search

brain-bican / whole_mouse_brain_taxonomy

Atlas of whole mouse brain
0 stars 0 forks source link

Add annotation transfers #3

Open dosumis opened 1 week ago

dosumis commented 1 week ago

https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-023-06812-z/MediaObjects/41586_2023_6812_MOESM8_ESM.xlsx

Cluster table includes:

column description
CTX.cluster_id The best matching cluster id in the previous published CTX_HPF taxonomy (https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-10x)
CTX.cluster_label The best matching cluster label in the previous published CTX_HPF taxonomy
CTX.supertype_id The best matching supertype id in the previous published CTX_HPF taxonomy
CTX.supertype_label The best matching supertype label in the previous published CTX_HPF taxonomy
CTX.subclass_id The best matching subclass id in the previous published CTX_HPF taxonomy
CTX.subclass_id The best matching subclass label in the previous published CTX_HPF taxonomy
CTX.neighborhood_id The best matching neighborhood id in the previous published CTX_HPF taxonomy
CTX.neighborhood_label The best matching neighborhood label in the previous published CTX_HPF taxonomy
CTX.size The number of cells included in the previous published CTX_HPF taxonomy

e.g.

CTX.cluster_id CTX.cluster_label CTX.supertype_id CTX.supertype_label CTX.subclass_id CTX.subclass_id CTX.neighborhood_id
238 238_Car3_2 45 Car3 21 Car3 4
238 238_Car3_3 45 Car3 21 Car3 4

We need a taxonomy for https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-10x

This corresponds to https://cellxgene.cziscience.com/collections/e3aa612b-0d7d-4d3f-bbea-b8972a74dd4b. We should be able to build a taxonomy directly from the 10x dataset (https://cellxgene.cziscience.com/e/d7291f04-fbbb-4d65-990a-f01fa44e915b.cxg/) using CAS-tools. But we should also check whether an existing AIT taxonomy is available. @patrick-lloyd-ray -can you check this?

Once this is in place, we can then translate then use the table to generate annotation transfer entries in this taxonomy

TODO: Check paper for annotation transfer method details (not found so far, but may be buried?)

dosumis commented 4 days ago

Options for building taxonomy:

CAS tools from https://cellxgene.cziscience.com/e/d7291f04-fbbb-4d65-990a-f01fa44e915b.cxg/

But also in JSON here: https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-10x @hkir-dev has python that can work with the JSON. Might be additional info in their we can use. Update: JSON has brain regions as well as cell types, so might not look like the others we've processed. Working with this is therefore lower priority.