ArticleNAR genomics and bioinformatics2026
UniProt data pruning and the growing invisibility of the dark proteome.
Article in NAR genomics and bioinformatics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
The protein resource UniProtKB has undergone a major, multi-stage reorganization of its protein space, implemented from release 2025_04 through release 2026_02. Analysis of UniProtKB and UniParc records accessed on 20 January 2026 showed that 125.9 million entries were last present in UniProtKB in 2025 and are now represented in UniParc, while ~200.0 million entries remained in UniProtKB at the access date. Of these, 58.9 million were designated for removal in release 2026_02, whereas 141.2 million were classified as retained. The reorganization retains all reviewed UniProtKB/Swiss-Prot entries (the expert-curated subset of UniProtKB), along with proteins from selected reference proteomes and unreviewed entries with additional biologically important data, including experimentally determined three-dimensional structures. The expected benefits include reduced redundancy, easier navigation, and a protein set that is more tractable for annotation and routine searches. However, the reorganization may reduce the visibility of protein sequences from uncultured microorganisms and metagenomic surveys, phylogenetically underrepresented lineages, particularly many archaeal groups, proteins belonging to the so-called "dark proteome," and strain-level variants of well-studied species such as
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