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Development of Ontology-anchored Grid-based Data Services to Facilitate Integrative Clinical and Translational Science

Development of Ontology-anchored Grid-based Data Services to Facilitate Integrative Clinical and Translational Science. Introduction Rakesh Dhaval The Ohio State University Medical Center. Topics. Use Case TRIAD openMDR TRIAD – openMDR Workflow Questions. Use Case.

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Development of Ontology-anchored Grid-based Data Services to Facilitate Integrative Clinical and Translational Science

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  1. Development of Ontology-anchored Grid-based Data Services to Facilitate Integrative Clinical and Translational Science Introduction Rakesh Dhaval The Ohio State University Medical Center

  2. Topics • Use Case • TRIAD • openMDR • TRIAD – openMDR Workflow • Questions

  3. 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.

  4. Hypothesis Discovery Hypothesis Formulation Observation & Surveillance Bedside-Bench Translational Research Clinical Practice Basic Sciences Bench-Bedside Pre-Clinical Research Analysis & Dissemination Clinical Research Translational Research

  5. Topics • Use Case • TRIAD • openMDR • TRIAD – openMDR Workflow • Questions

  6. The Translational Research Informatics and Data Management Grid (TRIAD) TRI D

  7. 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 TRIAD middleware

  8. 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

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

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

  11. Example Use Case

  12. Use Case: Technical Implementation

  13. Enhanced Data Services • Data service generation wizards for common data centric applications Class Model & Assertions CDEs & Semantics

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

  15. Topics • Use Case • TRIAD • openMDR • TRIAD – openMDR Workflow • Questions

  16. OpenMDR-based • Federated WorkFlow openMDR - TRIAD based domain modeling and annotation workflow

  17. openMDR: Components

  18. openMDR:mdrCORE • Metadata Registry - Capable of storing, versioning, and maintaining semantic and representational metadata. • Utilizing/enhancing the UK cancergridcgMDR ISO11179 database. • Built on eXist database. • Metadata is annotated with conceptual information from a local or remote lexEVSsystem(s). • Web based front-end for creating and curating semantic metadata.

  19. 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 cgMDRmdrConnector 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.

  20. openMDR:mdrEAPlugin • 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

  21. openMDR:mdrDomainModelGenerator • 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.

  22. Topics • Use Case • TRIAD • openMDR • TRIAD – openMDRWorkFlow • Questions

  23. TRIAD - openMDR Based Service Creation Workflow openMDR - TRIAD based Service Creation workflow

  24. OpenMDR Service Creation Phases CDE curation in Local instance of openMDR - using concepts from Local or Remote (NCI) LexEVSinstance 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

  25. Topics • Use Case • TRIAD • openMDR • TRIAD – openMDRWorkFlow • Questions

  26. 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

  27. 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

  28. 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

  29. 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.

  30. 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

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

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

  33. Data Model

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

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

  36. Logical Model : Enter Class Name

  37. Logical Model :Add Class Attributes • Select ‘Details’ tab and click ‘Attributes’ button

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

  39. Logical Model :Add Association • Select ‘Associate’ tool from Class Tools menu • Drag from Source to Target class Source Target

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

  41. Logical Model

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

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

  44. ORM : Export XMI

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

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

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

  48. 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

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

  50. MetaData:Common Data Elements

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