Cell type ontologies of the Human Cell Atlas

Nat Cell Biol. 2021 Nov;23(11):1129-1135. doi: 10.1038/s41556-021-00787-7. Epub 2021 Nov 8.


Massive single-cell profiling efforts have accelerated our discovery of the cellular composition of the human body while at the same time raising the need to formalize this new knowledge. Here, we discuss current efforts to harmonize and integrate different sources of annotations of cell types and states into a reference cell ontology. We illustrate with examples how a unified ontology can consolidate and advance our understanding of cell types across scientific communities and biological domains.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Atlases as Topic*
  • Biological Ontologies
  • Biomarkers / metabolism
  • Cell Biology*
  • Cell Lineage*
  • Cells / classification*
  • Cells / metabolism
  • Cells / pathology
  • Data Mining
  • Disease
  • Gene Ontology
  • Genomics
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Phenotype
  • Single-Cell Analysis*
  • Systems Integration
  • Transcriptome


  • Biomarkers