JMIR Publications

ABSTRACT

Background:

Effective data management is crucial in clinical studies for precise tracking, secure storage, and reliable analysis of samples. Traditional systems often encounter challenges like barcode recognition errors, inadequate data detail, and diminished performance under heavy workloads.

Objective:

This paper aims to enhance clinical data management by improving barcode robustness, increasing data granularity, and boosting system throughput. These improvements address key challenges in barcode informatics systems, as highlighted in prior studies, to better support real clinical applications. Additionally, we aim to validate the design criteria on various gastrointestinal (GI) related studies, ensuring it can be easily integrated into other clinical data management workflows.

Methods:

We evaluated the robustness of various barcode technologies under significant blurring conditions, implemented a dynamic organ-specific archive in the REDCap database for various clinical study data collection criteria, and utilized Docker to containerize the informatics software for different studies. Additionally, we proposed a local cache system to reduce interaction times with REDCap for large-scale data records. Experimental setups include assessing barcode recognition accuracy under various levels of image blurring, showcasing different study types managed with the organ-specific archive, and measuring system throughput and response times with and without the proposed local cache system.

Results:

Our findings demonstrate that the DataMatrix barcode exhibits superior resilience, maintaining high recognition accuracy under blurred conditions. The dynamic organ-specific archive in REDCap enabled precise tracking of sample origins, improving data granularity. Docker containerization streamlines software deployment and ensures consistency across studies. The local cache system significantly reduces interaction times with REDCap, decreasing operating time by nearly eightfold compared to the naïve strategy when handling large patient datasets.

Conclusions:

The proposed enhancements significantly improve barcode robustness, data granularity, and system throughput in the informatics system, addressing key limitations identified in previous studies. These optimizations ensure efficient data management and robust support for diverse clinical research needs. Clinical Trial: Combinatorial Single Cell Strategies for a Crohn's Disease Gut Cell Atlas (NCT04113733, https://clinicaltrials.gov/study/NCT04113733?cond=NCT04113733&rank=1&tab=table) BCCMA: Targeting Gut-Microbiome in Veterans Deployment Related Gastrointestinal and Liver Diseases: Dysbiosis, PTSD, and Epithelial and Immune Biology in Inflammatory Bowel Disease in Veterans (I01CX002473-01A2, https://research.va.gov/about/funded_research/proj-details-FY2024.cfm?pid=759730) Dysregulated Polyamine Metabolism in H. pylori-associated Gastric Inflammation and Disease Progression (I01CX002171-01, https://research.va.gov/about/funded_research/proj-details-FY2024.cfm?pid=759730) The Role of CCL11 in Inflammatory and Sporadic Colorectal Cancer. (I01CX002662-01A2, https://www.research.va.gov/about/funded_research/proj-details-FY2025.cfm?pid=802842) CCL11 as a New Therapeutic Target for Colitis and Colon Cancer (I01BX004366-01A2, https://research.va.gov/about/funded_research/proj-details-FY2024.cfm?pid=636361)