TRIAD: Walkthrough and Demonstration

Rakesh Dhaval
Applications Architect, The Ohio State University Medical Center

Department of Biomedical Informatics

 Topics
Review of Use Case
Model Development in Enterprise Architect
Data Model Development
Logical Model Development
Object Relational Mapping
Semantic Annotation
Create Data Elements in openMDR
Annotate Model with Data Elements
Acknowledgements
Questions

Department of Biomedical Informatics

 Use Case

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

utilizing 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

 Topics
Review of Use Case
UML Model Development
Data Model Development
Logical Model Development
Object Relational Mapping
Semantic Annotation
Create Data Elements in openMDR
Annotate Model with Data Elements
TRIAD Portal
Acknowledgements
Questions
Department of Biomedical Informatics
 UML Model Development

Create a Data Create a Map the Semantically Model is

Model Logical Model Logical Model Annotate the complete and
(database (UML class to the Data UML Model ready for review
schema) using diagram) using Model using using the and load into
Enterprise Enterprise caAdapter openMDR EA caDSR/
Architect Architect Plugin openMDR

Logical
Data Model Mapping Semantics Load Model
Model

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 Import Data Model
Project > Database Engineering > Import DB Schema from
ODBC ...

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 Data Model

Department of Biomedical Informatics

 UML Model Development

Create a Data Create a Map the Semantically Model is

Model Logical Model Logical Model Annotate the complete and
(database (UML class to the Data UML Model ready for
schema) using diagram) using Model using using the compatibility
Enterprise Enterprise caAdapter openMDR EA review and load
Architect Architect Plugin into caDSR/
openMDR
Logical
Data Model Mapping Semantics Load Model
Model

Department of Biomedical Informatics

 Logical Model :
Add a Class
Select Class
Click pointer in diagram workspace

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 Logical Model :
Enter Class Name

Department of Biomedical Informatics

 Logical Model :
Add Class Attributes
Select Details tab and click Attributes button

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 Logical Model :
Add Class Attributes
Enter Name
Select Java Type
lang
Boolean
Character
Double
Float
Integer
Long
String
util
Date
Click Save

Department of Biomedical Informatics

 Logical Model :
Add Association
Select Associate tool from Class Tools menu

Drag from Source to Target class

Source Target

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 Logical Model :
Association Properties
Double-click association
Specify directionality under
General tab
Specify multiplicity under
Source and Target tabs

Department of Biomedical Informatics

 Logical Model

Department of Biomedical Informatics

 UML Model Development

Create a Data Create a Map the Semantically Model is

Model Logical Model Logical Model Annotate the complete and
(database (UML class to the Data UML Model ready for review
schema) using diagram) using Model using using the and load into
Enterprise Enterprise caAdapter openMDR EA caDSR/
Architect Architect Plugin openMDR

Logical
Data Model Mapping Semantics Load Model
Model

Department of Biomedical Informatics

 ORM : Export XMI
Right-click on Logical View
Select Import/Export > Export Package to XMI file...

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ORM : Export XMI

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 ORM : caAdapter
Select File > New > Model Mapping Service > Object
Model to Data Model Map Specification

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 ORM : caAdapter
Open the XMI file that was exported from EA

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 ORM : caAdapter
Drag and drop to associate objects and
tables, attributes and columns

Department of Biomedical Informatics

 Topics
Review of Use Case
UML Model Development
Data Model Development
Logical Model Development
Object Relational Mapping
Semantic Annotation
Create Data Elements in openMDR
Annotate Model with Data Elements
TRIAD Portal
Acknowledgements
Questions
Department of Biomedical Informatics
 UML Model Development

Create a Data Create a Map the Semantically Model is

Model Logical Model Logical Model Annotate the complete and
(database (UML class to the Data UML Model ready for review
schema) using diagram) using Model using using the and load into
Enterprise Enterprise caAdapter openMDR EA caDSR/
Architect Architect Plugin openMDR

Logical
Data Model Mapping Semantics Load Model
Model

Department of Biomedical Informatics

 MetaData:
Common Data Elements

Department of Biomedical Informatics

 Topics
Review of Use Case
UML Model Development
Data Model Development
Logical Model Development
Object Relational Mapping
Semantic Annotation
Create Data Elements in openMDR
Annotate Model with Data Elements
TRIAD Portal
Acknowledgements
Questions
Department of Biomedical Informatics
 Semantic Annotation

Creating New Data Elements using openMDR

Metadata Registry

Demo

Department of Biomedical Informatics

 Topics
Review of Use Case
UML Model Development
Data Model Development
Logical Model Development
Object Relational Mapping
Semantic Annotation
Create Data Elements in openMDR
Annotate Model with Data Elements
TRIAD Portal
Acknowledgements
Questions
Department of Biomedical Informatics
 Semantic Annotation

Annotate the Clinical Model in Enterprise

Architect Tool

Demo

Department of Biomedical Informatics

 Semantic Annotations
New concept created using openMDR
Logical model:
Object: Visit
Attribute: dischargeDisposition
Data element: Discharge Disposition
cagrid.org_0edff23f-c0fa-4a18-ac06-97e4893d42e8_0.1
caTissue link
Logical model:
Object: Patient
Attribute: studyNumber
Data element: Participant Identifier java.lang.Long (public ID: 2513658)
Other
Logical model:
Object: Patient
Attribute: Gender
Data element: Participant Gender Person Gender Text Type (public ID:
2513661)

Department of Biomedical Informatics

 Topics
Review of Use Case
UML Model Development
Data Model Development
Logical Model Development
Object Relational Mapping
Semantic Annotation
Create Data Elements in openMDR
Annotate Model with Data Elements
TRIAD Portal
Acknowledgements
Questions
Department of Biomedical Informatics
 TRIAD Portal Demo
User Interface for Investigator to Query Data
TRIAD Portal Under Development

Demo

Department of Biomedical Informatics

 Topics
Review of Use Case
UML Model Development
Data Model Development
Logical Model Development
Object Relational Mapping
Semantic Annotation
Create Data Elements in openMDR
Annotate Model with Data Elements
TRIAD Portal
Acknowledgements
Questions
Department of Biomedical Informatics
 Acknowledgements
CTSA: http://ctsaweb.org/
NCI caBIG
caGrid toolset:
https://cabig.nci.nih.gov/index_html/sharable/
cagrid_overview
caGrid Knowledge Center:
https://cabig-kc.nci.nih.gov/CaGrid/KC/index.php/
Main_Page
Active caGrid Community

Department of Biomedical Informatics

 Topics
Review of Use Case
UML Model Development
Data Model Development
Logical Model Development
Object Relational Mapping
Semantic Annotation
Create Data Elements in openMDR
Annotate Model with Data Elements
TRIAD Portal
Acknowledgements
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