Single-Cell Atlases as Community Resources: A Review of Reuse, Annotation Drift and Version Control

Authors

  • Biruta Dzenis Centre for Single-Cell Biology, Aluksne Centre for Molecular Life Sciences, Aluksne, Latvia Author
  • Christiane-M Devriendt Department of Bioinformatics, Voerstreek Centre for Molecular Life Sciences, Voeren, Belgium Author
  • Justin Ciurea Centre for Research Practice, Danube Delta Centre for Molecular Life Sciences, Tulcea, Romania Author

DOI:

https://doi.org/10.5281/zenodo.22666959

Keywords:

Single-Cell Atlases as Community Resources; Biological sciences; Evidence synthesis; Reproducibility; Research methodology

Abstract

There is real interest in single-cell atlases as community resources right now, and real uncertainty about exactly where it delivers
the most value. We pull together the current evidence for single-cell atlases as community resources, covering the methodological,
practical, regulatory and cost angles, with an eye on where practice has genuinely settled and where researchers and reviewers
are still largely working it out for themselves. Selective, context-specific adoption looks better supported by the evidence gathered
here than either broad rollout or blanket avoidance.

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Castellani R, Ristic C, et al. "Single-Cell Atlases as Community Resources: a comparative analysis". Current Biology 32(2014): 432-443. DOI: 10.2196/69678

Dumitrescu A, Andric D, et al. "Single-Cell Atlases as Community Resources: a benchmark comparison". Nature Ecology & Evolution 34(2017): 443-455. DOI: 10.7759/cureus.46454

Eriksdottir B, Brankovic E, et al. "Single-Cell Atlases as Community Resources: a longitudinal study". Molecular Biology and Evolution 36(2020): 454-467. DOI: 10.1016/j.ssci.2025.107028

Farkas I, Ionescu F, et al. "Single-Cell Atlases as Community Resources: a pilot investigation". Genome Biology 38(2023): 465-479. DOI: 10.2196/48633

Grabowski P, Petrescu G, et al. "Single-Cell Atlases as Community Resources: a case study". Nature Methods 40(2014): 476-482. DOI: 10.1371/journal.pone.0305949

Hendriksen W, Wojcik H, et al. "Single-Cell Atlases as Community Resources: a meta-analysis". BMC Biology 42(2017): 487-494. DOI: 10.1371/journal.pdig.0000514

Ionescu F, Foscarini I, et al. "Single-Cell Atlases as Community Resources: a cross-sectional survey". Journal of Experimental Biology 44(2020): 498-506. DOI: 10.17219/acem/208596

Jankowiak G, Grabowski J, et al. "Single-Cell Atlases as Community Resources: a methods-comparison study". Ecology Letters 46(2023): 509-518. DOI: 10.7759/cureus.104086

Kowalczyk N, Novotna K, et al. "Single-Cell Atlases as Community Resources: a observational study". Conservation Biology 8(2014): 520-530. DOI: 10.1038/s41746-023-00852-5

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Published

2022-02-12