��T��x�����;T�" +�* �>���,ph3����l���D�. View details for DOI 10.1136/amiajnl-2014-002902. Predicting the need for a reduced drug dose, at first prescription. Spinal cord injury (SCI) research is a data-rich field that aims to identify the biological mechanisms resulting in loss of function and mobility after SCI, as well as develop therapies that promote recovery after injury. Harpaz, R., Dumouchel, W., Shah, N. H., Madigan, D., Ryan, P., Friedman, C. The coming age of data-driven medicine: translational bioinformatics' next frontier, The National Center for Biomedical Ontology. 0 We present an approach for identifying DDI signals directly from the textual portion of EHRs.We recognize mentions of drug and event concepts from over 50 million clinical notes from two sites to create a timeline of concept mentions for each patient. The objective of this study was to test the feasibility and accuracy of identifying patient centered outcomes within the EHR.Data from patients with localized prostate cancer undergoing prostatectomy were used to develop and test algorithms to accurately identify patient-centered outcomes in post-operative EHRs - we used urinary incontinence as the use case. However, this annotation process cannot be easily automated and often requires expert curators. The main outcome measure was presence of terms indicating allergy or allergy medications use overrepresented in juvenile idiopathic arthritis patients with chronic uveitis. Ph.D. Student in Biomedical Informatics . Evolutionary Pressures on the Electronic Health Record: Caring for Complexity. 1265 Welch Road . Comparing high-dimensional confounder control methods for rapid cohort studies from electronic health records. The first set permits bad data points to be flagged with respect to a number of parameters and performs normalization in three different ways. These data provide an example of how a combination of experimental studies and data-mining approaches can be applied to prioritize drug safety signals for further investigation. However, their performance characteristics are generally unknown. Shah, N. H., LePendu, P., Bauer-Mehren, A., Ghebremariam, Y. T., Iyer, S. V., Marcus, J., Nead, K. T., Cooke, J. P., Leeper, N. J. Chen, R., Ryan, P., Natarajan, K., Falconer, T., Crew, K. D., Reich, C. G., Vashisht, R., Randhawa, G., Shah, N. H., Hripcsak, G. A predictive tool for identification of SARS-CoV-2 PCR-negative emergency department patients using routine test results. Banda, J. M., Evans, L., Vanguri, R. S., Tatonetti, N. P., Ryan, P. B., Shah, N. H. Rapid identification of slow healing wounds. The NCI thesaurus terms have a wide coverage and provide terms for about 86% of the samples. Doctors prescribe drugs for indications that are not FDA approved. To date, there have not been comparisons of the different semantic-similarity approaches on a single ontology. Researchers face the challenge of collecting, evaluating and integrating large amounts of diverse information to compose and evaluate a hypothesis. View details for DOI 10.1038/sdata.2014.43, View details for PubMedCentralID PMC4306188, View details for DOI 10.1136/amiajnl-2014-002733, View details for Web of Science ID 000343776700019. We provide a curated and standardized version of FAERS removing duplicate case records, applying standardized vocabularies with drug names mapped to RxNorm concepts and outcomes mapped to SNOMED-CT concepts, and pre-computed summary statistics about drug-outcome relationships for general consumption. See the complete profile on LinkedIn and discover Nigam’s connections and jobs at similar companies. We find that anonymized signals on drug interactions can be mined from search logs. Only seven drug-drug-event associations (<0.5 %) had support from the majority of evidence sources, and about one third (1777) had support from at least one of the evidence sources.Our proof-of-concept method for scoring putative drug-drug-event associations from EHRs offers a systematic and reproducible way of prioritizing associations for further study. In this review, we briefly survey available datasets in functional genomics, review methods for data integration and network alignment, and describe recent work on using network models to guide experimental validation. A., Bailenson, J., Hancock, J. Other thought leaders in clinical research suggest that EHRs should be used to lower the cost of trials by integrating point-of-care randomization and data capture into clinical processes. - Worked with Nigam Shah’s lab to develop semi-supervised ML algorithms with noisy labeling for phenotyping of patients with comorbidities - Used Observational Medical Outcomes Partnership (OMOP) common data model to develop algorithms for electronic ... Microsoft Word - CV_7_24_19.docx 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. The widespread implementation of electronic medical records (EHR) offers opportunities to assess patient-centered outcomes within the routine healthcare delivery system. View phone numbers, addresses, public records, background check reports and possible arrest records for Pratik Shah in California (CA). Cilostazol was not associated with an increase in any arrhythmic complication. 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. BioPortal also enables integrated search of biomedical data resources such as the Gene Expression Omnibus (GEO), ClinicalTrials.gov, and ArrayExpress, through the annotation and indexing of these resources with ontologies in BioPortal. The results demonstrate that logs of the search activities of populations of computer users can contribute to drug safety surveillance. 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. Given the state of the art, it appears text mining can be applied to extract useful ADE-related information from multiple textual sources. This large amount of pathway data in a computable form will support visualization, analysis and biological discovery. Our Web log mining approach has the potential to monitor responses to FDA alerts at a national level. Nigam Shah Learning from past patient data to provide better care. 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. The service makes a decision based on three criteria. Jung, K., Covington, S., Sen, C. K., Januszyk, M., Kirsner, R. S., Gurtner, G. C., Shah, N. H. DISCOVERING PATIENT PHENOTYPES USING GENERALIZED LOW RANK MODELS. Traditional drug safety alerts may not cover usages that are not FDA approved. An alternative approach, known as an a posteriori method, requires an expert to enumerate diagnoses and procedures that can affect the measurement of interest. Ontologies are commonly used in biomedicine to organize concepts to describe domains such as anatomies, environments, experiment, taxonomies etc. By using DO in this manner a use-case driven mechanism is also proposed to evaluate the utility of classification hierarchies. 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. 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. Feasibility of prioritizing drug-drug-event associations found in electronic health records. 4/17/2007 Nigam Shah 1060 Continentals way, Apt 408 Belmont, CA 94002 (650) 598-9531 EDUCATION 2005 Ph.D. Integrative Biosciences (IBIOS) The Pennsylvania State University, University Park, PA We believe that a successful learning health care system will require both approaches, and we suggest a model that resolves this escalating tension: a "green button" function within EHRs to help clinicians leverage aggregate patient data for decision making at the point of care. The position offers the opportunity to work with leading Stanford faculty in Informatics (Nigam Shah), Statistics (Robert Tibshirani), Computer Science (Emma Brunskill), and Causal Inference (Stefan Wager). 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. Scott Flemming (co-advisor Nigam Shah) Jonathan Lee; Allen Nie (co-advisor Chris Piech) Charlie Marx (rotation student) Undergraduates Kavita Selva Alex Nam Recent Alumni Pierre-Luc Bacon (Postdoc, next: assistant prof University of Montreal, MILA) Christina Yuan … Jaewon Yang, Julian McAuley, Jure Leskovec. We have developed analytical and visualization tools to automate the identification of expression profile groups with common gene ontology (GO) annotations based on the sub-cellular localization and function of the proteins encoded by the genes, as well as to automate promoter analysis for such gene groups. Here, we developed and evaluated a tool for hypothesis generation from gene or protein lists using ontological concepts present in manually curated text that describes those genes and proteins.As a consequence we have developed the method Statistical Tracking of Ontological Phrases (STOP) that expands the realm of testable hypotheses in gene set enrichment analyses by integrating automated annotations of genes to terms from over 200 biomedical ontologies. View Nigam Shah’s profile on LinkedIn, the world's largest professional community. We have defined transformations for all constructs in an effort to foster a standard common mapping between OBO and OWL. For the cross-institutional analysis, using five example filters on i2b2/VA data reduces the actual lexicon to 19.13% of the size of the UMLS and only sees a 2% reduction in matched terms.The corpus statistics presented here are instructive for building lexicons from the UMLS. In this chapter, we will discuss methods to perform enrichment analysis using any ontology available in the biomedical domain. PRESEN-TATIONS / POSTERS Daisy Ding*, Tony Duan*, Scott Fleming*, Saurabh Gombar, Kenneth Jung, Nigam Shah (September, 2019). Finally, we detect hundreds of comorbidity associations among Mendelian disorders, and we use probabilistic genetic modeling to demonstrate that Mendelian variants likely contribute nonadditively to the risk for a subset of complex diseases. The workshop will focus particularly on the extraction of Genotype-Phenotype, Genotype-Drug, and Phenotype-Drug relationships that are of interest to Pharmacogenomics. We also found that 40% of annotations can be mapped to terms from both ontologies, providing the potential to align the two ontologies based on experimental data. Tamang, S., Patel, M. I., Blayney, D. W., Kuznetsov, J., Finlayson, S. G., Vetteth, Y., Shah, N. Comment on: "Zoo or savannah? This article provides an overview of recent advances in pharmacovigilance driven by the application of text mining, and discusses several data sources-such as biomedical literature, clinical narratives, product labeling, social media, and Web search logs-that are amenable to text mining for pharmacovigilance. Based on clinical observation, we hypothesized that allergic conditions are associated with chronic uveitis in juvenile idiopathic arthritis patients.This study is a retrospective cohort study using Stanford's clinical data warehouse containing data from Lucile Packard Children's Hospital from 2000-2011 to analyze patient characteristics associated with chronic uveitis in a large juvenile idiopathic arthritis cohort. Nigam has 3 jobs listed on their profile. Bing Professor. Nigam Shah. Our study shows that not all events are equally detectable, suggesting that specific events might be monitored more effectively using other data sources. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. Image processing researchers can extract images and scores for training and testing classification algorithms. endstream endobj 72 0 obj <> endobj 73 0 obj <> endobj 74 0 obj <>stream In particular, depressed patients exhibit largely unpredictable responses to treatment. Kashyap, S., Gombar, S., Yadlowsky, S., Callahan, A., Fries, J., Pinsky, B. Using genome-wide association results, we demonstrate that common variants associated with complex diseases are enriched in the genes indicated by this "Mendelian code." Building the graph of medicine from millions of clinical narratives. To assess the validity of this black box warning, we employed a novel text-analytics pipeline to quantify the adverse events associated with Cilostazol use in a clinical setting, including patients with congestive heart failure (CHF).We analyzed the electronic medical records of 1.8 million subjects from the Stanford clinical data warehouse spanning 18 years using a novel text-mining/statistical analytics pipeline. Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., Wu, G., D'Eustachio, P., Schaefer, C., Luciano, J., Schacherer, F., Martinez-Flores, I., Hu, Z., Jimenez-Jacinto, V., Joshi-Tope, G., Kandasamy, K., Lopez-Fuentes, A. C., Mi, H., Pichler, E., Rodchenkov, I., Splendiani, A., Tkachev, S., Zucker, J., Gopinath, G., Rajasimha, H., Ramakrishnan, R., Shah, I., Syed, M., Anwar, N., Babur, O., Blinov, M., Brauner, E., Corwin, D., Donaldson, S., Gibbons, F., Goldberg, R., Hornbeck, P., Luna, A., Murray-Rust, P., Neumann, E., Reubenacker, O., Samwald, M., van Iersel, M., Wimalaratne, S., Allen, K., Braun, B., Whirl-Carrillo, M., Cheung, K., Dahlquist, K., Finney, A., Gillespie, M., Glass, E., Gong, L., Haw, R., Honig, M., Hubaut, O., Kane, D., Krupa, S., Kutmon, M., Leonard, J., Marks, D., Merberg, D., Petri, V., Pico, A., Ravenscroft, D., Ren, L., Shah, N., Sunshine, M., Tang, R., Whaley, R., Letovksy, S., Buetow, K. H., Rzhetsky, A., Schachter, V., Sobral, B. S., Dogrusoz, U., McWeeney, S., Aladjem, M., Birney, E., Collado-Vides, J., Goto, S., Hucka, M., Le Novere, N., Maltsev, N., Pandey, A., Thomas, P., Wingender, E., Karp, P. D., Sander, C., Bader, G. D. Roeder, C., Jonquet, C., Shah, N. H., Baumgartner, W. A., Verspoor, K., Hunter, L. In Silico Functional Profiling of Human Disease-Associated and Polymorphic Amino Acid Substitutions. To date, 12 publications have been based on these raw public data. A., Sirota, M., Kenkare, P., Thompson, C. A., Yu, P. P., Gomez, S. L., Sledge, G. W., Kurian, A. W., Shah, N. H. The use of machine learning for the identification of peripheral artery disease and future mortality risk. In this study, we systematically analyzed UMLS Metathesaurus terms by analyzing their occurrences in over 18 million MEDLINE abstracts. The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. New opportunities have emerged to harness data sources that have not been used within the traditional framework. These inputs are further processed into statistics used by a discriminative classifier which outputs the probability that a given drug-disorder pair represents a valid ADE association. View details for DOI 10.1038/sdata.2016.26, View details for PubMedCentralID PMC4872271. Nigam Shah, Emma Brunskill. While not as precise as manually curated terms, we find that the additional enriched concepts have value when coupled with traditional enrichment analyses using curated terms.Multiple ontologies have been developed for gene and protein annotation, by using a dataset of both manually curated GO terms and automatically recognized concepts from curated text we can expand the realm of hypotheses that can be discovered. 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. View details for Web of Science ID 000270371700015, View details for PubMedCentralID PMC2745685, View details for Web of Science ID 000257304400014. View details for PubMedCentralID PMC3861917. Our Java implementation of the mapping is part of the official Gene Ontology project source.Our transformation system provides a lossless roundtrip mapping for OBO ontologies, i.e. Chronic nonhealing wounds have a prevalence of 2% in the United States, and cost an estimated $50 billion annually. In addition, the efficacies of first and second line treatments were evaluated using Cox proportional hazard models for control of Hemoglobin A1c. One of the key difficulties in realizing the full potential of ontologies in biomedical research is the isolation of various communities involved: some workers spend their career developing ontologies and ontology-related tools, while few researchers (biologists and physicians) know how ontologies can accelerate their research. We describe application of these methods to identify stress-induced genes whose transcript abundance is likely to be controlled by common regulatory mechanisms and summarized our findings in a temporal model of the stress response. To enable such observational studies from EHR in real time, particularly in emergencies, rapid confounder control methods that can handle numerous variables and adjust for biases are imperative. This paper demonstrates that this KR shortcoming leads users to interpret the files in ways that can be erroneous. Woei-Jyh Lee, Louiqa Raschid, Padmini Srinivasan, Nigam Shah, Daniel Rubin, and Natasha Noy. In the case of the GO, this background set is provided by the Gene Ontology Annotations. BioPortal: ontologies and integrated data resources at the click of a mouse. Digital northern analysis revealed that 55% of the stress-inducible genes are rarely transcribed in unstressed plants and 17% of them were not previously represented in Arabidopsis expressed sequence tag databases. More information about Neil Shah. Try the Course for Free. The metric based only on the ontology structure correlated most with expert opinion. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection. We have used data from the Stanford Hospital to attempt to address these issues. B., Murray, M. F., Myers, K. D., Wilemon, K., Shah, N. H., Knowles, J. W. Increased monocyte count as a cellular biomarker for poor outcomes in fibrotic diseases: a retrospective, multicentre cohort study. Advised by Professor Nigam Shah Princeton University, Princeton, NJ 2014 – 2018 B.S.E. Data science fellow About us: We are a group of about twenty doctors, engineers, informatics professionals and students focused on enabling better care using existing health data. These annotations are not mapped to concepts in any ontology, making it difficult to integrate these datasets across repositories. Bivariate-associated variables were used in a multivariate logistic regression adjusted for age, gender, and race. 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. Nigam H. Shah is a research scientist at the Stanford Center for Biomedical Informatics group and member of the National Center for Biomedical Ontology. Stanford, CA 94305-5479 View details for DOI 10.1186/1471-2105-7-196, View details for Web of Science ID 000239302400001, View details for PubMedCentralID PMC1522024. Chronic uveitis is a common and serious comorbid condition of juvenile idiopathic arthritis, with insidious presentation and potential to cause blindness. Whitepages people search is the most trusted directory. Toward the goal of personalizing treatment for depression, we develop and evaluate computational models that use electronic health record (EHR) data for predicting the diagnosis and severity of depression, and response to treatment.We develop regression-based models for predicting depression, its severity, and response to treatment from EHR data, using structured diagnosis and medication codes as well as free-text clinical reports. Schuler, A., Callahan, A., Jung, K., Shah, N. H. What This Computer Needs Is a Physician Humanism and Artificial Intelligence. Finding Progression Stages in Time-evolving Event Sequences. The definition of an HOI is generally considered a complex and time consuming task for health care professionals.In our clinical note-based pharmacovigilance research, we often operate upon potentially hundreds of ontologies at once, expand query inputs, and we also increase the search space over clinical text as well as structured data. The privacy rule in the Health Insurance Portability and Accountability Act (HIPAA) of 1996 may require revision to support this novel use of patient data. Availability and Supplementary information: http://www.personal.psu.edu/nhs109/Programs/, View details for DOI 10.1093/bioinformatics/btg253, View details for Web of Science ID 000185701100017, View details for Web of Science ID 000188997700143. h��X�n�F}�W�Ӣ����Mv�V�e[��,: ��G�%f%r@R�G�[}!EѲwv�K`�jI쮪S�NU��v�Ц��J..��#����(�)HI� E��Q���hs�Ji���,��q�'���W��a�~�ϏH�S�$��~K~� A,#��A^�k�����c��M��"����|c��B"���pV���؞��]F ��e��HN���g�6���ZZ��6�^ 6^�R�c��|θоw��5)��� �q{0w��C�nГ�D�k�Q��Ql���zk�վc�� ^ Of those, more than 73% lack supporting scientific evidence. Feasibility of prioritizing drug-drug-event associations found in electronic health records. View details for DOI 10.1186/2041-1480-2-S1-S3. Mildred Cho. The key attributes that distinguish the two sub-groups appear to have support in published literature clinical practice related to CKD. We demonstrate how this mapping enables ontology driven integration and querying of tissue microarray 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. Adverse drug events cause substantial morbidity and mortality and are often discovered after a drug comes to market. View details for PubMedCentralID PMC4322575, View details for DOI 10.1186/1546-0096-11-45, View details for Web of Science ID 000328822300001, View details for Web of Science ID 000328251900020, View details for DOI 10.1136/amiajnl-2013-001933. The resources come from a variety of repositories maintained by organizations from around the world. Finally, we prioritize well-supported novel usages for further investigation on the basis of drug safety and cost. 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. Ross, E. G., Shah, N. H., Dalman, R. L., Nead, K. T., Cooke, J. P., Leeper, N. J. The second is connectivity, or the ontologies that are most often mapped to by other ontologies. Our approach provides the basis for ontology-driven data integration for translational research on gene and protein expression data. View details for DOI 10.1136/amiajnl-2011-000744, View details for Web of Science ID 000314151400025, View details for PubMedCentralID PMC3392861. Larson, D. B., Magnus, D. C., Lungren, M. P., Shah, N. H., Langlotz, C. P. Estimating the efficacy of symptom-based screening for COVID-19. Longhurst, C. A., Harrington, R. A., Shah, N. H. Mining the internet for drug information. less than 1 minute read. PDE3,4 and 10 inhibitors, including dipyridamole, were found to promote β-cell replication in an adenosine receptor-dependent manner. We envision this method will have broad applications for examining difficult to test clinical hypotheses and to aid in post-marketing drug safety surveillance. 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. Verspoor, K., Oellrich, A., Collier, N., Groza, T., Rocca-Serra, P., Soldatova, L., Dumontier, M., Shah, N. Synergistic drug combinations from electronic health records and gene expression. We evaluate hypotheses of varying levels of detail about the genetic network controlling galactose metabolism in Saccharomyces cerevisiae to demonstrate the feasibility of deploying such semantic computing tools over a growing body of structured knowledge in Bio2RDF.HyQue is a query-based hypothesis evaluation system that can currently evaluate hypotheses about the galactose metabolism in S. cerevisiae. However, the lack of a common classification system hinders the comprehensive and systematic profiling of research activities. 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. We propose a signal-detection strategy that combines the adverse event reporting system (AERS) of the Food and Drug Administration and electronic health records (EHRs) by requiring signaling in both sources. 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. In this work we generalize our methods to map text annotations of gene expression datasets to concepts in the UMLS. Physician information-seeking behavior has typically been analyzed through survey-based approaches and literature reviews. Our approach provides the basis for a data-driven ontology alignment by mapping annotations of experimental data. 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. Agarwal, V., Han, L., Madan, I., Saluja, S., Shidham, A., Shah, N. H. LEARNING ATTRIBUTES OF DISEASE PROGRESSION FROM TRAJECTORIES OF SPARSE LAB VALUES. We conducted a large-scale study of Web search log data gathered during 2010. Adverse drug events (ADEs) are undesired harmful effects resulting from use of a medication, and occur in 30% of hospitalized patients. Jung, K., LePendu, P., Iyer, S., Bauer-Mehren, A., Percha, B., Shah, N. H. A time-indexed reference standard of adverse drug reactions. Wittkop, T., Teravest, E., Evani, U. S., Fleisch, K. M., Berman, A. E., Powell, C., Shah, N. H., Mooney, S. D. Practice-based evidence: profiling the safety of cilostazol by text-mining of clinical notes. In fact, bio-ontologies are beginning to proliferate in step with accruing biological data. The average improvement ranged from 31% to almost threefold for different evaluation categories. Our emphasis is on highlighting the key events in the field and pointing at promising research areas for the future. We can differentiate patients with severe baseline depression from those with minimal or mild baseline depression (AUC 0.72). One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or 'ontologies'. Spontaneous reporting systems (SRS) data, which are the mainstay of traditional drug safety surveillance, are used for hypothesis generation and to validate the newer approaches. Practice-based Evidence for the Evaluation of New Cholesterol Treatment Guidelines. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. The Metathesaurus from the Unified Medical Language System (UMLS) is a widely used ontology resource, which is mostly used in a relational database form for terminology research, mapping and information indexing. A., Fleming, S. L., Wilfley, D. E., Terence Wilson, G., Milstein, A., Jurafsky, D., Arnow, B. Tirmizi, S. H., Aitken, S., Moreira, D. A., Mungall, C., Sequeda, J., Shah, N. H., Miranker, D. P. Selected papers from the 13th Annual Bio-Ontologies Special Interest Group Meeting. The study focused on ADRs related to three high-profile serious adverse reactions. We address this shortcoming by providing a reference standard to support prospective performance evaluations. The key functionality of this system is to enable users to locate biomedical data resources related to particular ontology concepts. The Unified Medical Language System (UMLS) Metathesaurus is widely used for biomedical natural language processing (NLP) tasks.