Closed dosumis closed 1 year ago
CC @hkir-dev
Note - it may be worth contacting Siletti to clear up any ambiguities once a first pass at mapping has been done.
@bvarner-ebi - have made as start at this as want to some example mappings for a demo.
This is a uniq'd list of entries in Subtype auto-annotation
column + some potential mappings:
Table entry | Mapping |
---|---|
ABC PIA | |
ARACH | |
ARTERIOLE ARTERY | |
ARTERIOLE CAP | |
CAP | |
CB-GRAN | cerebellar granule cell (CL:0001031) |
CB-GranLayerInt | |
CB-MolLayerInt1 | |
CB-MolLayerInt1 CB-MolLayerInt2 | |
CB-MolLayerInt2 | |
CB-PURK | Purkinje cell (CL:0000121) |
CB-PurkLayerInt | |
CHAND | |
COP | |
DG-GRAN | TBA - |
FIBMYO | |
INT-LAMP5 | |
INT-LAMP5-LHX6 | |
INT-PVALB | |
INT-SST | |
INT-SST INT-SST-CHODL | |
INT-SST-CHODL | |
INT-VIP | |
L5-ET | |
L5-ET VonEcon | TBA - von Economo neuron |
MSN-D1 | |
MSN-D1 MSN-D2 MSN-ECC | |
MSN-D1 MSN-ECC | |
MSN-D2 | |
PIA | |
PIA PVF | |
UBC | |
VENOUS |
This comment is in progress. Template copied from comment above.
Table entry | Mapping |
---|---|
ABC PIA | ?fibroblast in pia mater |
ARACH | ?fibroblast in arachnoid mater |
ARTERIOLE ARTERY | CL:1000412 'endothelial cell of arteriole' |
ARTERIOLE CAP | CL:1000412 'endothelial cell of arteriole' | CL:002144 'capillary endothelial cell' |
CAP | CL:0002144 'capillary endothelial cell' |
CB-GRAN | CL:0001031 'cerebellar granule cell' |
CB-GranLayerInt | ?NTR- cerebellar granular layer interneuron |
CB-MolLayerInt1 | ?NTR- cerebellar molecular layer interneuron 1 |
CB-MolLayerInt1 CB-MolLayerInt2 | - |
CB-MolLayerInt2 | ?NTR- cerebellar molecular layer interneuron 2 |
CB-PURK | CL:0000121 'Purkinje cell' |
CB-PurkLayerInt | ?NTR- cerebellar purkinje layer interneuron |
CHAND | CL:4023083 'chandelier cell' |
COP | CL:4023059 'differentiation-committed oligodendrocyte precursor' |
DG-GRAN | CL:4023062 'dentate gyrus neuron' | CL:2000089 'dentate gyrus of hippocampal formation granule cell' |
FIBMYO | CL:0002590 'smooth muscle cell of the brain vasculature' | CL:0000186 myofibroblast |
INT-LAMP5 | CL:4023070 'caudal ganglionic eminence derived GABAergic cortical interneuron' | CL:4023011 'lamp5 GABAergic cortical interneuron' |
INT-LAMP5-LHX6 | ? check if this warrants a new term |
INT-PVALB | CL:4023069 'medial ganglionic eminence derived GABAergic coritcal interneuron' | CL:4023018 'pvalb GABAergic cortical interneuron' |
INT-SST | CL:4023069 'medial ganglionic eminence derived GABAergic coritcal interneuron' | CL:4023017 'sst GABAergic cortical interneuron' |
INT-SST INT-SST_CHODL | - |
INT-SST-CHODL | CL:4023069 'medial ganglionic eminence derived GABAergic coritcal interneuron' | CL:4023121 'sst chodl GABAergic cortical interneuron' |
INT-VIP | CL:4023070 'caudal ganglionic eminence derived GABAergic cortical interneuron' | CL:4023016 'vip GABAergic cortical interneuron' |
L5-ET | CL:4023041 'L5 extratelencephalic projecting glutamatergic cortical neuron' |
L5-ET VonEcon | NTR done: CL:4030039 'von Economo neuron' |
MSN-D1 | CL:4023026 'direct pathway medium spiny neuron' |
MSN-D1 MSN-D2 MSN-ECC | - |
MSN-D1 MSN-ECC | - |
MSN-D2 | CL:4023029 'indirect pathway medium spiny neuron' |
MSN-ECC | NTR done: CL:4030057 'eccentric medium spiny neuron' |
PIA | ?fibroblast in pia mater |
PIA PVF | ?fibroblast in pia mater |
UBC | ? |
VENOUS | CL:0002543 'vein endothelial cell' |
Next steps: @bvarner-ebi to work with @hkir-dev to get these mappings into the while human brain PCL build. @dosumis to contact Siletti to suggest meeting to discuss further & ask if she is happy to provide answers to more questions.
@hkir-dev, can you comment on the mappings above and if you need further input from me?
Notes on mappings: Question marks (?) signify best guesses. Hyphens (-) are next to aggregates of other entries - I don't have a recommendation on how those should be mapped. Otherwise, if there is no question mark, those terms can be mapped to the dataset entries.
My understand is that @dosumis would like to move forward using the confident mappings (those with no "?").
Paper: https://doi.org/10.1101/2022.10.12.511898 Siletti et al., 2022 bioRxiv Transcriptomic diversity of cell types across the adult human brain supplementary-material
Supplementary material table 2 has two columns that are potentially mappable to cell types:
Supercluster
- Shawn worked on mapping and adding terms - see #1743 for details. This work is mostly done but it might be worth following up the unchecked items on Shawn's list - particularly grouping of types derived from upper and lower rhombic lip.Subtype auto-annotation
: Review contents of this column - referring back to text of paper to work out if we should add a new cell type to CL or whether we have an existing type that could be mapped to.This is a uniq'd list of entries in
Subtype auto-annotation
column + some potential mappings. But note - it can be useful to look at the context of the rest of the row in table 1 to work out what is being referred to.