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A reference cell tree will serve science better than a reference cell atlas.

Silvia Domcke1, Jay Shendure2

  • 1Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.

Cell
|March 17, 2023
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Summary
This summary is machine-generated.

Single-cell biology needs a standardized system for naming cell types. A proposed "consensus ontogeny" offers a data-driven, tree-based nomenclature for precise scientific communication.

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Area of Science:

  • Single-cell biology
  • Genomics
  • Bioinformatics

Background:

  • The rapid generation of single-cell molecular profiles lacks a unified system for cell type definition and organization.
  • Current methods for clustering and annotating cell types are largely ad hoc, hindering consistent scientific communication.

Purpose of the Study:

  • To propose a principled, unified, and well-moored system for defining, naming, and organizing cell types in single-cell biology.
  • To advocate for a data-driven, tree-based nomenclature rooted in a consensus ontogeny as a reference taxonomy.
  • To explore the practical construction, representation, and segmentation of such a reference cell tree.

Main Methods:

  • Critique of atlas or periodic table-like discretization as a metaphor for cell type taxonomy.
  • Advocacy for a data-driven, tree-based nomenclature.
  • Conceptual framework for a consensus ontogeny incorporating lineage histories and molecular states.

Main Results:

  • A proposed reference cell tree based on consensus ontogeny offers a universal framework.
  • This framework supports precise scientific communication by integrating lineage and molecular information.
  • The system is designed to be stable and extendable for future discoveries.

Conclusions:

  • A consensus ontogeny-based, tree-like nomenclature is essential for advancing single-cell biology.
  • This approach provides a stable and universal standard for cell type classification.
  • Implementing this framework will enhance precision and consistency in scientific discourse across generations.