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 (rwinslow@jhu.edu)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 (sgranite@jhu.edu)

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