Simplifying the transformation of laboratory test data for integration into the ImmPort database - Project Summary/Abstract The sharing of data in biomedical research, including data generated from clinical trials, is paramount for ensuring reproducibility, improving study design, increasing analytic power via concatenation of disparate data sets, and identifying and testing new hypotheses. With more data being made publicly available, there is a critical need to facilitate their re-use. The reusability of publicly available clinical trial datasets is more complex when data are shared in an unstructured format, as compared to in a structured database, due to the need for arduous manual annotation of individual files to permit secondary analyses. One platform to share individual participant level clinical trial data is the Immunology Database and Analysis Portal (ImmPort), a NIH/NIAID-funded public warehouse providing open access to clinical and mechanistic data from immunological and clinical studies. The overall aim of this proposal is to enhance the reusability of clinical trial data shared through ImmPort and to encourage their re-use. Specifically, the goal is to develop an automated tool to simplify the transformation of laboratory test data from clinical trials into the format of the ImmPort submission template. Upload of the data in this template format is necessary for integration into the structured database. Otherwise, the data will be made available to the public as custom formatted study files, complicating their re-use. The complexity in current upload protocols is what prevents many data submitters from fully annotating their clinical data for integration into ImmPort’s structured database. The tool will be an extension of our prototype ImmPort curation approach that facilitates the formatting of assessment data for submission to ImmPort. The tool will rely on a manually curated data dictionary to give context to the data in the study files. With that data dictionary and minimal additional manual input, the approach automates the complex file formatting steps required to transform the data into the laboratory test submission template. The tool will be developed to guide users through the annotation process with a graphical user interface, making full annotation of lab test clinical trial data more accessible to researchers without informatics expertise. Additionally, to increase confidence and proficiency in re-using clinical study data publicly available through ImmPort, a comprehensive tutorial based on a secondary analysis of two food allergy related clinical trials shared through ImmPort will be developed. The tutorial, created in R, will cover various ways of data retrieval, processing, and an in-depth analysis with visualizations. Overall, this proposal aims to enhance the reusability of clinical trial data available through ImmPort, thereby increasing the return on investment for biomedical research and benefiting scientific knowledge and clinical care.
