Releases: obophenotype/provisional_cell_ontology
v2025-01-08 Release
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
2024-07-12 Release
Contributors
Assets 12
2024-01-05 Release
- Whole Human Brain Ontology added
- PCL ontologies deleted from the master branch (except base release) due to size limitations and will be published as release artefacts.
2023-02-23 Release
Legacy PCL identifiers are added as exact synonyms to the replaced terms.
2022-10-19 Release
Update Individuals IDs to match Taxonomy
2022-09-02 Release
Merge pull request #41 from obophenotype/pcl-cl-product add pcl-cl-full product
2022-04-27 Release
Merge pull request #35 from obophenotype/2022-04-27-Release 2022-04-27 Release
2022-03-02 Release
- Update BDS component
2022-02-09 Release
- Updated BDSO component
2021-02-02 Release
- redirected makefile to download new bdso component
- updated bdso component