A semi-automated tool for improving Assessments and Lab Tests data annotation in ImmPort
- 1Cincinnati Children's Hospital Medical Center/University of Cincinnati
Abstract
Public data sharing in immunological and clinical research is essential for transparency, reproducibility, and secondary analysis. However, many datasets in repositories such as ImmPort lack sufficient structured data to enable reuse. ImmPort's Assessments and Lab Tests templates -- which capture critical clinical information -- are often incomplete or omitted due to their complexity and the manual effort required. To address this challenge, an application with a graphical user interface requiring no programming was developed to facilitate population of these templates. The tool streamlines the submission process by reducing time and complexity for data contributors while ensuring template formatting. It integrates ImmPort files, study-specific data files, and a curated data dictionary to automate the mapping of study variables to the required fields within each template. The tool was evaluated on seven ImmPort studies with diverse designs. It successfully generated submission-ready templates that passed ImmPort's internal validation and will be incorporated into the repository. By improving the feasibility and completeness of templates, this approach enhances the quality, findability, and reusability of data within ImmPort.
Related
- Rclade: automated taxonomic collapsing and geological-timescale annotation of time-calibrated phylogenetic trees in R
- eNeuro Assessments: A Standardized Way to Communicate Research Quality
- Widefield OCT-Angiography and Fluorescein Angiography Assessments of Nonperfusion in Diabetic Retinopathy and Edema Treated with Anti–Vascular Endothelial Growth Factor
- The FOG‐COA Protocol: Validation of Freezing of Gait Clinical Outcomes Assessments in Parkinson's Disease
- Beyond snapshots: A dynamic framework for continuous motor unit tracking to enhance neurophysiological assessments
BibTeX
@misc{tursi2026semiautomated,
title = {{A semi-automated tool for improving Assessments and Lab Tests data annotation in ImmPort}},
author = {A. R. Tursi and J. D. Fortriede and K. Burns and N. Saba and P. Pirani and M. D. Strub and P. Dunn and H. Schaefer and S. Andorf},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.02.756287},
url = {https://www.biorxiv.org/content/10.64898/2026.10.02.756287v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - A semi-automated tool for improving Assessments and Lab Tests data annotation in ImmPort
AU - A. R. Tursi
AU - J. D. Fortriede
AU - K. Burns
AU - N. Saba
AU - P. Pirani
AU - M. D. Strub
AU - P. Dunn
AU - H. Schaefer
AU - S. Andorf
PY - 2026
DA - 2026/10/02
PB - bioRxiv
DO - 10.64898/2026.10.02.756287
UR - https://www.biorxiv.org/content/10.64898/2026.10.02.756287v1
AB - Public data sharing in immunological and clinical research is essential for transparency, reproducibility, and secondary analysis. However, many datasets in repositories such as ImmPort lack sufficient structured data to enable reuse. ImmPort's Assessments and Lab Tests templates -- which capture critical clinical information -- are often incomplete or omitted due to their complexity and the manual effort required. To address this challenge, an application with a graphical user interface requiring no programming was developed to facilitate population of these templates. The tool streamlines the submission process by reducing time and complexity for data contributors while ensuring template formatting. It integrates ImmPort files, study-specific data files, and a curated data dictionary to automate the mapping of study variables to the required fields within each template. The tool was evaluated on seven ImmPort studies with diverse designs. It successfully generated submission-ready templates that passed ImmPort's internal validation and will be incorporated into the repository. By improving the feasibility and completeness of templates, this approach enhances the quality, findability, and reusability of data within ImmPort.
ER -