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PRGN Data Elements Harmonization

PRGN Data Elements Harmonization. PGRN Team Division of Biomedical Informatics Mayo Clinic. Objectives. Provide support the PGRN through: Standardization of terminology Standardization of data elements Harmonization of data elements Creation of data dictionaries Data transformation

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PRGN Data Elements Harmonization

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  1. PRGNData Elements Harmonization PGRN Team Division of Biomedical Informatics Mayo Clinic

  2. Objectives • Provide support the PGRN through: • Standardization of terminology • Standardization of data elements • Harmonization of data elements • Creation of data dictionaries • Data transformation • Mapping to standards • Converting data values • Prospective or retrospective studies

  3. NCBO CaDSR LexEVS Vocabularies Mayo MDR … Data Element Registry & Harmonization Platform

  4. Mayo Ext Vocab Vocab … DE DE Data Element Registry & Harmonization Platform • Data Element Registry & Harmonization Platform • Create/Edit Domain entities like clinical studies • Create/Edit/Import Data Elements (e.g. Study attributes) • Data elements may have mappings to repositories like CaDSR, NCBO, MDR and local vocabularies. • Data element lookup services using LexEVS APIs. • Data Elements and Vocabularies inside and outside Mayo.

  5. Mayo Ext Vocab Vocab … DE DE Reference Models (e.g. 11179 and extensions) Data Element Registry & Harmonization Platform • Using the platform: • User creates DE mappings and export it to knowledgebase - a collection of user dictionaries. • KB is based on data models e.g. XMDR 11179 + extensions and/or combination of suitable models. • Platform can also save mapping in XML or custom formats – future extensions. Knowledgebase (Dictionaries)

  6. Mayo Ext Vocab Vocab … DE DE Data Element Registry & Harmonization Platform Knowledgebase (Dictionaries)

  7. Mayo Ext Vocab Vocab … DE DE Data Element Registry & Harmonization Platform Knowledgebase (Dictionaries) User Application Data elements in user application mapping to user-defined data elements defined in user dictionary Data elements in user application mapping to standard data elements mapped in user dictionary

  8. Mayo Ext Vocab Vocab … DE DE Data Element Registry & Harmonization Platform Knowledgebase (Dictionaries) User Application User application can then utilizes these mappings; it may create its own mapping for its own processes.

  9. Mayo Ext Vocab Vocab … DE DE Data Element Registry & Harmonization Platform Knowledgebase (Dictionaries) User Application

  10. Mayo Ext Vocab Vocab … DE DE Data Element Registry & Harmonization Platform Knowledgebase (Dictionaries) User Application User can add its own auxiliary processes like transformation routines to process incoming data before it is loaded into user databases.

  11. Mayo Ext Vocab Vocab … DE DE Data Element Registry & Harmonization Platform Knowledgebase (Dictionaries) User Application (Equipped with KB)

  12. Mayo Ext Vocab Vocab … DE DE Data Element Registry & Harmonization Platform Knowledgebase (Dictionaries) User Application (Equipped with KB) Incoming data Processing OUTPUT

  13. Proposed Modules • Terminology browser • New term proposals • Data element platform • Creation, harmonization, etc • Data dictionary • Creation, update, etc • Data transformer • Standardize legacy data, export • Application schema repository • Map local database schemas to data dictionaries • Development: modules can be built separately but should be designed under a common architecture

  14. Proposed Tasks • Investigate the status of the platform (eleMap) • Accessible? Open Source ? • Web Services or Embedded Library? • Search APIs – based on LexEVS ? • Search capabilities - Textual, Soundex/Double metaphone, Synonyms? • Output format support (MSExcel, … ?) • Design process to add/Edit study and variables using platform • Manual – using platform UI • Automatic – using platform APIs • Design the shared schema (Exchange) • Agree on a format which works for both (user and platform) • Transformation Rules in Schema/Value Sets/Permissible/Enumerated values

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