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CohortExplorer: A Generic Application Programming Interface for Entity Attribute Value Database Schemas.

Abhishek Dixit1, Richard J B Dobson

  • 1Institute of Psychiatry, NIHR Biomedical Research Centre for Mental Health & Biomedical Research Unit for Dementia, South London and Maudsley NHS Foundation Trust & Institute of Psychiatry, Kings College London, London, United Kingdom. abhishek.dixit@kcl.ac.uk.

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Summary
This summary is machine-generated.

Researchers can now easily query clinical data from multiple electronic data capture (EDC) and electronic data management (EDM) systems. CohortExplorer simplifies data exploration for studies using entity-attribute-value (EAV) schemas, improving research efficiency.

Keywords:
CDISC ODMSQLbiobank databaseclinical information systemsentity-attribute-value schema

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Area of Science:

  • Clinical Informatics
  • Data Management
  • Bioinformatics

Background:

  • Most clinical data systems use entity-attribute-value (EAV) schemas for flexibility.
  • EAV schemas present challenges for complex data querying using SQL.
  • Variations in EAV schemas across multiple systems hinder data integration.

Purpose of the Study:

  • To develop a generic application for efficient data and metadata exploration.
  • The application targets EAV schemas organized in a survey format, aligning with CDISC ODM.
  • To enable rapid and easy querying of clinical trial data.

Main Methods:

  • Developed CohortExplorer, a tool written in Perl.
  • Employs an SQL abstraction concept, treating queries as key-value pairs.
  • Designed for "plug-n-play" compatibility with EAV systems.

Main Results:

  • CohortExplorer facilitates the construction of complex queries via an abstracted interface.
  • Demonstrated utility with popular EAV frameworks: Opal (OBiBa) and REDCap.
  • Provides a user-friendly solution for exploring diverse clinical datasets.

Conclusions:

  • CohortExplorer is available under GPL-3+ license with source code on GitHub.
  • Currently supports Opal and REDCap; future versions will include OpenClinica and LabKey.
  • Further development is planned for hierarchical EAV schemas (e.g., i2b2).