Papers › Cell type nomenclature for the mammalian brain: Development and application of a...
Cell type nomenclature for the mammalian brain: Development and application of a systematic, extensible convention
Jeremy A. Miller, Nathan W. Gouwens, Bosiljka Tasic, Forrest Collman, Cindy T. J. van Velthoven, Trygve E. Bakken, Hongkui Zeng, Ed S. Lein, Amy Bernard
The recent advent of single cell RNA-sequencing and other high-throughput technologies has led to an explosion of cell type definitions across multiple organ systems. Consortia like the BRAIN Initiative Cell Census Network (BICCN) and the Human Cell Atlas (HCA) have begun to standardize and centralize the intake of data and associated metadata from these projects; however, the naming and organization of cell types has largely been left to individual investigators, resulting in widely varying nomenclature and limited alignment between taxonomies derived from overlapping datasets. To facilitate cross-dataset alignment and comparison, we created a working nomenclature convention for matching and tracking cell types across studies. The convention is qualitatively similar to how gene transcripts are tracked across different versions of GENCODE genome builds, allowing comparison of matched types with a common reference or any other taxonomy. It augments but does not change existing cell type names provided in original publications and can be directly applied to data from new or published studies. We applied this nomenclature to a series of published cell type data from the Allen Institute, highlighting its extensibility to classifications defined using multiple quantifiable modalities. Finally, we propose conventions for assigning accurate yet flexible cell types names in the mammalian cortex as a step towards a much larger community-wide effort to organize multi-source, data-driven information related to cell types. The convention presented here can be easily applied to cell type taxonomies from any organ system or organism.
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