Developing a Standardized but Extendable Framework to Increase the Findability of Infectious Disease Datasets

Authors

Ginger Tsueng
Marco A Alvarado Cano
José Bento
Candice Czech
Mengjia Kang
Lars Pache
Luke V Rasmussen
Tor C Savidge
Justin Starren
Qinglong Wu
Jiwen Xin
Michael R Yeaman
Xinghua Zhou
Andrew I Su
Chunlei Wu
Liliana Brown
Reed S Shabman
Laura D Hughes

Language

English

Publication Date

2-23-2023

Journal

Scientific Data

DOI

10.1038/s41597-023-01968-9

PMID

36823157

PMCID

PMC9950378

PubMedCentral® Posted Date

2-23-2023

PubMedCentral® Full Text Version

Post-print

Abstract

Biomedical datasets are increasing in size, stored in many repositories, and face challenges in FAIRness (findability, accessibility, interoperability, reusability). As a Consortium of infectious disease researchers from 15 Centers, we aim to adopt open science practices to promote transparency, encourage reproducibility, and accelerate research advances through data reuse. To improve FAIRness of our datasets and computational tools, we evaluated metadata standards across established biomedical data repositories. The vast majority do not adhere to a single standard, such as Schema.org, which is widely-adopted by generalist repositories. Consequently, datasets in these repositories are not findable in aggregation projects like Google Dataset Search. We alleviated this gap by creating a reusable metadata schema based on Schema.org and catalogued nearly 400 datasets and computational tools we collected. The approach is easily reusable to create schemas interoperable with community standards, but customized to a particular context. Our approach enabled data discovery, increased the reusability of datasets from a large research consortium, and accelerated research. Lastly, we discuss ongoing challenges with FAIRness beyond discoverability.

Keywords

Metadata, Reproducibility of Results, Communicable Diseases, Datasets as Topic, Humans, Data publication and archiving, Standards

Published Open-Access

yes

Recommended Citation

Tsueng, Ginger; Cano, Marco A Alvarado; Bento, José; et al., "Developing a Standardized but Extendable Framework to Increase the Findability of Infectious Disease Datasets" (2023). Faculty and Staff Publications. 5632.
https://digitalcommons.library.tmc.edu/baylor_docs/5632