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Friday, December 3 • 10:55am - 11:05am
OP 23 - The systematic assessment for the completeness of metadata information accompanying omics studies

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The systematic assessment for the completeness of metadata information accompanying omics studies

Presenting Author: Yu-Ning Huang, University of Southern California

Serghei Mangul, University of Southern California
Anushka Rajesh, University of Southern California
Jieting Hu, University of Southern California
Ruiwei Guo, University of Southern California
Man Yee Wong, University of Southern California
Jiaqi Fu, University of Southern California
Elizabeth Ling, University of Southern California
Irina Nakashidze, Batumi Shota Rustaveli State University
Steven Beringer, University of Southern California
Aditya Sarkar, Indian Institute of Technology Mandi

Abstract:Genomic data is easily accessible and available, owing to the ubiquity of public genomic repositories that allow researchers to share their study datasets. However, improperly annotated and incomplete metadata accompanying the raw data make the researchers almost impossible to reuse the data directly through the public repositories for secondary analysis and might slow down biomedical discoveries’ progress. Our study aims to assess the completeness of metadata accompanying omics studies in both publication and its related online repositories and make observations about how the process of data sharing could be made reliable. The study involved an initial literature survey in finding studies based on the seven therapeutic fields, sepsis, tuberculosis, cystic fibrosis, cardiovascular disease, acute myeloid leukemia, inflammatory bowel disease, and Alzheimer’s disease. We used computational tools (Python scripts) to extract metadata from the public repository, manually observed the availability of metadata in both publication and repositories, and then statistically visualized the results obtained from the analysis. By comparing the metadata availability on both platforms, orginal publications, and online repositories, we observed discrepancies between omics data and the corresponding metadata on public repositories. We advocate the need to have a standardized "checklist" for researchers to submit their study results and data to public repositories based on our results. Our study opens a comprehensive discussion about this potential solution to bridge the gap between omics data and metadata on repositories.


Yu-Ning Huang

University of Southern California

Friday December 3, 2021 10:55am - 11:05am MST
Ballroom Salon 1