The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression Omnibus data repository

Abstract

Recent advances in high-throughput sequencing technologies have enabled the collection and sharing of a massive amount of omics data, along with its associated metadata—descriptive information that contextualizes the data, including phenotypic traits and experimental design. Enhancing metadata availability is critical to ensure data reusability and reproducibility and to facilitate novel biomedical discoveries through effective data reuse. Yet, incomplete metadata accompanying public omics data may hinder reproducibility and reusability and limit secondary analyses. Our study assesses the completeness of metadata in over 253 scientific studies, covering more than 164,000 samples from both human and non-human mammalian studies. We find that over 25% of critical metadata are omitted, with only 74.8% of relevant phenotypes available in publications or public repositories. Notably, public repositories alone contain 62% of the phenotypes, surpassing the textual content of publications by 3.5%. Only 11.5% of studies completely shared all phenotypes, while 37.9% shared less than 40% of the phenotypes. Additionally, studies with non-human samples are more likely to include complete metadata compared to human studies. Similar trends are observed in an extended dataset comprising 61,000 studies and 2.1 million samples from the Gene Expression Omnibus (GEO) data repository. These findings highlight significant gaps in metadata sharing, underscoring the need for standardized practices to improve metadata availability. Enhanced metadata reporting would foster data reusability, support better-informed decision-making, and promote reproducible research across the biomedical field.