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Department of Biomedical Informatics
TRIAD: Walkthrough and Demonstration
Rakesh Dhaval
Applications Architect, The Ohio State University Medical Center
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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
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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 theTissue 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.
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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
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Department of Biomedical Informatics
UML Model Development
Create a
Logical Model
(UML classdiagram) using
Enterprise
Architect
Logical
Model
Create a Data
Model(databaseschema) using
Enterprise
Architect
Data Model
Semantically
Annotate theUML Modelusing the
openMDR EA
Plugin
Semantics
Map the
Logical Modelto the DataModel using
caAdapter
Mapping
Model is
complete andready for reviewand load into
caDSR/
openMDR
Load Model
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Department of Biomedical Informatics
Import Data Model
Project > Database Engineering > Import DB Schema fromODBC ...
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Department of Biomedical Informatics
Data Model
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Department of Biomedical Informatics
Logical Model :
Add a Class
Select Class Click pointer in diagram workspace
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Department of Biomedical Informatics
Logical Model :
Enter Class Name
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Department of Biomedical Informatics
Logical Model :
Add Class Attributes
Select Details tab and click Attributes button
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Department of Biomedical Informatics
Logical Model :
Add Class Attributes
Enter Name Select Java Type
lang Boolean Character Double Float Integer Long String
util Date Click Save
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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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Department of Biomedical Informatics
Logical Model :
Association Properties
Double-click association Specify directionality under
General tab
Specify multiplicity underSource and Target tabs
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Department of Biomedical Informatics
Logical Model
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Department of Biomedical Informatics
UML Model Development
Create a
Logical Model
(UML classdiagram) using
Enterprise
Architect
Logical
Model
Create a Data
Model
(databaseschema) using
Enterprise
Architect
Data Model
Semantically
Annotate the
UML Modelusing the
openMDR EA
Plugin
Semantics
Map the
Logical Model
to the DataModel using
caAdapter
Mapping
Model is
complete and
ready for reviewand load into
caDSR/
openMDR
Load Model
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Department of Biomedical Informatics
ORM : Export XMI
Right-click on Logical View Select Import/Export > Export Package to XMI file...
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Department of Biomedical Informatics
ORM : Export XMI
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Department of Biomedical Informatics
ORM : caAdapter
Select File > New > Model Mapping Service > ObjectModel to Data Model Map Specification
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Department of Biomedical Informatics
ORM : caAdapter
Open the XMI file that was exported from EA
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Department of Biomedical Informatics
ORM : caAdapter
Drag and drop to associate objects andtables, attributes and columns
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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
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Department of Biomedical Informatics
UML Model Development
Create a
Logical Model
(UML classdiagram) using
Enterprise
Architect
Logical
Model
Create a Data
Model
(databaseschema) using
Enterprise
Architect
Data Model
Semantically
Annotate the
UML Modelusing the
openMDR EA
Plugin
Semantics
Map the
Logical Model
to the DataModel using
caAdapter
Mapping
Model is
complete and
ready for reviewand load into
caDSR/
openMDR
Load Model
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Department of Biomedical Informatics
MetaData:
Common Data Elements
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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
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Department of Biomedical Informatics
Semantic Annotation
Creating New Data Elements using openMDRMetadata Registry
Demo
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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
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Department of Biomedical Informatics
Semantic Annotation
Annotate the Clinical Model in EnterpriseArchitectTool
Demo
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Department of Biomedical Informatics
Semantic Annotations
New concept created using openMDR Logical model: Object: Visit Attribute: dischargeDisposition
Data element: Discharge Dispositioncagrid.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)
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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
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Department of Biomedical Informatics
TRIAD Portal Demo
User Interface for Investigator to Query DataTRIAD Portal Under Development
Demo
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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
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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
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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
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Department of Biomedical Informatics
Questions/Comments?
Thank you for your time and attention
TRIAD: Dave Ervin [email protected]
http://wiki.triadcommunity.org
openMDR: Rakesh Dhaval [email protected]
http://cagrid.org/display/mdr
caGrid Knowledge Center: [email protected]
