G3DMS: Design and Implementation of a Data Management System for the Diagnosis of Genetic Disorders

Abstract

<jats:p>Current health information systems used in genetic research centers and clinics in the Kingdom of Saudi Arabia have failed to enable researchers and health care physicians to utilize genetic and clinical data in their research. In this paper, we aim to design and implement a Genetic Disorders Diagnosis Data Management System (G3DMS) to support clinicians in the process of diagnosing genetic diseases and conducting genetic studies. A case study was undertaken to analyze a health information system in Saudi to understand its design problems via a brainstorming method. We then used the Barker’s system design method and a prototype to validate our proposed system via usability testing. This research has resulted in the development of the G3DMS that comprises: electronic data-capture forms for data entry; a customized query builder to display and modify patient data as well as form research queries; a module that allows historical data to be uploaded in the form of bulk data using a template; export data options to Excel and JavaScript Object Notation (JSON) format; and authorization access for healthcare researchers and clinicians. The G3DMS was implemented in the Princess Al-Jawhara Center of Excellence in Research of Hereditary Disorders, Jeddah, KSA.</jats:p>

GENE2D: A NoSQL Integrated Data Repository of Genetic Disorders Data

“…The physical integration approach is adopted to achieve the intended IDR for GENE2D. The design of the IDR incorporates the ETL process, which will take place at the source system in our case (G3DMS [15]), which has been developed and implemented in a Saudi genetic clinic. We developed our own customized methods for mapping to perform the ETL process.…”

“…The design methodology of the GENE2D system aims to achieve the final design solution in three fundamental design stages: The design process involves automated data extraction transformation and load (ETL) at the source using customized methods. First, the data extraction step results from reading data from the source (G3DMS) [15]) using PHP methods for MySQL. Then a physical schema based on the data structure model is developed.…”

“…Based on these findings, we decided to find a solution to the lack of an efficient system that is able to contribute to the process of managing data, while diagnosing genetic conditions in Saudi genetic clinics and research centers. As a result, the novel G3DMS (genetic disorders diagnosis data management system) was designed with a view to being applicable in any genetic clinic or research center [15]. Next, in this paper, we further aim to find a solution to solve the issue of data integration.…”

“…The proposed solution aims to provide large datasets for clinical research from multiple sources of genetic diagnostic data systems. To achieve this aim, we incorporate an integration framework into the G3DMS [15] using an integrated data repository based on the "not only Structured Query Language (SQL)" (NoSQL) database. The design and implementation of the NoSQL-based integrated data repository (IDR) of genetic disorders data (GENE2D) is demonstrated in this paper.…”

“…The clinical and genetic data of patients with genetic disorders is available in individual clinics that are collected and managed by the system we developed and implemented, namely the G3DMS [15]. The integration of data from these systems requires a centralized repository (IDR) to accommodate all data coming from multiple G3DMSs.…”