1. No category

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
• 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)
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)
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 opensource projects (e.g., i2b2, Globus Online, etc.)
– Form collaborations to develop new software components
• Address the special needs of the CV community
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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
NHLBI-FUNDED
Studies
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Multi-Ethnic Study of Atherosclerosis
Coronary Artery Disease Risk in Young Adults
Minority Health Grid
Jackson Heart
• Pediatric Heart Network
ECG Tool Initial Design/Workflow
Reynolds Workflow
Norav ECG Data
(RDT)
ECG Data
ECG Analysis Parameters
RDT -> HL7aECG
Reynolds ECG Analysis
Algorithms
Data Storage
Services
Analytical
Services
Results
Analysis
Results
Services
Physionet Workflow
Physionet ECG Data
(WFDB – header, data)
WFDB ECG Data
Metadata XML
Physionet ECG Analysis
Algorithms
Results
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
– caGrid WebSSO used Java Architectures Special Interest Group
Central Authentication Service (JA-SIG CAS)
• Portlets implemented:
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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
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
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
ECG Tool Revised Design/Workflow
WFDB, HL7aECG
RDT, GE MUSE
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’s WaveForm
DataBase (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
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
Current CVRG Web Interfaces
XNAT-CVI
ECGrid Toolkit
Web Data Services (JHU Cloud)
CVRG Portal
Galaxy
MR/CT/US
Analyses
ECG
Analyses
Web Analysis Services
(Amazon EC2 & JHU Cloud)
Bioportal
BioPortalal
Web-Browser
Software as a Service
Ontology
(RESTful Web Service)
Live Demonstration
• CVRG Demonstration Portal
– Galaxy
– eXtensible NeuroImaging Toolkit – CV
Imaging (XNAT-CVI)
– ECGrid Toolkit
• CVRG website -> Portal
– http://www.cvrgrid.org
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
Web References
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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/
Acknowledgements
Johns Hopkins University
Michael Miller
Raimond Winslow
Laurent Younes
Siamak Ardekani
Stephen Granite
David Hopkins
Kyle Reynolds
Michael Shipway
Christian Jurado
NHLBI
Jennifer Larkin
NHLBI R24 HL085343
Emory University
Joel Saltz
Andrew Post
Tahsin Kurc
Richard Willard
Himanshu Rathod
Wake Forest University
J. Jeffrey Carr
Yaorong Ge
Ricardo Peral
University of Chicago
Ian Foster
Ravi Madduri
Liu Bo