Introduction

Rakesh Dhaval
Applications Architect, The Ohio State University Medical Center

Department of Biomedical Informatics

 Topics

Use Case
TRIAD
openMDR
TRIAD openMDR Workflow
Questions

Department of Biomedical Informatics

 Use Case

A clinical researcher is conducting an outcomes study in which they want

to utilize data collected during the course of standard clinical care, as well
as bio-specimen data from the Tissue Bank.

For patients that have consented to have their tissue specimen stored in the
Tissue Bank with specific sexGenotype, ethnicity and gender - The
researcher is interested in knowing Pre-Operating Room Diagnosis and
Procedure, as well as Post-Operating Room Diagnosis and Procedure.

The researcher would like to be able integrate and analyze all of this
information as a single data set.

Department of Biomedical Informatics

 Translational Research
Hypothesis
Discovery
Hypothesis Observation &
Formulation Surveillance

Bedside-Bench

Translational Clinical Practice

Basic Sciences Research

Bench-Bedside

Pre-Clinical Analysis &

Research Clinical Dissemination
Research

Department of Biomedical Informatics

 Topics

Use Case
TRIAD
openMDR
TRIAD openMDR Workflow
Questions

Department of Biomedical Informatics

TRI D

Department of Biomedical Informatics

 TRIAD Introduction
TRIAD = CTSA + caGrid
Data Service Wizards
Federated and Localized Metadata Management
caBIG - Cancer Biomedical Informatics Grid
Grid - Controlled and coordinated resource sharing and problem solving in
dynamic, scalable virtual organizations.
caGrid - Provides the software infrastructure that underlies the tools and
applications of caBIG

Distributed Syntactic & Security & Socio-

Data & Semantic Regulatory technical
Knowledge Interoperability Frameworks Factors

TRIAD middleware

Department of Biomedical Informatics

 TRIAD Design
TRIAD is an instance of caGrid that leverages existing, core components:
Service oriented architecture utilizing Axis, Globus, and caGrid extensions.
Data model management via the Global Model Exchange.
Customizable security infrastructure leveraging GAARDS.
Graphical strongly typed grid service creation using Introduce.
Extendable and customizable web service infrastructure.

TRIAD extends caGrid:

Additional options for data service creation, security policy, metadata management, etc.
Federated and/or local metadata management utilized for semantically annotated grid
service creation
Out of the box data services for popular tools such as I2B2 and RedCAP
Integration with commercial and open-source CTMS platforms

TRI D
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 Compatibility and
Interoperability
caBIG provides standards-based compatibility
guidelines for creating software systems that are
syntactically and semantically interoperable.

Reference: caGrid Executive Introduction Slides

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 Knowledge Engineering
Framework
Requirements Analysis
Determine needs, stakeholders and conditions to meet for new product or process

Knowledge Acquisition
Transformation of knowledge into a form used by knowledge-based system

Domain and Data Modeling

Conceptual modeling of system describing entities and their relationships

Semantic Annotation
Process of normalizing and standardizing data and models to allow for information exchange

Borlawsky TB, et al. Development of an Agile Knowledge Engineering Framework in Support of Multi-Disciplinary Translational Research. Proc AMIA Translational Bioinformatics Summit,
2009.

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Example Use Case

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Use Case: Technical
Implementation

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 Enhanced Data Services
Data service generation wizards for common data
centric applications

Class Model &

Assertions

CDEs & Semantics

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 TRIAD Development Process
caCORE is a robust set of tools and resources to support
the development of caBIG-compatible systems
NCI offers comprehensive training for caCORE tools

Create Semantically Harmonized Data Model Generate Grid-ify

Data
Resource

Create an Perform Transform the Generate Code Generate a

Information Semantic Model into and Interfaces Grid Service
Model using a Integration Metadata using using the using Introduce
modeling tool using the the Domain caCORE SDK
EA Plugin Model Gen. Code Generator

Information
Vocabularies CDEs APIs Grid
Models

Reference: Dr. Robert Freimuth, Vocabulary Knowledge Center Director

Department of Biomedical Informatics
 Topics

Use Case
TRIAD
openMDR
TRIAD openMDR Workflow
Questions

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 OpenMDR-based
Federated WorkFlow

openMDR - TRIAD based domain modeling and annotation workflow

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openMDR: Components

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 openMDR:mdrCORE

Metadata Registry - Capable of storing,

versioning, and maintaining semantic and
representational metadata.
Utilizing/enhancing the UK cancergrid cgMDR
ISO11179 database.
Built on eXist database.
Metadata is annotated
with conceptual
information from a local
or remote lexEVS
system(s).
Web based front-end
for creating and
curating semantic
metadata.

Department of Biomedical Informatics

 openMDR:mdrQuery

API and Grid Service for querying across

many disparate semantic metadata
repositories
caGrid grid service - capable of talking to
caDSR and many openMDR systems enabling
federated query of common data elements.
Enhances and wraps the cgMDR mdrConnector
in order to parse the received information into a
common format.
caGrid service enables it to be deployed in any
local or production grid environment and can be
configured and modified to talk to many
semantic metadata systems.

Department of Biomedical Informatics

 openMDR:mdrEAPlugin

Semantic Annotation Tool

Enables semantic annotation of federated
semantics
Utilizes MDRQuery service for locating and
utilizing CDEs from multiple semantic metadata
sources
Options for Search Filters
Enables Search within Context
Tags are created that identify CDE via local
unique id
No need to leave the EA environment

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 openMDR:mdrDomainModel
Generator
Process an MDR Plugin annotated model
and create service metadata which will
enable the service to be a semantically
annotated grid service and easily
discovered
The metadata can be used to generate a data
service using the Introduce Data Service
Wizard.

Department of Biomedical Informatics

 Topics

Use Case
TRIAD
openMDR
TRIAD openMDR WorkFlow
Questions

Department of Biomedical Informatics

 TRIAD - openMDR Based
Service Creation Workflow

openMDR - TRIAD based Service Creation workflow

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 OpenMDR Service Creation
Phases
CDE curation in Local instance of openMDR - using concepts from
Local or Remote (NCI) LexEVS instance
Create an information model - create logical model, data model and
Map Object Model to Data Model in Enterprise Architect (EA)
Annotate logical model with CDE's in EA - using openMDR EA
plugin.
Export annotated XMI
Create domain model file (XML file) with grid service metadata
Generate a system using caCORE SDK 4.X by supplying your
UML model as input
Create Grid Service - Use Introduce grid Service Authoring Toolkit

Department of Biomedical Informatics

 Topics

Use Case
TRIAD
openMDR
TRIAD openMDR WorkFlow
Questions

Department of Biomedical Informatics

 Questions/Comments?
Thank you for your time and attention

TRIAD: Dave Ervin david.ervin@osumc.edu

http://wiki.triadcommunity.org

openMDR: Rakesh Dhaval rakesh.dhaval@osumc.edu

http://cagrid.org/display/mdr

caGrid Knowledge Center: knowledge@osu-citih.org

Department of Biomedical Informatics