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Dixit A, Dobson RJ. CohortExplorer: A Generic Application Programming Interface for Entity Attribute Value Database Schemas. JMIR Med Inform. 2014;2(2):e32doi: 10.2196/medinform.3339.
Dixit, A., & Dobson, R. J. (2014). CohortExplorer: A Generic Application Programming Interface for Entity Attribute Value Database Schemas. JMIR medical informatics, 2(2), e32. https://doi.org/10.2196/medinform.3339
Dixit, Abhishek, and Dobson, Richard J B. "CohortExplorer: A Generic Application Programming Interface for Entity Attribute Value Database Schemas." JMIR medical informatics vol. 2,2 (2014): e32. doi: https://doi.org/10.2196/medinform.3339
Dixit A, Dobson RJ. CohortExplorer: A Generic Application Programming Interface for Entity Attribute Value Database Schemas. JMIR Med Inform. 2014 Dec 01;2(2):e32. doi: 10.2196/medinform.3339. PMID: 25601296; PMCID: PMC4288104.
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JMIR Med Inform. 2014 Dec 01;2(2):e32. doi: 10.2196/medinform.3339.

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

JMIR medical informatics

Abhishek Dixit, Richard J B Dobson

Affiliations

  1. Institute 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. [email protected].

PMID: 25601296 PMCID: PMC4288104 DOI: 10.2196/medinform.3339

Abstract

BACKGROUND: Most electronic data capture (EDC) and electronic data management (EDM) systems developed to collect and store clinical data from participants recruited into studies are based on generic entity-attribute-value (EAV) database schemas which enable rapid and flexible deployment in a range of study designs. The drawback to such schemas is that they are cumbersome to query with structured query language (SQL). The problem increases when researchers involved in multiple studies use multiple electronic data capture and management systems each with variation on the EAV schema.

OBJECTIVE: The aim of this study is to develop a generic application which allows easy and rapid exploration of data and metadata stored under EAV schemas that are organized into a survey format (questionnaires/events, questions, values), in other words, the Clinical Data Interchange Standards Consortium (CDISC) Observational Data Model (ODM).

METHODS: CohortExplorer is written in Perl programming language and uses the concept of SQL abstract which allows the SQL query to be treated like a hash (key-value pairs).

RESULTS: We have developed a tool, CohortExplorer, which once configured for a EAV system will "plug-n-play" with EAV schemas, enabling the easy construction of complex queries through an abstracted interface. To demonstrate the utility of the CohortExplorer system, we show how it can be used with the popular EAV based frameworks; Opal (OBiBa) and REDCap.

CONCLUSIONS: The application is available under a GPL-3+ license at the CPAN website. Currently the application only provides datasource application programming interfaces (APIs) for Opal and REDCap. In the future the application will be available with datasource APIs for all major electronic data capture and management systems such as OpenClinica and LabKey. At present the application is only compatible with EAV systems where the metadata is organized into surveys, questionnaires and events. Further work is needed to make the application compatible with EAV schemas where the metadata is organized into hierarchies such as Informatics for Integrating Biology & the Bedside (i2b2). A video tutorial demonstrating the application setup, datasource configuration, and search features is available on YouTube. The application source code is available at the GitHub website and the users are encouraged to suggest new features and contribute to the development of APIs for new EAV systems.

Keywords: CDISC ODM; SQL; biobank database; clinical information systems; entity-attribute-value schema

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