We are proud to announce the first release of PCL incorporating an ontology cell types covering the whole mouse brain. This is based on the work of Zizhen Yao, Hongkui Zheng and colleagues and includes of over 5000 cell types.
Yao, Z., van Velthoven, C.T.J., Kunst, M. et al. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain. Nature 624, 317–332 (2023). https://doi.org/10.1038/s41586-023-06812-z
All terms have auto-rolled definitions and formal relationships incorporating classifications, markers and brain regions, where available, as well as links to underlying data. Anatomical domains correspond to those in the Allen Standard Mouse Brain Atlas Ontology.
Examples:
Pinealocytes
VIP neurons
This provisional work will be refined in future releases. We aim to incorporate a version of it into the Cell Ontology by June 2025.
The underlying data can be browsed and searched on the Allen Brain Cell Atlas - https://tinyurl.com/yvxa3sm9
Integrated h5ad files of the underlying data (one per class area available from):
- http://cellular-semantics.cog.sanger.ac.uk/public/merged_CS20230722_CLAS_01.h5ad
- http://cellular-semantics.cog.sanger.ac.uk/public/merged_CS20230722_CLAS_02.h5ad
- http://cellular-semantics.cog.sanger.ac.uk/public/merged_CS20230722_CLAS_03.h5ad
- ...
- http://cellular-semantics.cog.sanger.ac.uk/public/merged_CS20230722_CLAS_33.h5ad
- http://cellular-semantics.cog.sanger.ac.uk/public/merged_CS20230722_CLAS_34.h5ad
It will also be available to browse and query in the next release of the Cell Ontology Knowledge Graph.
Full Changelog: v2024-07-12...v2025-01-08