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A web-based data visualization tool for the MIMIC-II database

Joon Lee, Evan Ribey, James R. Wallace
2015 BMC Medical Informatics and Decision Making  
The Explore feature enables the user to select a patient cohort within MIMIC-II and visualize the distributions of various administrative, demographic, and clinical variables within the selected cohort  ...  The Compare feature enables the user to select two patient cohorts and visually compare them with respect to a variety of variables.  ...  ER was supported by the School of Public Health and Health Systems, University of Waterloo, as well as the Undergraduate Research Internship Program of the University of Waterloo, as a co-op student.  ... 
doi:10.1186/s12911-016-0256-9 pmid:26846781 pmcid:PMC4743095 fatcat:teabpq5o25g5hlzcymhn5ycizy

Modular design, application architecture, and usage of a self-service model for enterprise data delivery: The Duke Enterprise Data Unified Content Explorer (DEDUCE)

Monica M. Horvath, Shelley A. Rusincovitch, Stephanie Brinson, Howard C. Shang, Steve Evans, Jeffrey M. Ferranti
2014 Journal of Biomedical Informatics  
Methods: Our query platform, the Duke Enterprise Data Unified Content Explorer (DEDUCE), supports enhanced data exploration, cohort identification, and data extraction from our enterprise data warehouse  ...  Purpose: Data generated in the care of patients are widely used to support clinical research and quality improvement, which has hastened the development of self-service query tools.  ...  tools.  ... 
doi:10.1016/j.jbi.2014.07.006 pmid:25051403 pmcid:PMC4335712 fatcat:impkw7bjhnhpxfmdgu6apacf2q

Visual Computing for Big Data Analysis in Prostate Cancer Research [article]

Jürgen Bernard, Thorsten May, Dirk Pehrke, Thorsten Schlomm, Jörn Kohlhammer
2017 Eurographics State of the Art Reports  
cohorts of patients for clinical tests, as well as generate and validate hypotheses.  ...  This visual-interactive system, developed in close collaboration with medical researchers, helps clinicians efficiently and effectively visualize single and multiple patient histories at a glance, create  ...  clinical data bases easily, build and explore patient cohorts in a never seen effectiveness, build and validate hypotheses without effort, and prepare clinical studies efficiently.  ... 
doi:10.2312/egm.20171044 fatcat:4lhw2ov46jaurox7q2z7o2mhua

A scoping review of clinical decision support tools that generate new knowledge to support decision making in real time

Anna Ostropolets, Linying Zhang, George Hripcsak
2020 JAMIA Journal of the American Medical Informatics Association  
Objective A growing body of observational data enabled its secondary use to facilitate clinical care for complex cases not covered by the existing evidence.  ...  We identified 8 expert-based and 17 data-driven tools. Sixteen (64%) tools were developed in the United States, with the others mostly in Europe.  ...  The tool preserves the ability to transparently explore "what-if" scenarios for cohorts of patients.  ... 
doi:10.1093/jamia/ocaa200 pmid:33120430 fatcat:mkd5vgaynzar7fabodfb7kjmde

WebMeV: A Cloud Platform for Analyzing and Visualizing Cancer Genomic Data [article]

Yaoyu E. Wang, Lev Kuznetsov, Antony Partensky, Jalil Farid, John Quackenbush
2017 bioRxiv   pre-print
WebMeV (https://mev.tm4.org) is an open-source, web-based tool that gives users access to sophisticated tools for analysis of RNA-Seq and other data in an interface designed to democratize data access.  ...  to use analysis tools has remained a barrier to the effective use of such data.  ...  Acknowledgements The authors would like to thank Alex Holman PhD, Brian Lawney PhD for thoughtful discussions and initial testing.  ... 
doi:10.1101/147884 fatcat:62ct3uitdfcdddho6c77omksz4

WebMeV: A Cloud Platform for Analyzing and Visualizing Cancer Genomic Data

Yaoyu E. Wang, Lev Kutnetsov, Antony Partensky, Jalil Farid, John Quackenbush
2017 Cancer Research  
WebMeV (http://mev.tm4.org) is an open-source, web-based tool that gives users access to sophisticated tools for analysis of RNA-Seq and other data in an interface designed to democratize data access.  ...  analysis tools has remained a barrier to the effective use of such data.  ...  Acknowledgments The authors would like to thank Alex Holman, PhD, and Brian Lawney, PhD, for thoughtful discussions and initial testing.  ... 
doi:10.1158/0008-5472.can-17-0802 pmid:29092929 fatcat:px6n6wgoubgvhhsr5leo3fgmzu

COVIZ

Cicero A. L. Pahins, Behrooz Omidvar-Tehrani, Sihem Amer-Yahia, Valérie Siroux, Jean-Louis Pepin, Jean-Christian Borel, João L. D. Comba
2019 Proceedings of the VLDB Endowment  
We demonstrate COVIZ, an interactive system to visually form and explore patient cohorts.  ...  COVIZ seamlessly integrates visual cohort formation and exploration, making it a single destination for hypothesis generation.  ...  The system will then show a series of statistics for the selected cohort in an efficient manner.  ... 
doi:10.14778/3352063.3352075 fatcat:jlydz7rdonc47kqpwibfsa5acy

The European medical information framework: A novel ecosystem for sharing healthcare data across Europe

Simon Lovestone, EMIF Consortium
2019 Learning Health Systems  
novel biomarkers and selecting potential patient samples for pharmacological intervention.  ...  The EMIF platform was built around two main data-types: electronic health record data and research cohort data, and the platform architecture composed of a set of tools designed to enable data discovery  ...  ) for revising the manuscript in response to reviewer's comments.  ... 
doi:10.1002/lrh2.10214 pmid:32313838 pmcid:PMC7156868 fatcat:fko7c5zkijad5j5dbvskkolrgu

A richly interactive exploratory data analysis and visualization tool using electronic medical records

Chih-Wei Huang, Richard Lu, Usman Iqbal, Shen-Hsien Lin, Phung Anh Nguyen, Hsuan-Chia Yang, Chun-Fu Wang, Jianping Li, Kwan-Liu Ma, Yu-Chuan Li, Wen-Shan Jian
2015 BMC Medical Informatics and Decision Making  
We introduced and demonstrated this tool by using EMRs of 14,567 Chronic Kidney Disease (CKD) patients.  ...  The output results are shown in a Sankey diagram-style timeline, which is a particular kind of flow diagram for showing factors' states and transitions over time.  ...  National Science Foundation and UC Davis RISE program, Taiwan Ministry of Science and Technology, grant  ... 
doi:10.1186/s12911-015-0218-7 pmid:26563282 pmcid:PMC4643519 fatcat:ze2kergroze3zffgzxh2lsl7my

Computed Tomography–Based Differentiation of Benign and Malignant Craniofacial Lesions in Neurofibromatosis Type I Patients: A Machine Learning Approach

Cheng-Jiang Wei, Cheng Yan, Yan Tang, Wei Wang, Yi-Hui Gu, Jie-Yi Ren, Xi-Wei Cui, Xiang Lian, Jin Liu, Hui-Jing Wang, Bin Gu, Tao Zan (+2 others)
2020 Frontiers in Oncology  
Three validation cohorts were used: validation cohort 1 (random selection of 90% of the patients in the training cohort), validation cohort 2 (an independent cohort of 9 NF1 patients with benign craniofacial  ...  With more clinical data accumulating in the model, this system may support clinical doctors in the primary screening of true MPNSTs from benign lesions in NF1 patients.  ...  Three validation cohorts were used: validation cohort 1 (random selection of 90% of the patients in the training cohort), validation cohort 2 (an independent cohort of 9 NF1 patients with benign craniofacial  ... 
doi:10.3389/fonc.2020.01192 pmid:32850344 pmcid:PMC7411852 fatcat:2c5ozml3czhxzd3qname5y4s2i

Access to Transplantation and Transplant Outcome Measures (ATTOM): study protocol of a UK wide, in-depth, prospective cohort analysis

Gabriel C Oniscu, Rommel Ravanan, Diana Wu, Andrea Gibbons, Bernadette Li, Charles Tomson, John L Forsythe, Clare Bradley, John Cairns, Christopher Dudley, Christopher J E Watson, Eleanor M Bolton (+8 others)
2016 BMJ Open  
BMJ Open 2016;6:e010377. doi:10.1136/bmjopen-2015-010377 Tool Time of administration Patient cohort EuroQoL five dimensions (EQ-5D) health status tool Recruitment 6 months 1 year* All cohorts  ...  selected as controls for transplanted patients (figure 1).  ... 
doi:10.1136/bmjopen-2015-010377 pmid:26916695 pmcid:PMC4769394 fatcat:5olvazxy4bgnzb5psotp6e7h44

Visual cluster analysis in support of clinical decision intelligence

David Gotz, Jimeng Sun, Nan Cao, Shahram Ebadollahi
2011 AMIA Annual Symposium Proceedings  
In addition to providing efficient and accurate records for individual patients, large databases of EHRs contain valuable information about overall patient populations.  ...  To address this challenge, we describe an approach based on patient similarity which analyzes an EHR database to extract a cohort of patient records most similar to a specific target patient.  ...  The primary use case for an EHR is to digitally capture all medical data for an individual patient and to provide efficient access to the stored data at the point of care.  ... 
pmid:22195102 pmcid:PMC3243281 fatcat:n6dp74p5jbhc7bla5xggv2bqu4

A Toolbox Approach to Flexible and Efficient Data Mining [chapter]

Ole M. Nielsen⋆, Peter Christen, Markus Hegland, Tatiana Semenova, Timothy Hancock
2001 Lecture Notes in Computer Science  
Our toolbox provides a number of routines for basic data mining tasks on top of which the user can add more functions -mainly domain and data collection dependent -for complex and time consuming data mining  ...  This paper describes a flexible and efficient toolbox based on the scripting language Python, capable of handling common tasks in data mining.  ...  The authors also like to thank Christopher Kelman (CDHAC) and the members of the CSIRO CMIS Enterprise Data Mining group for their contributions to this project.  ... 
doi:10.1007/3-540-45357-1_16 fatcat:v3u3byilnfas3cwwi2zaew4bga

QSP Toolbox: Computational Implementation of Integrated Workflow Components for Deploying Multi-Scale Mechanistic Models

Yougan Cheng, Craig J. Thalhauser, Shepard Smithline, Jyotsna Pagidala, Marko Miladinov, Heather E. Vezina, Manish Gupta, Tarek A. Leil, Brian J. Schmidt
2017 AAPS Journal  
Commonly accepted modeling strategies, workflows, and tools have promise to greatly improve the efficiency of QSP methods and improve productivity.  ...  The toolbox also includes scripts for developing and applying virtual populations to mechanistic exploration of biomarkers and efficacy.  ...  Arthur Goldsipe of MathWorks® on improving aspects of the QSP Toolbox.  ... 
doi:10.1208/s12248-017-0100-x pmid:28540623 fatcat:p6vcknp2s5bwzh2rvwhmcs3e5m

PhenoStacks: Cross-Sectional Cohort Phenotype Comparison Visualizations

Michael Glueck, Alina Gvozdik, Fanny Chevalier, Azam Khan, Michael Brudno, Daniel Wigdor
2017 IEEE Transactions on Visualization and Computer Graphics  
These summary charts can be used to identify starting points for deeper exploration of the details of the data (Fig. 1A) .  ...  This work contributes PhenoStacks, a visual analysis tool that enables genetics scientists and researchers to explore phenotypic variation in cross-sectional cohorts of patients with a rare genetic disease  ... 
doi:10.1109/tvcg.2016.2598469 pmid:27514055 fatcat:3ul4wurtmfelbk4yjrnb5desua
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