ArticleScientific data2019
The variable quality of metadata about biological samples used in biomedical experiments.
Article in Scientific data, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers, 2 of them syntheses that pooled it.
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Who cites it
61 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Understanding the Nature of Metadata: Systematic Review.Journal of medical Internet research · 2022Pooled it
- A systematic review of datasets that can help elucidate relationships among gene expression, race, and immunohistochemistry-defined subtypes in breast cancer.Cancer biology & therapy · 2021Pooled it
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- Toward total recall: Enhancing data FAIRness through AI-driven metadata standardization.GigaScience · 2026Article
- HVRLocator: a computationally efficient tool for identifying hypervariable regions in large 16S rRNA datasets.GigaScience · 2026Article
- Large-scale manual curation and harmonization of metadata from metagenomic and cancer genomic repositories: challenges and solutions.Database : the journal of biological databases and curation · 2026Article
- The Mpox contextual data specification package: a data curation toolkit to support collaborative pathogen genomic surveillance.Microbial genomics · 2026Article
- Knowledge Engineering for Open Science: Building and Deploying Knowledge Bases for Metadata Standards.AI magazine · 2026Article
- Large-scale Manual Curation and Harmonization of Metadata from Metagenomic and Cancer Genomic Repositories: Challenges and Solutions.bioRxiv : the preprint server for biology · 2025Article
- A Photomicrographic Dataset of Rocks for the Accurate Classification of Minerals.Scientific data · 2025Article
- The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression Omnibus data repository.Genome biology · 2025Article
- Toward Sex-Specific Biomaterials Innovation: A Perspective.ACS biomaterials science & engineering · 2025Review
- Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies.Cell genomics · 2025Review
- aurora: a machine learning gwas tool for analyzing microbial habitat adaptation.Genome biology · 2025Article
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- An approach to making life sciences FAIR-FAIR-DS as a tool for Aspergillus fumigatus.Database : the journal of biological databases and curation · 2025Article
- Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database.GigaScience · 2025Article
- Uncovering hundreds of exogenous and endogenous RNA viral RdRp sequences amongst uncharacterized sequences in public protein databases.Virus evolution · 2025Article
- Metadata harmonization from biological datasets with language models.Bioinformatics advances · 2025Article
1 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
We present an analytical study of the quality of metadata about samples used in biomedical experiments. The metadata under analysis are stored in two well-known databases: BioSample-a repository managed by the National Center for Biotechnology Information (NCBI), and BioSamples-a repository managed by the European Bioinformatics Institute (EBI). We tested whether 11.4 M sample metadata records in the two repositories are populated with values that fulfill the stated requirements for such values. Our study revealed multiple anomalies in the metadata. Most metadata field names and their values are not standardized or controlled. Even simple binary or numeric fields are often populated with inadequate values of different data types. By clustering metadata field names, we discovered there are often many distinct ways to represent the same aspect of a sample. Overall, the metadata we analyzed reveal that there is a lack of principled mechanisms to enforce and validate metadata requirements. The significant aberrancies that we found in the metadata are likely to impede search and secondary use of the associated datasets.
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