ArticleGenome biology2025
The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression Omnibus data repository.
Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed.
- Harnessing Probiotic LAB and Bacteriocins for Clean-Label Food Processing and Biopreservation: Omics, Molecular Innovations and Industrial Applications.Probiotics and antimicrobial proteins · 2026Review
- Reporting and representation of population descriptors in public RNA-seq databases.Cell genomics · 2026Article
- Mechanistic Insights into Wildlife Cancer and Conservation Strategies Under the One Health Framework.Veterinary sciences · 2026Review
- Large-scale automated detection reveals pervasive sex imbalance in biomedical research.bioRxiv : the preprint server for biology · 2026Article
- RD-OMICS: An Integrative Multi-Omics Data Inventory in Rare Diseases.bioRxiv : the preprint server for biology · 2026Article
- The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression Omnibus data repository.Genome biology · 2025Article
- Discordant effects of maternal age on the human MII oocyte transcriptome.Molecular human reproduction · 2025Article
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27 authors.
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Abstract
backgroundRecent 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.
resultsOur 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.
conclusionsThese 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.