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The CardioVascular Research Grid: A Resource Supporting National Collaborations in Heart Research NHLBI R24 HL085343 Stephen J. Granite, MS, MBA The Johns Hopkins University Institute for Computational Medicine. Cardiovascular (CV) Community Needs. - PowerPoint PPT Presentation
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The CardioVascular Research Grid:
A Resource Supporting National Collaborations in Heart Research
NHLBI R24 HL085343
Stephen J. Granite, MS, MBAThe Johns Hopkins University
Institute for Computational Medicine
Cardiovascular (CV) Community NeedsCardiovascular (CV) Community Needs• Describe both CV data and data collection methods
CV-specific ontologies Semantic description facilitates re-use of data
• Standards-based representation and management of multi-scale CV data
There are unique CV data types for which no standards exist Time-evolving CV Electrophysiology (EP), electrocardiogram (ECG), and multi-
modal image data
• Query across multiple types of primary and derived data located and maintained at different sites
Data integration Federated querying
The CardioVascular Research Grid The CardioVascular Research Grid (CVRG) Project Addresses These Needs(CVRG) Project Addresses These Needs
• CVRG = a community resource for the distributed management, semantic description, federation, and analysis of both primary and derived CV data
• CVRG is developing new CV-specific data management resources
delivering CV data analysis tools and customized workflows
creating easy to use, customized interfaces for accessing its resources
providing these resources in a secure manner
The CVRG Approach to Technology The CVRG Approach to Technology DevelopmentDevelopment
• Don’t re-invent the wheel When possible, re-use or extend software components from other BioGrid
projects (e.g., BIRN and the cancer Biomedical Informatics Grid (caBIG))
• Address the special needs of the CV community Time-evolving imagery ECG and EP data CV-specific ontologies Integration of multi-scale data sets Specific data analysis workflows
• Assure that the CV community drives technology development Subject Matter Expert Ontology Review CV Working Groups
The CVRG Development TeamThe CVRG Development TeamEmory UniversityProject PI’s and Investigators:Joel Saltz (caGrid)Tahsin Kurc (caGrid)Developers:Mark Grand (Lead Developer)Michel Monsour (Study Data Interfaces)Tony Pan (Imaging Interfaces)Ashish Sharma (Imaging Interfaces)
caGrid Knowledge CenterJustin Permar (caGrid)Steve Langella (Security)
UCSD (BIRN; Yrs 1-2)Mark EllismanJeff GretheRamil Manansala
Johns Hopkins UniversityResource PI: Raimond Winslow ([email protected])Project PI’s and Investigators:Donald Geman (Machine Learning)Michael Miller (Cardiac CA)Daniel Naiman (Machine Learning)Tilak Ratnanather (Cardiac CA)Raimond Winslow (ECG & EP Services)Laurent Younes (Cardiac CA)Project Manager: Stephen Granite ([email protected])
Developers:Timothy Brown (Cardiac CA Interfaces)Bill Girten (ECG Interfaces)David Hopkins (Website & Portal)Anthony Kolasny (Cardiac CA Interfaces)Luan Le (Imaging Interfaces)Kyle Reynolds (Systems Support)Michael Shipway (Machine Learning Interfaces)Matthew Toerper (Imaging Interfaces)
What Data Services Does CVRG Provide?What Data Services Does CVRG Provide?
CVRG PortalPortlet AccessFederated Querying
CVRG PortalPortlet AccessFederated Querying
Developed by CVRG
Developed by NCI-caBIG
Other Open Source
ProteomicsData Service
PACS (DCM4CHE),DICOM DataService
Virtual PACS
ECG DataService
Study Data Service(OpenClinica)
mRNAExpressionData Service
SNP/GWASData Service Other CVRG Nodes
Grid-enabling Existing SystemsGrid-enabling Existing Systems
Data Service (“Lighthouse”)
Abstract Model(Terminology,
Semantics, Objects,…)
caGridIntroduce
NCI EVS,NCBOBioPortal
ManagedLocally
CVRG Node 1(OSU)
ECG DataService
CVRG Node 2(Emory)
CVRG Node 3(JHU)
CVRG Portal
Portlet AccessFederated Querying
CVRG Portal
Portlet AccessFederated Querying
Federated Queries
Real Database(Oracle, DB2,…)
Study Data Service(OpenClinica)
What Analysis Services Does CVRG What Analysis Services Does CVRG Provide?Provide?
Heart Shape & Motion Analyses(LDDMM, PTA)
Machine Learning;Rweb, geWorkbench
ECG AnalysisServices
Other CVRG Nodes
CVRG PortalWorkflow Access
CVRG PortalWorkflow Access
Developed by CVRG
Developed by NCI-caBIG
Other Open Source
ECG Data Management and Analysis:ECG Data Management and Analysis:An Example of Novel Tool DevelopmentAn Example of Novel Tool Development
• Problem: ECGs = most common type of biomedical time-series data Primary data not always saved in digital format
Paper by default & multi-image DICOM in conjunction with ultrasound Typically, only analytically derived data are stored
Difficult for clinical researchers to compare derived data (i.e., proprietary analysis methods)
• Challenges: No comprehensive data model/database implementation for managing digital ECG data
existed at the start of the CVRG Currently, no hardened ECG ontology is available for use in annotation Few open-source web-based ECG analysis tools available to the CV community (e.g.,
Physionet; http://www.physionet.org/)
• Solution: Develop these resources
ECG Analysis WorkflowsECG Analysis Workflows
Physionet Workflow
Reynolds Workflow
Data Storage Services
Norav ECG Data (RDT)
Norav ECG Data (RDT)
Physionet ECG Data(WFDB – header, data)
Physionet ECG Data(WFDB – header, data)
ECG Data Analytical Services
ECG Analysis Parameters ECG Analysis Parameters
Analysis ResultsServices
RDT -> HL7aECGRDT -> HL7aECG
WFDB ECG Data WFDB ECG Data
Reynolds ECG Analysis Algorithms
Reynolds ECG Analysis Algorithms
Physionet ECG Analysis Algorithms
Physionet ECG Analysis Algorithms
ResultsResults
ResultsResultsMetadata XML Metadata XML
Alpha CVRG Portal DemoAlpha CVRG Portal Demo• Alpha CVRG Portal leverages caGrid Portal and Web Single Sign-
On (WebSSO) caGrid Portal leverages LifeRay open-source Portal Server (
http://www.liferay.com/) caGrid WebSSO leverages JA-SIG Central Authentication Service (
http://www.jasig.org/cas/)
• Portlets implemented: Beta Signup ECG Storage/Analysis Workflow (end-to-end for both workflows) Imaging Storage & Analysis (i.e., virtualPACS utilization and Large
Diffeomorphic Deformation Metric Mapping (LDDMM)) ProteinDB utilization
• Beta Signup/ECG Workflow Demo
Ontologies:Ontologies:• Emerging Strategy
• When ontologies/tools are available from BIRN, caBIG and the NCBO (http://bioportal.bioontology.org/), use them
• Develop new ontologies that are of special importance in CV research
• CV EP Ontology• Version 1 complete
• ECG Ontology• Version 1 nearing completion
• CV Imaging Ontologies• Beginning stages, with the National Alliance for Medical Image Computing (NAMIC)
• Deposit new CV ontologies at NCBO
• These ontologies are then available for use by BIRN and caBIG
Collaboration With the CVRG ProjectCollaboration With the CVRG Project• CVRG Collaboration Proposals (PAR-07-426, as amended in NOT-08-103)
• Development of a Hypertrophic Cardiomyopathy Consortium (Abraham)
• Federation and Analysis of MESA Genetic and Imaging Data Using the CVRG (Lima)
• Data Ontologies for Integrating Cardiovascular Epidemiological Studies (Rice)
• Final LOI August 21 2009, final proposal submission September 21 2009
• One BRP collaboration proposal submitted
• CardioVascular Imaging Informatics (CVRG & NAMIC Collaboration, PI = Kikinis)
• NCBO Driving Biological Project
• Ontology-Based Annotation of Biomedical Time-Series Data (Winslow)
• Physionet (analytical services)
• Site beta testers (request account on CVRG portal)
• Working Groups, Conference on CardioVascular Informatics
CVRG Web ResourcesCVRG Web Resources• CVRG Website – Information about the CVRG (
http://www.cvrgrid.org/)
• CVRG Portal – Web environment for accessing all tools
• Link on the CVRG Website
• CVRG Wiki – Technical information on all services• Link on the CVRG Website• Software dependencies and revisions• Build information• Installation instructions
Questions and DiscussionQuestions and Discussion