Cell type ontologies of the Human Cell Atlas

Abstract

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 formalise this new knowledge. Here, we review current cell ontology efforts to harmonise and integrate different sources of annotations of cell types and states. We illustrate with examples how a unified ontology can consolidate and advance our understanding of cell types across scientific communities and biological domains. MainWith collaboration of over 2,000 scientists across more than 1,000 institutes from 76 countries to date, the Human Cell Atlas (HCA) has generated comprehensive molecular profiles of tens of millions of single cells across 18 different organs and systems, which in turn, are advancing our understanding of the definition of cell types and states 1, 2 . The technological revolution in single-cell and spatial genomics is rapidly expanding the compendium of known cell types, and accelerating discoveries of a large variety of novel cell populations.

Towards Tabula Gallus

“…Tabula Gallus will generate a compendium of single-cell transcriptome data from Gallus gallus, characterize each cell type, and provide the tools for studying the biology of this species, like other ongoing cell atlas projects (Tabula Muris and Tabula Sapiens/Human Cell Atlas for mice and human, respectively) [88][89][90][91] (https://tabula-muris. ds.czbiohub.org (accessed on 10 December 2021); https://www.humancellatlas.org (accessed on 10 December 2021); https://tabula-sapiens-portal.ds.czbiohub.org (accessed on 10 December 2021)).…”

“…Thus, the first step towards "Tabula Gallus" would be to create an integrated website to catalog those datasets and facilitate international collaboration between many researchers. The precedents would be Tabula Muris and Tabula Sapiens/Human Cell Atlas [88][89][90][91]. Moreover, to combine further information such as validated gene expression data and images (see below), the species-specific community websites like GEISHA (http://geisha.arizona.edu (accessed on 10 December 2021)) may provide excellent starting points as a resource for chicken biology as in the cases for other model animals (e.g., https://flybase.org (accessed on 10 December 2021), https://wormbase.org/ (accessed on 10 December 2021)).…”

“…Tabula Gallus will generate a compendium of single-cell transcriptome data from Gallus gallus , characterize each cell type, and provide the tools for studying the biology of this species, like other ongoing cell atlas projects (Tabula Muris and Tabula Sapiens/Human Cell Atlas for mice and human, respectively) [ 88 , 89 , 90 , 91 ] ( (accessed on 10 December 2021); (accessed on 10 December 2021); (accessed on 10 December 2021)). Tabula Gallus will potentially become an international collaboration among many researchers.…”

“…The Tabula Gallus is currently at an early stage (~20 scRNA-seq studies using chicks as of early 2022) [ 89 , 90 , 91 , 92 , 93 , 94 , 95 , 96 , 97 , 98 , 99 , 100 , 101 , 102 , 103 , 104 , 105 , 106 , 107 , 108 ]. Nonetheless, a couple of fledging studies support the feasibility of this project revealing diverse cell types and their states in the chick limb buds [ 96 , 102 ], the early primitive streak stage [ 95 , 103 ], neural crests [ 94 , 100 ], and the developing neural retina [ 98 , 107 ].…”

Single-cell Bayesian deconvolution

“…The degree to which this heterogeneity affects, or even dictates, cellular decision making in most situations is still an open question. This issue is of paramount importance in processes such as mammalian development, where hundreds (if not thousands 4 ) of distinct cell types (cell states) emerge from a small number of identical undifferentiated cells [5][6][7] . Identifying the molecular mechanisms underlying these cell-fate decision programs and their interplay with cellular heterogeneity 8,9 requires a rigorous quantification of cellular states across large numbers of cells.…”