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Update CellTypes_v1.tsv
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- Changed "gamma delta T cell" (without dash) to the official EFO term "gamma-delta T cell" (with dash, CL:0000798)
- Changed "pericyte cell" to "pericyte" (CL:0000669).
- Changed EFO ID for "transit amplifying cell" from DB:0000024 to CL:0009010. 
- Added new cell types for Elmentaite dataset (annotation from celltypist intestine): 
BEST4+ intestinal epithelial cell, human
T follicular helper cell
capillary endothelial cell
colon macrophage
endothelial cell of artery
tuft cell of colon
vein endothelial cell
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@hatjek
hatjek authored Aug 7, 2023
1 parent 0bd219a commit e0084e4
Showing 1 changed file with 14 additions and 7 deletions.
21 changes: 14 additions & 7 deletions besca/datasets/nomenclature/CellTypes_v1.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -95,8 +95,8 @@ CD8-positive, alpha-beta T cell CD8-positive, alpha-beta T cell CL:0000625 CD8Tc
Mueller cell Mueller cell CL:0000636 Mueller 5 astrocyte CL:0000127 macrogial cell CL:0000126 glial cell CL:0000125 neural cell CL:0002319 animal cell CL:0000548
Bergmann glial cell Bergmann glial cell CL:0000644 BergmannGlial 5 astrocyte CL:0000127 macrogial cell CL:0000126 glial cell CL:0000125 neural cell CL:0002319 animal cell CL:0000548
basal cell basal cell CL:0000646 Basal 5 epithelial fate stem cell CL:0000036 somatic stem cell CL:0000723 stem cell CL:0000034 precursor cell CL:0011115 animal cell CL:0000548
mesangial cell mesangial cell CL:0000650 Mesangial 3 pericyte cell CL:0000669 connective tissue cell CL:0002320 animal cell CL:0000548
pericyte cell pericyte cell CL:0000669 Pericyte 2 connective tissue cell CL:0002320 animal cell CL:0000548
mesangial cell mesangial cell CL:0000650 Mesangial 3 pericyte CL:0000669 connective tissue cell CL:0002320 animal cell CL:0000548
pericyte pericyte CL:0000669 Pericyte 2 connective tissue cell CL:0002320 animal cell CL:0000548
glutamatergic neuron glutamatergic neuron CL:0000679 GlutamatergicN 3 neuron CL:0000540 neural cell CL:0002319 animal cell CL:0000548
muscle precursor cell muscle precursor cell CL:0000680 MusclePC 2 precursor cell CL:0011115 animal cell CL:0000548
radial glial cell radial glial cell CL:0000681 RadialGlial 3 glial cell CL:0000125 neural cell CL:0002319 animal cell CL:0000548
Expand Down Expand Up @@ -130,7 +130,7 @@ plasma cell plasma cell CL:0000786 Plasma 3 lymphocyte of B lineage CL:00009
memory B cell memory B cell CL:0000787 MemBcell 4 B cell CL:0000236 lymphocyte of B lineage CL:0000945 hematopoietic cell CL:0000988 animal cell CL:0000548
naive B cell naive B cell CL:0000788 NaiBcell 4 B cell CL:0000236 lymphocyte of B lineage CL:0000945 hematopoietic cell CL:0000988 animal cell CL:0000548
CD8-positive, alpha-beta cytotoxic T cell CD8-positive, alpha-beta cytotoxic T cell CL:0000794 CytotoxCD8Tcell 5 CD8-positive, alpha-beta T cell CL:0000625 T cell CL:0000084 lymphocyte CL:0000542 hematopoietic cell CL:0000988 animal cell CL:0000548
gamma delta T cell gamma-delta T cell CL:0000798 gdTcell 4 T cell CL:0000084 lymphocyte CL:0000542 hematopoietic cell CL:0000988 animal cell CL:0000548
gamma-delta T cell gamma-delta T cell CL:0000798 gdTcell 4 T cell CL:0000084 lymphocyte CL:0000542 hematopoietic cell CL:0000988 animal cell CL:0000548
memory T cell memory T cell CL:0000813 MemTcell 4 T cell CL:0000084 lymphocyte CL:0000542 hematopoietic cell CL:0000988 animal cell CL:0000548
mature NK T cell mature NK T cell CL:0000814 NKTcell 4 T cell CL:0000084 lymphocyte CL:0000542 hematopoietic cell CL:0000988 animal cell CL:0000548
regulatory T cell regulatory T cell CL:0000815 RegTcell 4 T cell CL:0000084 lymphocyte CL:0000542 hematopoietic cell CL:0000988 animal cell CL:0000548
Expand Down Expand Up @@ -223,7 +223,7 @@ fibroblast of lung fibroblast of lung CL:0002553 LungFibroblast 3 fibroblast
intestinal epithelial cell intestinal epithelial cell CL:0002563 IntestinalEpithelial 3 endo-epithelial cell CL:0002076 epithelial cell CL:0000066 animal cell CL:0000548
mesenchymal stem cell of adipose mesenchymal stem cell of adipose CL:0002570 AdiposeMSC 5 mesenchymal stem cell CL:0000134 multi fate stem cell CL:0000048 stem cell CL:0000034 precursor cell CL:0011115 animal cell CL:0000548
Schwann cell Schwann cell CL:0002573 Schwann 3 glial cell CL:0000125 neural cell CL:0002319 animal cell CL:0000548
central nervous system pericyte central nervous system pericyte CL:0002575 CNSPericyte 3 pericyte cell CL:0000669 connective tissue cell CL:0002320 animal cell CL:0000548
central nervous system pericyte central nervous system pericyte CL:0002575 CNSPericyte 3 pericyte CL:0000669 connective tissue cell CL:0002320 animal cell CL:0000548
renal cortical epithelial cell renal cortical epithelial cell CL:0002584 RenalCorticalEpith 3 kidney epithelial cell CL:0002518 epithelial cell CL:0000066 animal cell CL:0000548
retinal blood vessel endothelial cell retinal blood vessel endothelial cell CL:0002585 RetinalVesselEndo 4 blood vessel endothelial cell CL:0000071 endothelial cell of vascular tree CL:0002139 endothelial cell CL:0000115 animal cell CL:0000548
retinal pigment epithelial cell retinal pigment epithelial cell CL:0002586 RetPigmentEpith 3 pigment cell CL:0000147 epithelial cell CL:0000066 animal cell CL:0000548
Expand Down Expand Up @@ -268,7 +268,7 @@ bone marrow hematopoietic cell bone marrow hematopoietic cell CL:1001610 BoneMar
microvascular endothelial cell microvascular endothelial cell CL:2000008 MicroVascEndo 5 microvascular endothelial cell CL:2000008 blood vessel endothelial cell CL:0000071 endothelial cell of vascular tree CL:0002139 endothelial cell CL:0000115 animal cell CL:0000548
cerebellum basket cell cerebellum basket cell CL:2000027 CerebellumBasket 5 basket cell CL:0000118 central nervous system neuron CL:2000029 neuron CL:0000540 neural cell CL:0002319 animal cell CL:0000548
central nervous system neuron central nervous system neuron CL:2000029 CNSNeuron 3 neuron CL:0000540 neural cell CL:0002319 animal cell CL:0000548
brain pericyte brain pericyte CL:2000043 BrainPericyte 4 central nervous system pericyte CL:0002575 pericyte cell CL:0000669 connective tissue cell CL:0002320 animal cell CL:0000548
brain pericyte brain pericyte CL:2000043 BrainPericyte 4 central nervous system pericyte CL:0002575 pericyte CL:0000669 connective tissue cell CL:0002320 animal cell CL:0000548
inflammatory monocyte DB:0000001 InflamMonocyte 4 monocyte CL:0000576 myeloid leukocyte CL:0000766 hematopoietic cell CL:0000988 animal cell CL:0000548
exhausted-like CD4-positive, alpha-beta T cell DB:0000002 ExhCD4Tcell 5 CD4-positive, alpha-beta T cell CL:0000624 T cell CL:0000084 lymphocyte CL:0000542 hematopoietic cell CL:0000988 animal cell CL:0000548
proliferating CD8-positive, alpha-beta T cell DB:0000003 ProlifCD8Tcell 5 CD8-positive, alpha-beta T cell CL:0000625 T cell CL:0000084 lymphocyte CL:0000542 hematopoietic cell CL:0000988 animal cell CL:0000548
Expand All @@ -291,8 +291,8 @@ proliferating B cell DB:0000018 ProlifBcell 4 B cell CL:0000236 lymphocyte of
proliferating monocyte DB:0000020 ProlifMonocyte 3 monocyte CL:0000576 myeloid leukocyte CL:0000766 hematopoietic cell CL:0000988 animal cell CL:0000548
proliferating T cell DB:0000021 ProlifTcell 3 T cell CL:0000084 lymphocyte CL:0000542 hematopoietic cell CL:0000988 animal cell CL:0000548
proliferating CD4-positive, alpha-beta T cell DB:0000022 ProlifCD4Tcell 5 CD4-positive, alpha-beta T cell CL:0000624 T cell CL:0000084 lymphocyte CL:0000542 hematopoietic cell CL:0000988 animal cell CL:0000548
proliferating transit amplifying cell DB:0000023 ProlifTAmplifying 5 transit amplifying cell DB:0000024 intestinal epithelial cell CL:0002563 endo-epithelial cell CL:0002076 epithelial cell CL:0000066 animal cell CL:0000548
transit amplifying cell DB:0000024 TAmplifying 4 intestinal epithelial cell CL:0002563 endo-epithelial cell CL:0002076 epithelial cell CL:0000066 animal cell CL:0000548
proliferating transit amplifying cell DB:0000023 ProlifTAmplifying 5 transit amplifying cell CL:0009010 intestinal epithelial cell CL:0002563 endo-epithelial cell CL:0002076 epithelial cell CL:0000066 animal cell CL:0000548
transit amplifying cell CL:0009010 TAmplifying 4 intestinal epithelial cell CL:0002563 endo-epithelial cell CL:0002076 epithelial cell CL:0000066 animal cell CL:0000548
SLC17A7-positive neuron DB:0000025 Neuron_SLC17A7 4 glutamatergic neuron CL:0000679 neuron CL:0000540 neural cell CL:0002319 animal cell CL:0000548
SLC17A6-positive neuron DB:0000026 Neuron_SLC17A6 4 glutamatergic neuron CL:0000679 neuron CL:0000540 neural cell CL:0002319 animal cell CL:0000548
SLC17A6_SLC17A7-positive neuron DB:0000027 Neuron_SLC17A6_SLC17A7 4 glutamatergic neuron CL:0000679 neuron CL:0000540 neural cell CL:0002319 animal cell CL:0000548
Expand Down Expand Up @@ -398,3 +398,10 @@ epicardial adipocyte epicardial adipocyte CL:1000309 EpicardialAdipocyte 3 f
SLC17A6_PVALB-positive neuron DB:0000085 Neuron_SLC17A6_PVALB 4 glutamatergic neuron CL:0000679 neuron CL:0000540 neural cell CL:0002319 animal cell CL:0000548
proliferating natural killer cell DB:0000086 ProlifNKcell 5 natural killer cell CL:0000623 innate lymphoid cell CL:0001065 lymphocyte CL:0000542 hematopoietic cell CL:0000988 animal cell CL:0000548
B myeloid cell doublet DB:0000087 BMyeloid 2 hematopoietic cell CL:0000988 animal cell CL:0000548
BEST4+ intestinal epithelial cell, human BEST4+ intestinal epithelial cell, human CL:4030026 BEST4enterocyte 5 enterocyte CL:0000584 intestinal epithelial cell CL:0002563 endo-epithelial cell CL:0002076 epithelial cell CL:0000066 animal cell CL:0000548
T follicular helper cell T follicular helper cell CL:0002038 FollicularTh 5 CD4-positive, alpha-beta T cell CL:0000624 T cell CL:0000084 lymphocyte CL:0000542 hematopoietic cell CL:0000988 animal cell CL:0000548
capillary endothelial cell capillary endothelial cell CL:0002144 CapillaryEndothelial 4 blood vessel endothelial cell CL:0000071 endothelial cell of vascular tree CL:0002139 endothelial cell CL:0000115 animal cell CL:0000548
colon macrophage colon macrophage CL:0009038 ColonMacrophage 4 macrophage CL:0000235 myeloid leukocyte CL:0000766 hematopoietic cell CL:0000988 animal cell CL:0000548
endothelial cell of artery endothelial cell of artery CL:1000413 EndothelialArtery 4 blood vessel endothelial cell CL:0000071 endothelial cell of vascular tree CL:0002139 endothelial cell CL:0000115 animal cell CL:0000548
tuft cell of colon tuft cell of colon CL:0009041 TuftColon 5 brush cell of epithelium proper of large intestine CL:0002203 brush cell CL:0002204 endo-epithelial cell CL:0002076 epithelial cell CL:0000066 animal cell CL:0000548
vein endothelial cell vein endothelial cell CL:0002543 VeinEndothelial 4 blood vessel endothelial cell CL:0000071 endothelial cell of vascular tree CL:0002139 endothelial cell CL:0000115 animal cell CL:0000548

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