intermediate files

output/FTU-CT-AnnTool-level-info.csv

@@ -1,4 +1,4 @@
-Organ,FTU Label in Uberon,FTU ID in Uberon,CL_ID,CL_Label_FTU,popv,celltypist_pkl,celltypist_L1,azimuth_L2,azimuth_L5,azimuth_L4,azimuth_L3,azimuth_finest,azimuth_L1
+Organ,FTU Label in Uberon,FTU ID in Uberon,CL_ID,CL_Label_FTU,popv,celltypist_L1,celltypist_pkl,azimuth_L5,azimuth_L2,azimuth_L1,azimuth_L3,azimuth_finest,azimuth_L4
 Kidney,Cortical Collecting Duct,UBERON:0004203,CL:1000715,kidney cortex collecting duct intercalated cell,0,0,0,0,0,0,0,0,0
 Kidney,Cortical Collecting Duct,UBERON:0004203,CL:4030015,kidney collecting duct alpha-intercalated cell,0,0,0,0,0,0,0,0,0
 Kidney,Cortical Collecting Duct,UBERON:0004203,CL:1001033,peritubular capillary endothelial cell,0,0,0,0,0,0,0,0,0

output/sanity_check/Dataset-source-cell-summary.csv

@@ -0,0 +1 @@
+

ref_data/FTU Cell Count Table - Cell_Type_Count.csv

@@ -1,19 +1,19 @@
 Organ,FTU Label in Uberon,FTU ID in Uberon,CT Label in CL,CT ID in CL,CT Label in 2D Object,#AS,#CT
-Kidney,Cortical Collecting Duct,UBERON:0004203,kidney collecting duct beta-intercalated cell,CL:4030005,Cortical Collecting Duct Intercalated Cell Type B,0,2
+Kidney,Cortical Collecting Duct,UBERON:0004203,kidney cortex collecting duct intercalated cell,CL:1000715,Cortical Collecting Duct Intercalated Cell Type B,0,2
 Kidney,Cortical Collecting Duct,UBERON:0004203,kidney collecting duct alpha-intercalated cell,CL:4030015,Cortical Collecting Duct Intercalated Cell Type A,0,4
 Kidney,Cortical Collecting Duct,UBERON:0004203,peritubular capillary endothelial cell,CL:1001033,Endothelium Peritubular Capillary,0,5
 Kidney,Cortical Collecting Duct,UBERON:0004203,kidney cortex collecting duct principal cell,CL:1000714,Cortical Collecting Duct Principal Cell,0,9
 Kidney,Outer Medullary Collecting Duct,UBERON:0004204,kidney outer medulla collecting duct intercalated cell,CL:1000717,Outer Medullary Collecting Duct Intercalated Cell Type A,0,5
 Kidney,Outer Medullary Collecting Duct,UBERON:0004204,kidney outer medulla collecting duct principal cell,CL:1000716,Outer Medullary Collecting Duct Principal Cell,0,10
 Kidney,Outer Medullary Collecting Duct,UBERON:0004204,peritubular capillary endothelial cell,CL:1001033,Endothelium Peritubular Capillary,0,2
-Kidney,Inner Medullary Collecting Duct,UBERON:0004204,kidney inner medulla collecting duct principal cell,CL:1000718,Inner Medullary Collecting Duct Cell,0,14
+Kidney,Inner Medullary Collecting Duct,UBERON:0004205,kidney inner medulla collecting duct principal cell,CL:1000718,Inner Medullary Collecting Duct Cell,0,14
 Kidney,Inner Medullary Collecting Duct,UBERON:0004205,peritubular capillary endothelial cell,CL:1001033,Endothelium Peritubular Capillary,0,5
-Kidney,Thick Ascending Limb,UBERON:0001291,kidney loop of Henle thick ascending limb epithelial cell,CL:1001106,Thick Ascending Limb Cell,0,9
-Kidney,Thick Ascending Limb,UBERON:0001291,peritubular capillary endothelial cell,CL:1001033,Endothelium Peritubular Capillary,0,5
-Kidney,Descending Thin Limb,UBERON:0001289,kidney loop of Henle thin descending limb epithelial cell,CL:1001111,Descending Thin Limb Cell,0,3
-Kidney,Descending Thin Limb,UBERON:0001289,vasa recta descending limb cell,CL:1001285,Descending Vasa Recta,0,3
-Kidney,Ascending Thin Limb,UBERON:0004193,kidney loop of Henle thin ascending limb epithelial cell,CL:1001107,Ascending Thin Limb Cell,0,3
-Kidney,Ascending Thin Limb,UBERON:0004193,vasa recta ascending limb cell,CL:1001131,Ascending Vasa Recta,0,5
+Kidney,Thick Ascending Limb Of Loop Of Henle,UBERON:0001291,kidney loop of Henle thick ascending limb epithelial cell,CL:1001106,Thick Ascending Limb Cell,0,9
+Kidney,Thick Ascending Limb Of Loop Of Henle,UBERON:0001291,peritubular capillary endothelial cell,CL:1001033,Endothelium Peritubular Capillary,0,5
+Kidney,Descending Limb of Loop of Henle,UBERON:0001289,kidney loop of Henle thin descending limb epithelial cell,CL:1001111,Descending Thin Limb Cell,0,3
+Kidney,Descending Limb of Loop of Henle,UBERON:0001289,vasa recta descending limb cell,CL:1001285,Descending Vasa Recta,0,3
+Kidney,Loop Of Henle Ascending Limb Thin Segment,UBERON:0004193,kidney loop of Henle thin ascending limb epithelial cell,CL:1001107,Ascending Thin Limb Cell,0,3
+Kidney,Loop Of Henle Ascending Limb Thin Segment,UBERON:0004193,vasa recta ascending limb cell,CL:1001131,Ascending Vasa Recta,0,5
 Kidney,Nephron,UBERON:0001285,cortical collecting duct,UBERON:0004203,Collecting Duct,1,0
 Kidney,Nephron,UBERON:0001285,proximal straight tubule,UBERON:0001290,Proximal Tubule,1,0
 Kidney,Nephron,UBERON:0001291,proximal convoluted tubule segment 2,UBERON:0004197,Proximal Tubule,1,0
@@ -42,11 +42,11 @@ Kidney,Renal Corpuscle,UBERON:0001229,efferent arteriole endothelial cell,CL:100
 Kidney,Renal Corpuscle,UBERON:0001229,parietal epithelial cell,CL:1000452,Parietal Epithelial Cell,0,12
 Kidney,Renal Corpuscle,UBERON:0001229,afferent arteriole endothelial cell,CL:1001096,Afferent Arteriole Endothelial Cell,0,19
 Kidney,Renal Corpuscle,UBERON:0001229,macula densa epithelial cell,CL:1000850,Macula Densa Epithelial Cell,0,7
-Large Intestine,Crypt Of Lieberkuhn,UBERON:0001984,large intestine crypt goblet cell,CL:1000321,Goblet Cells,0,53
-Large Intestine,Crypt Of Lieberkuhn,UBERON:0001984,enterocyte of epithelium of large intestine,CL:0002071,Absorptive Cells,0,136
-Large Intestine,Crypt Of Lieberkuhn,UBERON:0001984,neuroendocrine cell,CL:0000165,Enteroendocrine Cells,0,5
-Large Intestine,Crypt Of Lieberkuhn,UBERON:0001984,intestinal crypt stem cell of large intestine,CL:0009016,Epithelial Stem Cells,0,5
-Large Intestine,Crypt Of Lieberkuhn,UBERON:0001984,intestinal tuft cell,CL:0019032,Tuft Cell,0,5
+Large Intestine,Crypt Of Lieberkuhn of Large Intestine,UBERON:0001984,large intestine crypt goblet cell,CL:1000321,Goblet Cells,0,53
+Large Intestine,Crypt Of Lieberkuhn of Large Intestine,UBERON:0001984,enterocyte of epithelium of large intestine,CL:0002071,Absorptive Cells,0,136
+Large Intestine,Crypt Of Lieberkuhn of Large Intestine,UBERON:0001984,neuroendocrine cell,CL:0000165,Enteroendocrine Cells,0,5
+Large Intestine,Crypt Of Lieberkuhn of Large Intestine,UBERON:0001984,intestinal crypt stem cell of large intestine,CL:0009016,Epithelial Stem Cells,0,5
+Large Intestine,Crypt Of Lieberkuhn of Large Intestine,UBERON:0001984,intestinal tuft cell,CL:0019032,Tuft Cell,0,5
 Liver,Liver Lobule,UBERON:0004647,hepatic portal fibroblast,CL:0009100,Hepatic Portal Fibroblast,0,4
 Liver,Liver Lobule,UBERON:0004647,blood vessel smooth muscle cell,CL:0019018,Blood Vessel Smooth Muscle Cell,0,8
 Liver,Liver Lobule,UBERON:0004647,endothelial cell of artery,CL:1000413,Endothelial Cell,0,4
@@ -62,14 +62,14 @@ Lung,Bronchial Submucosal Gland,UBERON 8410043,airway submucosal gland duct cili
 Lung,Bronchial Submucosal Gland,UBERON 8410043,airway submucosal gland duct basal cell,CL:4033024,Basal Cell Of Submucosal Gland,0,12
 Lung,Bronchial Submucosal Gland,UBERON 8410043,mucus secreting cell of bronchus submucosal gland,CL:4033022,Mucus Cell,0,52
 Lung,Bronchial Submucosal Gland,UBERON 8410043,airway submucosal gland collecting duct epithelial cell,CL:4033023,Epithelial cell Of Submucosal Gland,0,2
-Lung,Bronchial Submucosal Gland,UBERON 8410043,serous secreting cell of bronchus submucosal gland,CL:0000313,Serous Cell,0,55
+Lung,Bronchial Submucosal Gland,UBERON 8410043,serous secreting cell of bronchus submucosal gland,CL:4033023,Serous Cell,0,55
 Lung,Bronchial Submucosal Gland,UBERON 8410043,myoepithelial cell of bronchus submucosal gland,CL:4033003,Myoepithelial cell,0,20
-Lung,Pulmonary Alveolus,UBERON:0002299,type II pneumocyte,CL:0002063,Type II Pneumocyte,0,6
-Lung,Pulmonary Alveolus,UBERON:0002299,lung pericyte,CL:0009089,Pericyte,0,2
-Lung,Pulmonary Alveolus,UBERON:0002299,type I pneumocyte,CL:0002062,Type I Pneumocyte,0,14
-Lung,Pulmonary Alveolus,UBERON:0002299,alveolar type 1 fibroblast cell,CL:4028004,Lung Matrix Fibroblast,0,7
-Lung,Pulmonary Alveolus,UBERON:0002299,secondary crest myofibroblast,CL:4033016,Secondary Crest Myofibroblast,0,9
-Lung,Pulmonary Alveolus,UBERON:0002299,alveolar capillary type 1 endothelial cell,CL:4028002,Capillary Endothelial Cell,0,27
+Lung,Alveolus of Lung,UBERON:0002299,type II pneumocyte,CL:0002063,Type II Pneumocyte,0,6
+Lung,Alveolus of Lung,UBERON:0002299,lung pericyte,CL:0009089,Pericyte,0,2
+Lung,Alveolus of Lung,UBERON:0002299,type I pneumocyte,CL:0002062,Type I Pneumocyte,0,14
+Lung,Alveolus of Lung,UBERON:0002299,alveolar type 1 fibroblast cell,CL:4028004,Lung Matrix Fibroblast,0,7
+Lung,Alveolus of Lung,UBERON:0002299,secondary crest myofibroblast,CL:4033016,Secondary Crest Myofibroblast,0,9
+Lung,Alveolus of Lung,UBERON:0002299,alveolar capillary type 1 endothelial cell,CL:4028002,Capillary Endothelial Cell,0,27
 Pancreas,Intercalated Duct,UBERON:0014726,epithelial cell of exocrine pancreas,CL:1001433,Ductal Epithelial Cell,0,25
 Pancreas,Intercalated Duct,UBERON:0014726,pancreatic centro-acinar cell,CL:0002080,Centroacinar Cell,0,2
 Pancreas,Intercalated Duct,UBERON:0014726,intercalated duct of pancreas,UBERON:0014726,intercalated duct,1,0
@@ -90,7 +90,7 @@ Pancreas,Islet of Langerhans,UBERON:0000006,,,Pericyte,0,1
 Prostate,Prostate Glandular Acinus,UBERON:0004179,fibroblast of subepithelial connective tissue of prostatic gland,CL:1000301,Fibroblast Of Subepithelial Connective Tissue Of Prostatic Gland,0,101
 Prostate,Prostate Glandular Acinus,UBERON:0004179,smooth muscle cell of prostate,CL:1000487,Smooth Muscle Cell Of Prostate,0,76
 Prostate,Prostate Glandular Acinus,UBERON:0004179,fibroblast of connective tissue of prostate,CL:1000299,Fibroblast Of Connective Tissue Of Prostate,0,20
-Prostate,Prostate Glandular Acinus,UBERON:0004179,prostate gland microvascular endothelial cell,CL:2000059,Prostate Gland Microvascular Endothelial Cell,0,3
+Prostate,Prostate Glandular Acinus,UBERON:0004179,,,Prostate Gland Microvascular Endothelial Cell,0,3
 Prostate,Prostate Glandular Acinus,UBERON:0004179,luminal cell of prostate epithelium,CL:0002340,Luminal Cell Of Prostate Epithelium,0,120
 Prostate,Prostate Glandular Acinus,UBERON:0004179,basal cell of prostate epithelium,CL:0002341,Basal Cell Of Prostate Epithelium,0,174
 Prostate,Prostate Glandular Acinus,UBERON:0004179,vascular associated smooth muscle cell,CL:0000359,Vascular Smooth Muscle Cell,0,4
@@ -99,7 +99,7 @@ Skin,Dermal Papilla,UBERON:0001992,skin fibroblast,CL:0002620,Skin Fibroblast,0,
 Skin,Dermal Papilla,UBERON:0001992,endothelial cell,CL:0000115,Blood Vessel,0,7
 Skin,Epidermal Ridge,UBERON:0013487,prickle cell,CL:0000649,Prickle Cell,0,104
 Skin,Epidermal Ridge,UBERON:0013487,epidermal Langerhans cell,CL:0002457,Epidermal Langerhans Cell,0,3
-Skin,Epidermal Ridge,UBERON:0013487,basal cell of epidermis,CL:0002187,Basal Cell,0,35
+Skin,Epidermal Ridge,UBERON:0013487,basal cell,CL:0000646,Basal Cell,0,35
 Skin,Epidermal Ridge,UBERON:0013487,Merkel cell,CL:0000242,Merkel Cell,0,2
 Skin,Epidermal Ridge,UBERON:0013487,melanocyte of skin,CL:1000458,Melanocyte,0,4
 Small Intestine,Villus,UBERON 0001213,natural killer cell,CL:0000623,Natural Killer Cell,0,4