Department of Biomedical Informatics Development of Ontology-anchored Grid-based Data Services to Facilitate Integrative Clinical and Translational Science Introduction Rakesh Dhaval 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 Bedside-Bench Bench-Bedside Basic Sciences Hypothesis Discovery Analysis & Dissemination Pre- Clinical Research Clinical Practice Observation & Surveillance Clinical Research Hypothesis Formulation Translational Research Translational Research

Department of Biomedical Informatics Topics Use Case TRIAD openMDR TRIAD – openMDR Workflow Questions

Department of Biomedical Informatics The Translational Research Informatics and Data Management Grid (TRIAD)

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 Data & Knowledge Syntactic & Semantic Interoperability Security & Regulatory Frameworks Socio- technical Factors TRIAD middleware

Department of Biomedical Informatics 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 TRIAD Design

Department of Biomedical Informatics Compatibility and Interoperability caBIG ® provides standards-based compatibility guidelines for creating software systems that are syntactically and semantically interoperable.

Department of Biomedical Informatics Knowledge Engineering Framework Semantic Annotation Process of normalizing and standardizing data and models to allow for information exchange Domain and Data Modeling Conceptual modeling of system describing entities and their relationships Knowledge Acquisition Transformation of knowledge into a form used by knowledge-based system Requirements Analysis Determine needs, stakeholders and conditions to meet for new product or process Borlawsky TB, et al. Development of an Agile Knowledge Engineering Framework in Support of Multi-Disciplinary Translational Research. Proc AMIA Translational Bioinformatics Summit, 2009.

Department of Biomedical Informatics Example Use Case

Department of Biomedical Informatics Use Case: Technical Implementation

Department of Biomedical Informatics Enhanced Data Services Data service generation wizards for common data centric applications Class Model & Assertions CDEs & Semantics

Department of Biomedical Informatics TRIAD Development Process Create an Information Model using a modeling tool Informatio n Models Perform Semantic Integration using the EA Plugin Vocabulari es Generate Code and Interfaces using the caCORE SDK Code Generator APIs Transform the Model into Metadata using the Domain Model Gen. CDEs Generate a Grid Service using Introduce Grid Reference: Dr. Robert Freimuth, Vocabulary Knowledge Center Director caCORE is a robust set of tools and resources to support the development of caBIG®-compatible systems NCI offers comprehensive training for caCORE tools

Department of Biomedical Informatics Topics Use Case TRIAD openMDR TRIAD – openMDR Workflow Questions

Department of Biomedical Informatics OpenMDR-based Federated WorkFlow openMDR - TRIAD based domain modeling and annotation workflow

Department of Biomedical Informatics openMDR: Components

Department of Biomedical Informatics 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. openMDR:mdrCORE

Department of Biomedical Informatics 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. openMDR:mdrQuery

Department of Biomedical Informatics Semantic Annotation Tool »Enables semantic annotation of federated semantics »Utilizes MDRQuery service for locating and utilizing CDE’s 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 openMDR:mdrEAPlugin

Department of Biomedical Informatics 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. openMDR:mdrDomainModel Generator

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

Department of Biomedical Informatics ① CDE curation in Local instance of openMDR - using concepts from Local or Remote (NCI) LexEVS instance ② Create an information model - create logical model, data model and Map Object Model to Data Model in Enterprise Architect (EA) ③ Annotate logical model with CDE's in EA - using openMDR EA plugin. ④ Export annotated XMI ⑤ Create domain model file (XML file) with grid service metadata ⑥ Generate a system using caCORE SDK 4.X by supplying your UML model as input ⑦ Create Grid Service - Use Introduce grid Service Authoring Toolkit OpenMDR Service Creation Phases

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 openMDR: Rakesh Dhaval caGrid Knowledge Center:

Department of Biomedical Informatics Development of Ontology-anchored Grid-based Data Services to Facilitate Integrative Clinical and Translational Science 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 Logical Model (UML class diagram) using Enterprise Architect Logical Model Create a Data Model (database schema) using Enterprise Architect Data Model Semantically Annotate the UML Model using the openMDR EA Plugin Semantics Map the Logical Model to the Data Model using caAdapter Mapping Model is complete and ready for review and load into caDSR/ openMDR Load Model

Department of Biomedical Informatics Import Data Model Project > Database Engineering > Import DB Schema from ODBC...

Department of Biomedical Informatics Data Model

Department of Biomedical Informatics UML Model Development Create a Logical Model (UML class diagram) using Enterprise Architect Logical Model Create a Data Model (database schema) using Enterprise Architect Data Model Semantically Annotate the UML Model using the openMDR EA Plugin Semantics Map the Logical Model to the Data Model using caAdapter Mapping Model is complete and ready for compatibilit y review and load into caDSR/ openMDR Load Model

Department of Biomedical Informatics Logical Model : Add a Class Select Class Click pointer in diagram workspace

Department of Biomedical Informatics Logical Model : Enter Class Name

Department of Biomedical Informatics Logical Model : Add Class Attributes Select ‘Details’ tab and click ‘Attributes’ button

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’

Department of Biomedical Informatics Logical Model : Add Association Select ‘Associate’ tool from Class Tools menu Drag from Source to Target class SourceTarget

Department of Biomedical Informatics 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 Logical Model (UML class diagram) using Enterprise Architect Logical Model Create a Data Model (database schema) using Enterprise Architect Data Model Semantically Annotate the UML Model using the openMDR EA Plugin Semantics Map the Logical Model to the Data Model using caAdapter Mapping Model is complete and ready for review and load into caDSR/ openMDR Load Model

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

Department of Biomedical Informatics ORM : Export XMI

Department of Biomedical Informatics ORM : caAdapter Select File > New > Model Mapping Service > Object Model to Data Model Map Specification

Department of Biomedical Informatics ORM : caAdapter Open the XMI file that was exported from EA

Department of Biomedical Informatics 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 Logical Model (UML class diagram) using Enterprise Architect Logical Model Create a Data Model (database schema) using Enterprise Architect Data Model Semantically Annotate the UML Model using the openMDR EA Plugin Semantics Map the Logical Model to the Data Model using caAdapter Mapping Model is complete and ready for review and load into caDSR/ openMDR Load 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_0.1cagrid.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: ) Other –Logical model: Object: Patient Attribute: Gender –Data element: Participant Gender Person Gender Text Type (public ID: )

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: NCI caBIG –caGrid toolset: d_overview d_overview –caGrid Knowledge Center: kc.nci.nih.gov/CaGrid/KC/index.php/Main_Pagehttps://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 openMDR: Rakesh Dhaval caGrid Knowledge Center: