Generate new taxonomy for mouse cortex

[dosumis]

On CxG https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-10x
JSON from Allen: https://idk-etl-prod-download-bucket.s3.amazonaws.com/aibs_mouse_ctx-hpf_10x/dend.json

JSON has accessions and useful metadata.

Update: Some cell set labels are missing in JSON. ALternative source of accessions that seems to have at least some of the missing labels:

https://www.cell.com/cms/10.1016/j.cell.2021.04.021/attachment/5cad417f-9a4d-4ffd-954d-a4421ad747ac/mmc3.xlsx

[ubyndr]

Repo is at https://github.com/Cellular-Semantics/mouse_cortex_taxonomy

[dosumis]

TODO: Try to fill in missing accessions from supplementary material spreadsheet.

[ubyndr]

These are the labelsets that do not have a cell_set_accession at the moment.

[{'labelset': 'subclass_label', 'cell_label': 'L5 IT CTX'},
 {'labelset': 'subclass_label', 'cell_label': 'L4/5 IT CTX'},
 {'labelset': 'subclass_label', 'cell_label': 'L2/3 IT ENTl'},
 {'labelset': 'subclass_label', 'cell_label': 'Endo'},
 {'labelset': 'subclass_label', 'cell_label': 'L6 IT CTX'},
 {'labelset': 'subclass_label', 'cell_label': 'CR'},
 {'labelset': 'subclass_label', 'cell_label': 'L2/3 IT PPP'},
 {'labelset': 'subclass_label', 'cell_label': 'Astro'},
 {'labelset': 'subclass_label', 'cell_label': 'SUB-ProS'},
 {'labelset': 'subclass_label', 'cell_label': 'Sncg'},
 {'labelset': 'subclass_label', 'cell_label': 'Vip'},
 {'labelset': 'subclass_label', 'cell_label': 'L6b CTX'},
 {'labelset': 'subclass_label', 'cell_label': 'Lamp5'},
 {'labelset': 'subclass_label', 'cell_label': 'Oligo'},
 {'labelset': 'subclass_label', 'cell_label': 'L2 IT ENTl'},
 {'labelset': 'subclass_label', 'cell_label': 'L6 IT ENTl'},
 {'labelset': 'subclass_label', 'cell_label': 'L5 PPP'},
 {'labelset': 'subclass_label', 'cell_label': 'L6b/CT ENT'},
 {'labelset': 'subclass_label', 'cell_label': 'CA1-ProS'},
 {'labelset': 'subclass_label', 'cell_label': 'L5/6 IT TPE-ENT'},
 {'labelset': 'class_label', 'cell_label': 'Non-Neuronal'}]