1 / 17

Providing the cardiovascular community with rich web interfaces to integrate cardiovascular tools, data and analysis

Providing the cardiovascular community with rich web interfaces to integrate cardiovascular tools, data and analysis. Stephen J. Granite, MS, MBA CVRG Program Manager NHLBI R24-HL085343 http://www.cvrgrid.org. Data Management Needs of the Cardiovascular (CV) Community.

eunice
Download Presentation

Providing the cardiovascular community with rich web interfaces to integrate cardiovascular tools, data and analysis

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Providing the cardiovascular community with rich web interfaces to integrate cardiovascular tools, data and analysis Stephen J. Granite, MS, MBA CVRG Program Manager NHLBI R24-HL085343 http://www.cvrgrid.org

  2. Data Management Needs of the Cardiovascular (CV) Community • CV-specific ontologies for describing data and data collection protocols • Must address unique CV data types • Time-evolving electrophysiology (EP), electrocardiogram (ECG), and multi-modal image data • Software tools for managing diverse types of CV data • Must be well documented, easy to install/use, secure, and work out of the box • Ability to query multiple data sources located and maintained at different sites • Project design often requires that specific types of data be collected and managed at different sites (e.g., MR Reading Centers, ECG Reading Centers, etc)

  3. The CVRG Project Mission: Serve the needs of basic and clinical cardiovascular researchers by providing seamless, customized, secure access to study datasets and analysis tools Team: Institute for Computational Medicine, Johns Hopkins University (Winslow, Miller) Image Lab, Wake Forest University (Carr, Ge) Center for Comprehensive Informatics, Emory University (Saltz, Post) Computation Institute, University of Chicago (Foster, Madduri)

  4. The CVRG Approach to Technology Development • Don’t re-invent the wheel • When possible, re-use or extend software components from National Center for Biomedical Computing (NCBC) & other open-source projects (e.g., i2b2, Globus Online, etc.) • Form collaborations to develop new software components • Address the special needs of the CV community • Time-evolving imagery • ECG and EP data • CV-specific vocabularies • Integration of multi-scale data sets • Specific data analysis workflows • Let the CV community drive technology development

  5. NHLBI-FUNDED Studies • Multi-Ethnic Study of Atherosclerosis • Coronary Artery Disease Risk in Young Adults • Minority Health Grid • Jackson Heart • Pediatric Heart Network

  6. ECG Tool Initial Design/Workflow Reynolds Workflow ECG Analysis Parameters Norav ECG Data (RDT) Reynolds ECG Analysis Algorithms Results RDT -> HL7aECG ECG Data Data Storage Services Analytical Services Analysis Results Services Physionet Workflow WFDB ECG Data Physionet ECG Data (WFDB – header, data) Physionet ECG Analysis Algorithms Results Metadata XML

  7. CVRG Web Interfaces: Initial Approach • Alpha CVRG Portal leveraged caGrid Portal and Web Single Sign-On (WebSSO) • caGrid Portal built upon Liferay 4.1 open-source Portal Server • caGridWebSSO used Java Architectures Special Interest Group Central Authentication Service (JA-SIG CAS) • Portlets implemented: • Beta Signup • ECG Storage/Analysis Workflow (end-to-end for both workflows) • Imaging Storage & Analysis • Heart shape and motion analysis • ProteinDB utilization Beta Signup/ECG Workflow Demo

  8. Initial Approach Lessons Learned • Portal (e.g., Liferay 4.1) • All the work is done on the server • Changing the tabs requires a web browser refresh • Resets the portlet displayed so data entry starts all over again • New requirements appeared during development • Need to dynamically display and annotate an ECG • Dynamic refresh of portlets themselves difficult • Ability to display an embedded scrolling graph next to impossible • Call to tools outside of a portlet required extensions to Liferay itself • Portal environment customization should be minimized

  9. Investigation of Web 2.0 • Web 2.0 interfaces/tools • Work can be divided between the server & web browser • Components can be placed in web pages or executed standalone, making changes dynamic • Yahoo User Interface (YUI) • Open-source JavaScript library • Used by i2b2 in Web Client • Google Web Toolkit & API Library (GWT) • Open-source Java project with plugin for Eclipse • Allows Java developers to produce rich JavaScript tools without knowledge of syntax • Used by LabKey & WebProtege

  10. ECG Tool Revised Design/Workflow WFDB, HL7aECG RDT, GE MUSE

  11. CVRG Web Interfaces: Revised Approach • Prototype ECG Gadget (renamed ECGrid Toolkit) • Built using GWT & Google Visualization API • Can exist in a portal, a web page, a dashboard, a flash drive and/or a handheld device (e.g., iPhone) • Expanded avenues of tool access, “putting it in the users’ hands” • Functions on multiple platforms and multiple browsers • Functionality implemented: • Integrated the ECG workflows into one unified workflow • Accepts multiple ECG formats stores in Physionet’sWaveFormDataBase (WFDB) format • Extended the capability of scrolling ECG visualization • Allows for annotation within the waveform, using National Center for Biomedical Ontology (NCBO) REST Services real-time Prototype ECGrid Toolkit Demo

  12. Revised Approach Lessons Learned • Web 2.0 applications are more dynamic • Flexibility in deployment require development of authorization/authentication components as well • Portal/Web 2.0 combination maximizes strengths/minimizes weaknesses • Portal serves as an interface access point • Allows addition/removal of interfaces without a portal reboot • Interfaces can be run on servers separate from the portal • Appear centralized when they actually are distributed

  13. Current CVRG Web Interfaces XNAT-CVI ECGrid Toolkit Web Data Services (JHU Cloud) BioPortalal CVRG Portal Web-Browser Software as a Service MR/CT/US Analyses ECG Analyses Galaxy Ontology (RESTful Web Service) Web Analysis Services (Amazon EC2 & JHU Cloud)

  14. Live Demonstration • CVRG Demonstration Portal • Galaxy • eXtensibleNeuroImaging Toolkit – CV Imaging (XNAT-CVI) • ECGrid Toolkit • CVRG website -> Portal • http://www.cvrgrid.org

  15. Future Development • In Process • Integration of NSF Cybersecurity Infrastructure Logon (CILogon) into CVRG Portal • Alternative Shibboleth method developed using Johns Hopkins Enterprise Authentication (for testing purposes) • Deployment of Survey portlet for user feedback on CVRG tools • Planned • Healthy Heart Imaging cohort to be made available to the community for clinical trial controls via XNAT-CVI instance at Wake Forest • ECGs corresponding to Image datasets to be made available via ECGrid Toolkit at Johns Hopkins • ECG analysis services to be made available via Galaxy, to demonstrate workflow sharing and re-use

  16. Web References • CVRG - http://www.cvrgrid.org/ • JHU Institute for Computational Medicine – http://www.icm.jhu.edu/ • Wake Forest University Image Lab – http://www.wakehealth.edu/imagelab/ • Emory University Center for Comprehensive Informatics – http://cci.emory.edu/cms/index.html • University of Chicago Computation Institute - http://www.ci.anl.gov/ • Liferay – http://www.liferay.com/community/welcome/dashboard • JA-SIG CAS - http://www.jasig.org/cas/ • YUI - http://developer.yahoo.com/yui/ • i2b2 Web Client - https://www.i2b2.org/ • GWT - http://code.google.com/webtoolkit/ • LabKey - https://www.labkey.org/ • WebProtege - http://protegewiki.stanford.edu/index.php/WebProtege • NCBO Bioportal – http://bioportal.bioontology.org/ • Physionet – http://www.physionet.org/ • CILogon - http://www.cilogon.org/

  17. Acknowledgements Johns Hopkins University Emory University Michael Miller RaimondWinslow Laurent Younes SiamakArdekani Stephen Granite David Hopkins Kyle Reynolds Michael Shipway Christian Jurado Joel Saltz Andrew Post TahsinKurc Richard Willard HimanshuRathod Wake Forest University J. Jeffrey Carr YaorongGe Ricardo Peral NHLBI University of Chicago Jennifer Larkin Ian Foster Ravi Madduri Liu Bo NHLBI R24 HL085343

More Related