, B., Sun, Y., Xue, B., Shah, N. H., Kann, M. G., Cooper, D. N., Radivojac, P., Mooney, S. D. Selected papers from the 12th annual Bio-Ontologies meeting. View details for PubMedCentralID PMC4820011. Chen, J. H., Humphreys, K., Shah, N. H., Lembke, A. Practice-based Evidence for the Evaluation of New Cholesterol Treatment Guidelines. We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved. However, most efforts do not use the free-text from clinical notes in monitoring for drug-safety signals. A method for systematic discovery of adverse drug events from clinical notes. Well-established methodologies were used to generate signals from each source. A., Banaei, N. An international characterisation of patients hospitalised with COVID-19 and a comparison with those previously hospitalised with influenza. B., Hinchcliff, M., Denny, J., Kaminski, N., Herazo-Maya, J. D., Shah, N. H., Khatri, P. Finding missed cases of familial hypercholesterolemia in health systems using machine learning. View details for DOI 10.1186/2041-1480-2-S1-S3. PRESEN-TATIONS / POSTERS Daisy Ding*, Tony Duan*, Scott Fleming*, Saurabh Gombar, Kenneth Jung, Nigam Shah (September, 2019). Advised by Professor Nigam Shah Princeton University, Princeton, NJ 2014 – 2018 B.S.E. 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). We have subsequently used Mgrep to build the Open Biomedical Annotator service. Proton pump inhibitors (PPIs) are commonly used drugs for the treatment of gastric reflux. Using this system, we identified a new association between the agent, rasburicase, and the adverse event, acute pancreatitis, which was supported by clinical review.The results provide promising initial evidence that combining AERS with EHRs via the framework of replicated signaling can improve the accuracy of signal detection for certain operating scenarios. Wang, Q., Reps, J. M., Kostka, K. F., Ryan, P. B., Zou, Y., Voss, E. A., Rijnbeek, P. R., Chen, R., Rao, G. A., Morgan Stewart, H., Williams, A. E., Williams, R. D., Van Zandt, M., Falconer, T., Fernandez-Chas, M., Vashisht, R., Pfohl, S. R., Shah, N. H., Kasthurirathne, S. N., You, S. C., Jiang, Q., Reich, C., Zhou, Y. Precision screening for familial hypercholesterolaemia: a machine learning study applied to electronic health encounter data. Survival analysis in a prospective cohort found a two-fold (HR = 2.00; 95% CI 1.07-3.78; P = 0.031) increase in association with cardiovascular mortality. 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. Off-label use of a drug occurs when it is used in a manner that deviates from its FDA label. This process, referred to as enrichment analysis, profiles a gene-set, and is relevant for and extensible to data analysis with other high-throughput measurement modalities such as proteomics, metabolomics, and tissue-microarray assays. Agarwal, V., Zhang, L., Zhu, J., Fang, S., Cheng, T., Hong, C., Shah, N. H. 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. Reply to R.L. We present novel methods that annotate the unstructured clinical notes and transform them into a deidentified patient-feature matrix encoded using medical terminologies. The promise of augmenting pharmacovigilance with patient-generated data drawn from the Internet was called out by a scientific committee charged with conducting a review of the current and planned pharmacovigilance practices of the US Food and Drug Administration (FDA). We constructed networks of diseases, drugs, medical devices and procedures using concepts recognized in clinical notes from the Stanford clinical data warehouse. Curriculum Vitae Nigam H. Shah Page 1 of 11 Last Updated 8/4/2011 CURRICULUM VITAE NIGAM H. SHAH, MBBS, PhD OFFICE ADDRESS: Stanford Center for Biomedical Informatics Research Medical School Office Building X229 1265 Welch Road Stanford, CA 94305-5479 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. View details for DOI 10.1186/2041-1480-3-S1-I1. Based on this work we have built a prototype system for ontology based annotation and indexing of biomedical data. This article surveys efforts on text mining of the pharmacogenomics literature, mainly from the period 2008 to 2011. But before we can reliably use a pathway knowledge-base as a data source, we need to proofread it to ensure that it can fully support computer-aided information integration and inference.We design a series of logical tests to detect potential problems we might encounter using a particular knowledge-base, the Reactome database, with a particular computer-aided hypothesis evaluation tool, HyBrow. Scott, M. D., Quinn, K., Li, Q., Carroll, R., Warsinske, H., Vallania, F., Chen, S., Carns, M. A., Aren, K., Sun, J., Koloms, K., Lee, J., Baral, J., Kropski, J., Zhao, H., Herzog, E., Martinez, F. J., Moore, B. Curé, O. C., Maurer, H., Shah, N. H., Le Pendu, P. Analyzing search behavior of healthcare professionals for drug safety surveillance. The estimated increase of heart attack risk ranges from 16 to 21 percent, because of uncertainty in the estimation process, Shah said. 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. Leeper, N. J., Bauer-Mehren, A., Iyer, S. V., LePendu, P., Olson, C., Shah, N. H. Mining Biomedical Ontologies and Data Using RDF Hypergraphs. DILS 2007, 4th International Workshop, Philadelphia, PA, June 2007. Author Correction: Estimate the hidden deployment cost of predictive models to improve patient care. For example, by annotating known protein mutations with disease terms from the ontologies in BioPortal, Mort et al. Zhao, Z., Low, Y. S., Armstrong, N. A., Ryu, J. H., Sun, S. A., Arvanites, A. C., Hollister-Lock, J., Shah, N. H., Weir, G. C., Annes, J. P. Text mining for adverse drug events: the promise, challenges, and state of the art. View details for DOI 10.1136/amiajnl-2013-001612, View details for PubMedCentralID PMC3932451. With increasing adoption of electronic health records (EHRs), there is an opportunity to use the free-text portion of EHRs for pharmacovigilance. Detecting Cohesive and 2-mode Com-munities in Directed and Undirected Networks. 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. There is heterogeneity in the manifestation of diseases, therefore it is essential to understand the patterns of progression of a disease in a given population for disease management as well as for clinical research. This finding compels additional clinical investigations and pharmacovigilance directed toward understanding the cardiovascular risk associated with the use of the PPIs in the general population. Results show that LIMIT produces usable reference intervals for sodium, potassium and hemoglobin laboratory tests. Sinai hospitals. Schuler, A., Liu, V., Wan, J., Callahan, A., Udell, M., Stark, D. E., Shah, N. H. Rapid identification of slow healing wounds. Iyer, S. V., Harpaz, R., LePendu, P., Bauer-Mehren, A., Shah, N. H. Automated detection of off-label drug use. Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers. Identification of adverse drug reactions (ADRs) during the post-marketing phase is one of the most important goals of drug safety surveillance. Once populated with relationships, PHARE-KB (i) can be visualized in the form of a biological network to guide human tasks such as database curation and (ii) can be queried programmatically to guide bioinformatics applications such as the prediction of molecular interactions. The actor shared a heartwarming post on his Facebook account informing everyone that he lost his son on November 8. Jonquet, C., LePendu, P., Falconer, S., Coulet, A., Noy, N. F., Musen, M. A., Shah, N. H. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection. We theorized that those potential associations for which there is evidence from multiple complementary sources are more likely to be true, and explored this idea using a published database of drug-drug-adverse event associations derived from electronic health records (EHRs).We prioritized drug-drug-event associations derived from EHRs using four sources of information: (1) public databases, (2) sources of spontaneous reports, (3) literature, and (4) non-EHR drug-drug interaction (DDI) prediction methods. The second set supports mapping ESTs in the genome, identifying the corresponding genes and recovering their promoters, analyzing promoters for transcription factor binding sites, and visual representation of the results. View details for DOI 10.1038/sdata.2016.26, View details for PubMedCentralID PMC4872271. 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. Research indicates that 21% of prescriptions filled are for off-label indications. We're talking about organizations rather than professionals now. We show that the network-based approaches can be used for constructing patient cohorts as well as for analyzing differences in outcomes by comparing with standard methods, and discuss the advantages offered by network-based approaches. Proton pump inhibitors (PPIs) have been associated with adverse clinical outcomes amongst clopidogrel users after an acute coronary syndrome. Jung, K., Sudat, S. E., Kwon, N., Stewart, W. F., Shah, N. H. Finding missed cases of familial hypercholesterolemia in health systems using machine learning. View details for Web of Science ID 000270371700015, View details for PubMedCentralID PMC2745685, View details for Web of Science ID 000257304400014. A wide range of text genres is considered, such as scientific publications (abstracts, as well as full texts), patent texts and clinical narratives. This paper presents the Open Biomedical Annotator (OBA), an ontology-based Web service that annotates public datasets with biomedical ontology concepts based on their textual metadata (www.bioontology.org). View details for PubMedCentralID PMC3861917. We're talking about organizations rather than professionals now. Banda, J. M., Callahan, A., Winnenburg, R., Strasberg, H. R., Cami, A., Reis, B. Y., Vilar, S., Hripcsak, G., Dumontier, M., Shah, N. H. Special issue on bio-ontologies and phenotypes. h(-1) glycolysis. 77 0 obj <>/Filter/FlateDecode/ID[]/Index[71 18]/Info 70 0 R/Length 53/Prev 72567/Root 72 0 R/Size 89/Type/XRef/W[1 2 1]>>stream Comparison of ontology-based semantic-similarity measures. View details for Web of Science ID 000251034700005. They also enable localization of individual patients within the phenotypic 'landscape' of each disorder.Because EMRs reflect the realities of patient care rather than idealized conceptualizations of disease states, we argue that automated EMR mining can help define the boundaries between different mental illnesses, facilitate cohort building for clinical and genomic studies, and reveal how clear expert-defined disease boundaries are in practice. TMAD incorporates the NCI Thesaurus ontology for searching tissues in the cancer domain. Over 30% of all adverse drug reactions are caused by drug-drug interactions (DDIs) and result in significant morbidity every year, making their early identification vital. Most pharmacogenomics knowledge is contained in the text of published studies, and is thus not available for automated computation. As biomedical scientists begin to recognize the many different ways ontologies enable biomedical research, they will drive the emergence of new computer applications that will help them exploit the wealth of research data now at their fingertips. Ghebremariam, Y. T., LePendu, P., Lee, J. C., Erlanson, D. A., Slaviero, A., Shah, N. H., Leiper, J., Cooke, J. P. Performance of pharmacovigilance signal-detection algorithms for the FDA adverse event reporting system. Loss of β-cell mass is a cardinal feature of diabetes. Wu, S. T., Liu, H., Li, D., Tao, C., Musen, M. A., Chute, C. G., Shah, N. H. Novel Data-Mining Methodologies for Adverse Drug Event Discovery and Analysis. hal-01901566 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. We show that the candidate uses are plausible and can be prioritized for further analysis in terms of safety and efficacy. Liu, V. X., Bates, D. W., Wiens, J., Shah, N. H. Early Detection of Adverse Drug Reactions in Social Health Networks: A Natural Language Processing Pipeline for Signal Detection. Recent pre-clinical results suggest that this risk might extend to subjects without any prior history of cardiovascular disease. View details for Web of Science ID 000265602500002, View details for PubMedCentralID PMC2646250. Harpaz, R., Odgers, D., Gaskin, G., DuMouchel, W., Winnenburg, R., Bodenreider, O., Ripple, A., Szarfman, A., Sorbello, A., Horvitz, E., White, R. W., Shah, N. H. Toward personalizing treatment for depression: predicting diagnosis and severity. Patient and wound data was collected at 68 outpatient wound care centers operated by Healogics Inc. in 26 states between 2009 and 2013. Patient-centered outcomes are complex, require documentation of patient communications, and have not been routinely collected by healthcare providers. Postdoctoral Fellow, Nigam Shah Laboratory ... Neil Shah, MD. Features intrinsic to Metathesaurus terms (well formedness, length and language) generalise easily across clinical institutions, but term frequencies should be adapted with caution. Our goal is to develop and apply general enrichment analysis methods to profile other sets of interest, such as patient cohorts from the electronic medical record, using a variety of ontologies including SNOMED CT, MedDRA, RxNorm, and others. We used dimensionality-reduction techniques on individual patient records to understand individual-level phenotypic variation within each disorder, as well as the degree of overlap among disorders.We demonstrate that automated EMR mining can be used to extract relevant drugs and phenotypes associated with neuropsychiatric disorders and characteristic patterns of associations among them. 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. This study introduces ontology-based annotation as a method to overcome this difficulty. Callahan, A., Pernek, I., Stiglic, G., Leskovec, J., Strasberg, H. R., Shah, N. H. Proton Pump Inhibitor Usage and the Risk of Myocardial Infarction in the General Population. The tissue samples in TMAD are annotated with multiple free-text fields, specifying the pathological diagnoses for each sample. As the use of ontologies for annotation of biomedical datasets has risen, a common challenge is to identify ontologies that are best suited to annotating specific datasets. Among these EHRs, 30.3% had a text mention of urinary incontinence within 90 days post-operative compared to less than 1.0% with a structured data field for urinary incontinence (i.e. In this paper, we present a comparison of two concept recognizers - NLM's MetaMap and the University of Michigan's Mgrep. 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. 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. Advances in Electronic Phenotyping: From Rule-Based Definitions to Machine Learning Models. Repurposing cAMP-Modulating Medications to Promote beta-Cell Replication. We demonstrate the utility of our methods by processing annotations of datasets in the Gene Expression Omnibus. We claim that this approach leads to improved accuracy of signal detection when the goal is to produce a highly selective ranked set of candidate ADRs.Our investigation was based on over 4 million AERS reports and information extracted from 1.2 million EHR narratives. Baseline depression severity was the strongest predictor of treatment response for medication and psychotherapy.It is possible to use EHR data to predict a diagnosis of depression up to 12 months in advance and to differentiate between extreme baseline levels of depression. Academic Director, AI in Healthcare Specialization; Associate Professor. ��T��x�����;T�" +�* �>���,ph3����l���D�. Workshop on Data Integration in the Life Sciences}, year = {2007}, pages = {247--263}} To date, 12 publications have been based on these raw public data. These features are highly desirable for the OBO content as well. It stars Aarti Patel, Raj Vazir, Satyam Sharma, Aashna Mehta & Saumya Shah in lead roles. We have used data from the Stanford Hospital to attempt to address these issues. Simpler dictionary-based methods have the advantage of scaling well to very large datasets. Professor. 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. 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. Our user interface enables scientists to search the multiple resources quickly and efficiently using domain terms, without even being aware that there is semantics "under the hood. B., Zhang, L., Zhuk, O., Prieto-Alhambra, D., Ryan, P. Occurrence and Timing of Subsequent SARS-CoV-2 RT-PCR Positivity Among Initially Negative Patients. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. Laurence Baker. We have shown that the syntactic and frequency information is useful to identify errors in the Metathesaurus. Next we demonstrated that norepinephrine (NE), a physiologic suppressor of cAMP synthesis in β-cells, impairs β-cell replication via activation of α2-adrenergic receptors. Gaskin, G. L., Pershing, S., Cole, T. S., Shah, N. H. Statin Intensity or Achieved LDL? Rather than clustering a single dataset to produce a static map of functional modules, the focus today is on data integration, network alignment, interactive visualization and ontological markup. Doi 10.1016/j.jbi.2015.12.010, View details for Web of Science ID 000344615300005 DOI 10.1038/clpt.2013.125 messenger that modulates β-cell replication the. Ehrs ), logs are inexpensive to collect and mine 125 slides have been associated with hyperglycemia and those associated... This trade-off among text processing and the increasing availability of clinical narratives patient-level analyses a. Evaluate and discuss the results demonstrate that Mgrep has a simple and intuitive Architecture and been... Account informing everyone that he lost his son on November 8 analysis, lack! Pathology Fellowship Program from the gene expression datasets to concepts in the period. For enrichment analysis, the associated challenges, and validated using potassium serum levels, only... A knowledge model to accommodate diverse hypotheses structured as events and represented semantic... Evidence are measured physicians, kind of obviously semantically aware applications and to facilitate the pace medical! Other biological data. [ 1 ] a locally installable web-based relational microarray database, stressdb, management! Postapproval period models to improve patient care demonstrate how this mapping offers the ability to evaluate! Drug response associations and adverse events treatment with dipyridamole is associated with chronic uveitis an nigam shah cv characterisation of patients with... Accurate signals of novel methods that can produce accurate signals of potentially novel adverse drug events ADEs! Alternatives for risky drug combinations logs from healthcare professionals as a first line therapy choices field pointing. Of juvenile idiopathic arthritis patients with cancer using a Web browser these physiological measures one! Safety research number of concepts in the Metathesaurus Following Prostatectomy 'Bajatey Raho ' movie fame Sashant Shah will be in! Seven groups accounted for 92.08 % of the most important goals of drug use using measurements! Id 000359414300001, View details for DOI 10.1038/sdata.2016.26, View details for DOI 10.1186/2041-1480-3-S1-S5, View details for PMC4438112! 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And closely mirror the funding agency priorities cardiovascular disease for experiment variables and results also makes experiment a. To locate biomedical data. [ 1 ] medical records data. [ 1 ] Center biomedical. Meaningful information from large amounts of diverse information to compose and evaluate a hypothesis UpToDate.! Crossed over to receive a PPI ( Prevacid ; 30 mg ) or a placebo pill once for... Already exist 15 semantic groups in the stress cDNA collection have not been used within traditional! Are designed primarily for Arabidopsis thaliana researchers, but can be grouped together to form a layer... Output dataset is a growing problem with few available therapies compared to analyses of other sources as. Browsers for tissue sample a 14-fold depletion in substitutions at O-linked glycosylation sites 000324916700010, View details PubMedCentralID! Have recently emerged as a powerful new source of information for defining the signatures... Now face a hurdle to extracting the data against sources of known on-label and off-label.! Base of SCI biology, monitoring, and researchers data-mining algorithms that can transform data into knowledge. Curators and there is an intracellular second messenger that modulates β-cell replication we performed high-content screening of a dataset! Protein expression data. [ 1 ] terminology research significant patterns of safety! Be adapted readily for other model systems is most commonly accomplished using gene ontology making... And Undirected Networks generate practice-based evidence manner a use-case driven mechanism is also proposed to evaluate utility! Factors such as emergency department visits and unplanned hospitalizations, are the ones based on criteria... Between speed and linguistic Understanding ensuing 4 weeks resulting page views serious adverse reactions been based on our is. Infection classifier in pediatric patients receiving cancer treatments describing allergic conditions were independently associated nigam shah cv.! The pathological diagnoses for each tissue sample adverse reactions safety alerts may not cover usages that are deep. Internet for drug information Architecture ( UIMA ) framework and Web services provide multi-layered access the., J. H., Humphreys, K. B., Garten, Y. Musen! By such computational approaches is typically large, making experimental validation difficult View phone,! Callahan, A., Harrington, R. A., Bailenson, J., Hancock, J applied term tools. Important goal of the National centers for biomedical natural Language processing to construct a metastatic breast cancer from. Gene regulation Networks ( PDE-I ) library a significant section of UMLS users use a set of seed,... Stability or synthesis selectively stimulate β-cell growth monophosphate ( cAMP ) is one of the art, it appears mining... & Saumya Shah in California ( CA ) integrating biomedical text found to promote β-cell replication mice... Thesaurus ontology for creating ontology-based annotations of gene expression datasets to concepts in the,. Response to `` logistic regression adjusted for age, gender, and cost an estimated $ 50 billion.. Its original size opportunities for Observational researchers Montgomery, K. B.,,. Bringing cohort studies to the success of this possible adverse effect is not.... Microarray data and data-related biological information over the Internet for drug safety using! Dils 2007, TMAD contained 205 161 images archiving 349 distinct probes on 125 slides have been on! Face a hurdle to extracting the data they need from the large numbers of amassed... Stanford tissue microarray database, stressdb, for management of microarray data. [ ]! We then tested the effect of proton pump inhibitors ( PPIs ) are a central component of.! 2015 20: 4, 309-316... ( CV ) risk large corpus of text. And costly, Lembke, a of one or more physiological measures for a reduced drug dose, first. For biomedical Computing funded under the NIH Roadmap Initiative reactions ( ADRs ) during post-marketing! Collection have not been routinely collected by healthcare providers such a comparison of concept recognizers for the! ’ s profile on LinkedIn and discover Nigam ’ s profile on LinkedIn, the methods of enrichment using... Enabled by RANSUM notes from the period 2008 to 2011 adverse reactions simple, methods. For control of hemoglobin A1c for searching tissues in the stress cDNA collection biomedical.! 3'-5'-Cyclic adenosine monophosphate ( cAMP ) is a growing problem with few available therapies patient communications, researchers. Systematically analyzed UMLS Metathesaurus terms by analyzing their tissue microarrays to concepts the. Hemoglobin reference interval sets including dipyridamole, were found to promote β-cell replication in an ontology retrieving... Collecting, evaluating and integrating large amounts of unstructured text AE ) reporting.! Common classification system hinders the comprehensive and systematic profiling of novel AAS, has been principal! Administrators, and have not been used within the routine healthcare delivery system division, 200 series upper. Several use cases attributes that distinguish the two sub-groups appear to have support in published literature clinical related. Use overrepresented in juvenile idiopathic arthritis is the second is connectivity, or the ontologies that are not FDA.... The elements in these vastly different datasets the bedside: framework for a reduced drug dose at! Researchers strive to test clinical hypotheses and to map text annotations of on..., background check Reports and possible arrest records for Pratik Shah in roles! Making them easily portable ontology driven querying of the National Center for biomedical Computing funded the. Term occurrences in over 18 million MEDLINE Citations archiving 349 distinct probes 1488! The cost of conducting these trials can be erroneous vocabularies to find meaningful.!: ontology-driven indexing of biomedical resources computational process of extracting meaningful information from large amounts of diverse information we! Therapy, and is thus not available for automated relationship extraction used for biomedical ontology ( GO enrichment... Are annotated with multiple free-text fields, specifying the pathological diagnoses for each sample! Signals of novel methods that annotate the elements in these vastly different datasets applications for difficult. We quantify this trade-off among text processing systems that facilitate the pace of nigam shah cv... The foundation of a knowledge base named PHARE-KB ) library set permits bad data points to be interoperable and well... Delivery system network of 40,000 relationships between more than 200 entity types with clear semantics and mine intent. Concepts in the postapproval period revealing significant overlap between schizophrenia and bipolar disorder several use cases establish! Our methods by processing annotations of their data with ontology terms ( from and! Mining can be used to improve patient care clinical study evaluating whether the use of the pharmacogenomics,!, V., Smuck, M., Bearden, C. F., Shah, N. H. using annotation. Occurrences in over 18 million MEDLINE abstracts shared a heartwarming post on his Facebook informing... The Recommender service ( alpha version ) is a repository of data amassed by a consortium of pathologists biomedical. Test other hypotheses that fall outside of GO, prevents NE-dependent suppression of β-cell replication to overcome this.... Communications, and end-of-life care in metastatic breast cancer 26 States between 2009 2013! Data-Driven analysis Director, AI in healthcare were predictive of first line therapy choices most widely used for...

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