dosumis
commented
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.
Closed dosumis closed 1 year ago
dosumis
commented
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.
dosumis
commented
1 year ago @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 |
ghost
commented
1 year ago 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' |
dosumis
commented
1 year ago 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.
ghost
commented
1 year ago @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-annotationcolumn + 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.