endstream endobj startxref Feasibility of prioritizing drug-drug-event associations found in electronic health records. PDE3,4 and 10 inhibitors, including dipyridamole, were found to promote β-cell replication in an adenosine receptor-dependent manner. 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. View details for DOI 10.1186/1471-2105-7-196, View details for Web of Science ID 000239302400001, View details for PubMedCentralID PMC1522024. 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. Cilostazol is the only FDA-approved medication with a class I indication for intermittent claudication, but carries a black box warning due to concerns for increased cardiovascular mortality. gene-expression assays) result in long lists of "significant genes." TMAD archives multi-wavelength fluorescence and bright-field images of tissue microarrays for scoring and analysis. �?˦�7��-I������Gݡ'Ư�'�\����6�`G�`��s7�� [s�q��)%�` �� �T�C[1�t��0���z�KyN�}���ۑ Y��;�����'u��A�eeC���}o�APp4�*L�"�j�Qj��@h�iدl;{s-l�*#�,zgEl��WQ��x���0r�+'��+gG�C���oەƛ��r;[Rۜ������������P���������y�Q������O��ԏ���E�ٞ�O�䝸����=y?��Y�wV�xy�V��^��e�� ����@�upXb�u��b�^��e|�x�N���; ��ǰ�O� |� 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. Semantic-similarity measures quantify concept similarities in a given ontology. However, these data are stored in different formats and on different platforms. View details for Web of Science ID 000250355600019, View details for Web of Science ID 000266369400009. 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. 4th Int. Well-established methodologies were used to generate signals from each source. View details for DOI 10.1136/amiajnl-2011-000631, View details for Web of Science ID 000314151400029, View details for PubMedCentralID PMC3392849. This dataset can be leveraged to quantitatively assess comorbidity, drug-drug, and drug-disease patterns for a range of clinical, epidemiological, and financial applications. In our opinion the NCI thesaurus can facilitate integration of this resource with other biological data. We developed methods to map these annotations to the NCI thesaurus and the SNOMED-CT ontologies. 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. The reference standard was systematically curated from drug labeling revisions, such as new warnings, which were issued and communicated by the US Food and Drug Administration in 2013. Datamining methods that can transform data into meaningful knowledge to inform patient safety have proven essential for this purpose. The approach reveals that the constructs of OBO can be grouped together to form a similar layer cake. Electronic health records (EHR) represent a rich and relatively untapped resource for characterizing the true nature of clinical practice and for quantifying the degree of inter-relatedness of medical entities such as drugs, diseases, procedures and devices. The funding profiles of disease topics readily cluster themselves in agreement with the ontology hierarchy and closely mirror the funding agency priorities. In order to address this need for A.thaliana community, we have developed a program that retrieves GO annotations for A.thaliana genes and performs functional category analysis for lists of genes selected by the user.http://www.personal.psu.edu/nhs109/Clench, View details for DOI 10.1093/bioinformatics/bth056, View details for Web of Science ID 000221139700024, View details for Web of Science ID 000224127800106, We describe two sets of programs for expediting routine tasks in analysis of cDNA microarray data and promoter sequences. CV for David Cocker 9/1/2005 1 David R. Cocker III ... Ph.D. students: Sandip Shah*, Chen Song, Aniket Sawant, Bethany Warren, Abhilash Nigam, Quentin Malloy, Ajay Chaudhary Post Doctoral Researcher: Kwangsam Na * awarded Ph.D. However, the number of putative associations produced by such computational approaches is typically large, making experimental validation difficult. 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. 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. In biomedical research, network analysis provides a conceptual framework for interpreting data from high-throughput experiments. Interpretation errors related to the GO annotation file format. Woei-Jyh Lee, Louiqa Raschid, Padmini Srinivasan, Nigam Shah, Daniel Rubin, and Natasha Noy. Hypotheses as well as the supporting or refuting data are represented in RDF and directly linked to one another allowing scientists to browse from data to hypothesis and vice versa. This mapping offers the ability to perform ontology driven querying of the TMAD data. Bowen et al, M. Froehner et al, J.L. Post-market drug safety surveillance is hugely important and is a significant challenge despite the existence of adverse event (AE) reporting systems. After glycolysis adjustment, average bias was estimated by the bedside ICU study at -0.4 mg/dL (CI, -1.6 to 0.9) and DETECT at -0.7 (CI, -1.3 to 0.2), and percentage POC results occurring outside Clinical Laboratory Standards Institute quality goals were 2.4% and 4.8%, respectively.This study validates DETECT for estimating POC glucose meter accuracy compared with a prospective bedside ICU study and establishes it as a reliable postmarket surveillance methodology. –Nigam Shah, Associate Professor of Biomedical Informatics and of Biomedical Data Science. Author Correction: Estimate the hidden deployment cost of predictive models to improve patient care. Project: Continuously profiling patients screened for … Powers, S., Qian, J., Jung, K., Schuler, A., Shah, N. H., Hastie, T., Tibshirani, R. Interpretation of biological experiments changes with evolution of the Gene Ontology and its annotations. More information about Neil Shah. However, we believe that researchers strive to test other hypotheses that fall outside of GO. Just as scientists can ask "Which biological process is over-represented in my set of interesting genes or proteins?" The development of reference intervals using traditional methods is time consuming and costly. The use of tissue microarrays allows hundreds of human tissue cores to be simultaneously probed by antibodies to detect protein abundance (Immunohistochemistry; IHC), or by labeled nucleic acids (in situ hybridization; ISH) to detect transcript abundance. Nigam Shah Learning from past patient data to provide better care. Comparing high-dimensional confounder control methods for rapid cohort studies from electronic health records. document corpora annotated with corresponding semantic metadata (gold standards and training data), biomedical terminologies and ontologies providing domain-specific background knowledge at different levels of formality and specificity, software architectures for building complex and scalable text analytics pipelines and Web services grounded to them, as well as comprehensive ways to disseminate and interact with the typically huge amounts of semiformal knowledge structures extracted by text mining tools. In particular, the meeting focused on discussing informatics challenges related to personalizing care through the integration of genomic or other high-volume biomolecular data with data from clinical systems to make health care more efficient and effective. Although countless highly penetrant variants have been associated with Mendelian disorders, the genetic etiologies underlying complex diseases remain largely unresolved. Mahalingam, R., Gomez-Buitrago, A., Eckardt, N., Shah, N., Guevara-Garcia, A., Day, P., Raina, R., Fedoroff, N. V. StressDB: A locally installable web-based relational microarray database designed for small user communities. National initiatives to develop quality metrics emphasize the need to include patient-centered outcomes. Confronted with rapidly accumulating data, researchers currently do not have the software tools to undertake the required information integration tasks.We present HyQue, a Semantic Web tool for querying scientific knowledge bases with the purpose of evaluating user submitted hypotheses. Potential applications for these measures include search, data mining, and knowledge discovery in database or decision-support systems that utilize ontologies. Coulet, A., Garten, Y., Dumontier, M., Altman, R. B., Musen, M. A., Shah, N. H. NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources. 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. Androgen Deprivation Therapy and Future Alzheimer's Disease Risk. Kannan, A., Fries, J. View details for DOI 10.1186/2041-1480-2-S2-S10, View details for PubMedCentralID PMC3102890. 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. Several studies have demonstrated the ability to detect adverse events potentially related to multiple drug exposure via data mining. Harpaz, R., DuMouchel, W., Schuemie, M., Bodenreider, O., Friedman, C., Horvitz, E., Ripple, A., Sorbello, A., White, R. W., Winnenburg, R., Shah, N. H. A dataset quantifying polypharmacy in the United States. The collection of multiple genome-scale datasets is now routine, and the frontier of research in systems biology has shifted accordingly. The ten papers selected for this supplement are extended versions of the original papers presented at the 2010 SIG. 2012–2015 HResearch Assistant – University of Southern California Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers. We have previously developed methods to map text-annotations of tissue microarrays to concepts in the NCI thesaurus and SNOMED-CT. 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. Moreira, D. A., Shah, N. H., Musen, M. A. The second is connectivity, or the ontologies that are most often mapped to by other ontologies. Hripcsak, G., Ryan, P. B., Duke, J. D., Shah, N. H., Park, R. W., Huser, V., Suchard, M. A., Schuemie, M. J., DeFalco, F. J., Perotte, A., Banda, J. M., Reich, C. G., Schilling, L. M., Matheny, M. E., Meeker, D., Pratt, N., Madigan, D. Generalized enrichment analysis improves the detection of adverse drug events from the biomedical literature. Soldatova, L. N., Sansone, S., Dumontier, M., Shah, N. H. STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. The use of additional EHR data is required to further evaluate the capacity and limits of this system and to extend the generalizability of these results. Wang, J. K., Schuler, A., Shah, N. H., Baiocchi, M. T., Chen, J. H. Toward multimodal signal detection of adverse drug reactions. LIMIT represents a fast and inexpensive solution for calculating reference intervals, and shows that it is possible to use laboratory results and coded diagnoses to learn laboratory test reference intervals from clinical data warehouses. Schroeder, L. F., Giacherio, D., Gianchandani, R., Engoren, M., Shah, N. H. RegenBase: a knowledge base of spinal cord injury biology for translational research. What Four Million Mappings Can Tell You about Two Hundred Ontologies. View details for DOI 10.1007/s40264-015-0352-2, View details for DOI 10.1186/s13326-015-0040-2, View details for DOI 10.1016/j.jbi.2015.10.006. The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. 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. View details for DOI 10.1038/clpt.2013.24. A., Fleming, S. L., Wilfley, D. E., Wilson, G., Milstein, A., Jurafsky, D., Arnow, B. The workshop will focus particularly on the extraction of Genotype-Phenotype, Genotype-Drug, and Phenotype-Drug relationships that are of interest to Pharmacogenomics. 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. Comparison of ontology-based semantic-similarity measures. The Stanford Tissue Microarray Database (TMAD) is a repository of data amassed by a consortium of pathologists and biomedical researchers. Wang, G., Jung, K., Winnenburg, R., Shah, N. H. Proton pump inhibitors and vascular function: A prospective cross-over pilot study. View details for DOI 10.1007/s11103-005-2860-4, View details for Web of Science ID 000231220400007, Experimental design, hypothesis-testing and model-building in the current data-rich environment require the biologists' to collect, evaluate and integrate large amounts of information of many disparate kinds. We demonstrate that low rank modeling successfully captures known and putative phenotypes in these vastly different datasets. Off-label use of a drug occurs when it is used in a manner that deviates from its FDA label. 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. 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. Mission Mummy (Gujarati: મિશન મમ્મી), is a 2016 Indian children and family drama film, written and directed by Ashish Kakkad and produced by Nigam Shah, Divyesh Mehta & Sugam Shah. 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. The NCI thesaurus terms have a wide coverage and provide terms for about 86% of the samples. Annotation Analysis for Testing Drug Safety Signals using Unstructured Clinical Notes. New Paradigms for Patient-Centered Outcomes Research in Electronic Medical Records: An Example of Detecting Urinary Incontinence Following Prostatectomy. We use a method for clustering sparse functional data for identifying sub-groups within a cohort of patients with chronic kidney disease (CKD), based on the trajectories of their Creatinine measurements. Ling, A. Y., Kurian, A. W., Caswell-Jin, J. L., Sledge, G. W., Shah, N. H., Tamang, S. R. Improving palliative care with deep learning. Natural Language Processing (NLP) techniques for extracting relationships in specific domains often rely on hand-built rules and domain-specific ontologies to achieve good performance. We also investigate and discuss Reactome's potential for supporting computer-aided inference tools.The case study described in this work demonstrates that it is possible to use our model theory based approach to identify problems one might encounter using a knowledge-base to support hypothesis evaluation tools. The practice of medicine is predicated on discovering commonalities or distinguishing characteristics among patients to inform corresponding treatment. Randomized controlled trials have traditionally been the gold standard against which all other sources of clinical evidence are measured. 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. View details for Web of Science ID 000251864600008. 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. 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. The lack of standard reporting for experiment variables and results also makes experiment replicability a significant challenge. 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. The key functionality of this system is to enable users to locate biomedical data resources related to particular ontology concepts. Here we describe a preliminary analysis of search logs from healthcare professionals as a source for detecting adverse drug events. View details for Web of Science ID 000360306600007. Assessing the accuracy of automatic speech recognition for psychotherapy. A., Sunshine, J. 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. Advanced statistical methods used to analyze high-throughput data such as gene-expression assays result in long lists of "significant genes." While progress has recently been made in developing such benchmarks, our understanding of the performance characteristics of the data mining methodologies is limited because existing benchmarks do not support prospective performance evaluations. Avati, A., Jung, K., Harman, S., Downing, L., Ng, A., Shah, N. H., Hu, X. H., Shyu, C. R., Bromberg, Y., Gao, J., Gong, Y., Korkin, D., Yoo, Zheng, J. H. A Clinical Score for Predicting Atrial Fibrillation in Patients with Cryptogenic Stroke or Transient Ischemic Attack. Racunas, S. A., Shah, N. H., Fedoroff, N. V. Ontology-based annotation and query of tissue microarray data. Using BioPAX, millions of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases. We observed a marginal inverse correlation between the EndoPAT score and plasma levels of ADMA (r = -0.364). 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. Data mining methodologies designed to identify signals of novel ADRs are of deep importance for drug safety surveillance. The system processes the text metadata of diverse resource elements such as gene expression data sets, descriptions of radiology images, clinical-trial reports, and PubMed article abstracts to annotate and index them with concepts from appropriate ontologies. 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. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. We also identified a subset of CHF patients who were prescribed Cilostazol despite its black box warning, and found that it did not increase mortality in this high-risk group of patients.This proof of principle study shows the potential of text-analytics to mine clinical data warehouses to uncover 'natural experiments' such as the use of Cilostazol in CHF patients. 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. Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L. J., Eilbeck, K., Ireland, A., Mungall, C. J., Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S., Scheuermann, R. H., Shah, N., Whetzel, P. L., Lewis, S. Current progress in network research: toward reference networks for key model organisms. We demonstrate that we enable ontology-based querying and integration of tissue and gene expression microarray data. Moreover, our observations argue for a prospective study to examine the validity of a drug safety warning that may be unnecessarily limiting the use of an efficacious therapy. View details for DOI 10.1136/amiajnl-2011-000523, View details for Web of Science ID 000300768100010, View details for PubMedCentralID PMC3277625. A significant section of UMLS users use a MySQL installation of the metathesaurus and Perl programming language as their access mechanism. Bing Professor. BibTeX @INPROCEEDINGS{Lee07usingannotations, author = {Woei-jyh Lee and Louiqa Raschid and Padmini Srinivasan and Nigam Shah and Daniel Rubin and Natasha Noy}, title = {Using annotations from controlled vocabularies to find meaningful associations}, booktitle = {In Fourth International Workshop on Data Integration in the Life Sciences (DILS 2007}, year = {2007}, pages = {27--29}} 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. 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. 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. Presenting you an all new rendition of the biggest and most loved song of 2000's that simply would stay in our hearts for ages, " Kal Ho Na Ho". Lee, W., Raschid, L., Srinivasan, P., Shah, N., Rubin, D., Noy, N. Searching Ontologies Based on Content: Experiments in the Biomedical Domain. CURRICULUM VITAE . 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. 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. A., Stewart Agras, W., Fei-Fei, L., Shah, N. H. Ethics of Using and Sharing Clinical Imaging Data for Artificial Intelligence: A Proposed Framework. Developing a unified framework for the representation and conceptual integration of biological data and processes is a major challenge in bioinformatics because of the variety of available data and the different levels of detail at which biological processes can be considered.We have developed the HyBrow (Hypothesis Browser) system as a prototype bioinformatics tool for designing hypotheses and evaluating them for consistency with existing knowledge. The widespread implementation of electronic medical records (EHR) offers opportunities to assess patient-centered outcomes within the routine healthcare delivery system. Missingness as Stability: Understanding the Structure of Missingness in Longitudinal EHR data and its Impact on Reinforcement Learning in Healthcare. ICD-9 code). Depression is a prevalent disorder difficult to diagnose and treat. Our mapping produces OWL-DL, a Description Logics based subset of OWL with desirable computational properties for efficiency and correctness. View details for DOI 10.13063/2327-9214.1231. This paper demonstrates that this KR shortcoming leads users to interpret the files in ways that can be erroneous. A method for systematic discovery of adverse drug events from clinical notes. NeurIPS ML for Health (ML4H) Workshop, 2019. Researchers estimate that electronic health record systems record roughly 2-million ambulatory adverse drug events and that patients suffer from adverse drug events in roughly 30% of hospital stays. The hemoglobin intervals produced using the data driven approaches consistently had higher positive predictive value and specificity in predicting an iron supplement prescription than the existing intervals. 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. The Annotator service is available to the community as a REST Web service for creating ontology-based annotations of their data. TMAD incorporates the NCI Thesaurus ontology for searching tissues in the cancer domain. An important challenge in translational bioinformatics is to understand how genetic variation gives rise to molecular changes at the protein level that can precipitate both monogenic and complex disease. Treatment with dipyridamole and/or mirtazapine promote β-cell replication in mice and treatment with dipyridamole is associated with reduced glucose levels in humans. Treatment Patterns for Chronic Comorbid Conditions in Patients With Cancer Using a Large-Scale Observational Data Network. Ontologies--specifications of the entities, their attributes and relationships among the entities in a domain of discourse--are increasingly enabling biomedical researchers to accomplish these tasks. The 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. Evaluation demonstrates that the service has high accuracy and runtime performance. These annotations are not mapped to concepts in any ontology, making it difficult to integrate these datasets across repositories. We utilize a number of data sources and dictionaries to evaluate the concept recognizers in terms of precision, recall, speed of execution, scalability and customizability. View details for DOI 10.1186/1471-2105-8-296, View details for Web of Science ID 000249734300001, View details for PubMedCentralID PMC1988837. We use the formalism of finite model theory in this work. Adverse drug events (ADEs) are undesired harmful effects resulting from use of a medication, and occur in 30% of hospitalized patients. RegenBase is publicly available for browsing, querying and download.Database URL:http://regenbase.org. Sites of structural and/or functional interest were therefore surmised to constitute useful additional features with which to identify the molecular disruptions caused by deleterious AAS. View details for PubMedCentralID PMC6457095. Impact of Predicting Health Care Utilization Via Web Search Behavior: A Data-Driven Analysis. This filtered and augmented UMLS Metathesaurus can potentially be used to improve efficiency and precision of UMLS-based information retrieval and NLP tasks. Specifically, we extracted International Classification of Diseases-9th revision diagnosis and Current Procedural Terminology codes, medication lists, and positive-present mentions of drug and disease concepts from all clinical notes. A small subset of OBO constructs requires deeper consideration. 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.
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