Common Cell type Nomenclature for the mammalian brain: A systematic, extensible convention

TL;DR

The paper introduces the Common Cell type Nomenclature (CCN), a standardized, extensible system for naming and matching cell types across diverse single-cell RNA-sequencing datasets in the mammalian brain, enhancing data comparison and organization.

Contribution

It presents the CCN framework, enabling consistent cell type naming across studies and modalities, addressing variability in current taxonomies.

Findings

CCN can be applied to diverse datasets and modalities.

It improves cross-study cell type comparison.

Facilitates community-wide organization of cell type data.

Abstract

The advancement of single cell RNA-sequencing technologies has led to an explosion of cell type definitions across multiple organs and organisms. While standards for data and metadata intake are arising, organization of cell types has largely been left to individual investigators, resulting in widely varying nomenclature and limited alignment between taxonomies. To facilitate cross-dataset comparison, the Allen Institute created the Common Cell type Nomenclature (CCN) for matching and tracking cell types across studies that is qualitatively similar to gene transcript management across different genome builds. The CCN can be readily applied to new or established taxonomies and was applied herein to diverse cell type datasets derived from multiple quantifiable modalities. The CCN facilitates assigning accurate yet flexible cell type names in the mammalian cortex as a step towards community-wide efforts to organize multi-source, data-driven information related to cell type taxonomies from any organism.