Review azimuth annotations for new cell types

[dosumis]

No description provided.

[ghost]

https://azimuth.hubmapconsortium.org/references/

Human - PBMC

Annotation group	Note
celltype.l1	All mapped.
celltype.l2 (default)	All mapped, but some details lost. For example, "AXL+ Dendritic Cell" mapped to 'dendritic cell'; "Proliferating Natural Killer" mapped to 'natural killer cell'
celltype.l3	All mapped, but several mapped terms are more general. For example, all "gamma-delta T_%N" mapped to 'gamma-delta T cell'

Human - Pancreas

Annotation group	Note
annotation.l1	All mapped, but cell states noted in some "expanded labels" are lost and some assumptions are made. For example, "cycling" mapped to pancreatic endocrine cell and "immune" mapped to leukocyte.

Human - Lung v1

Annotation group	Note
annotation.l1	All mapped, but some variations in specificity.  For example, "Basophil/Mast" and "Platelet/Megakaryocyte" are mapped to 'myeloid cell'. "Capillary Aerocyte" is mapped to 'capillary endothelial cell'. Of note, 'alveolar capillary type 2 endothelial cell' has broad synonym "aerocyte" in CL.
annotation.l2	All mapped, but some variations in specificity.  "Differentiating Basal" is mapped to 'basal cell'. "Signaling Alveolar Epithelial Type 2" is mapped to 'type II pneumocyte'.

[emquardokus]

@dosumis this is the new pipeline being used for Azimuth cell annotations that the New York Genome Center (NYGC) team (Rahul Satija, Gesmira Molla and Austin Hartman) are using: https://github.com/hubmapconsortium/azimuth-annotate cells.
You might want to check this out and comment?

[dosumis]

@aleixpuigb - moving over to you as we don't have any more CAP priority datasets here. Job for remaining datasets is mostly to map labels to cell types and look for new cell types whilst doing it.

[aleixpuigb]

New mappings for the remaining datasets will be submitted in the azimuth-mapping repository:

• Human - PBMC
• Human - Motor Cortex
• Mouse - Motor Cortex
• Human - Pancreas
• Human - Fetal Development
• Human - Lung v1
• Human - Kidney
• Human - Bone Marrow
• Human - Lung v2 (HLCA)
• Human - Tonsil
• Human - Adipose
• Human - Heart
• Human - Liver

[emquardokus]

@aleixpuigb related issue: Review Specific Kidney cell type annotation mappings on Azimuth to find more detailed CL terms #1972

[aleixpuigb]

Since this has been moved to a different repo, all the mappings have been done, and the discussion is taking place in the google sheets, I will close this ticket as completed.