Automated report

hubmapconsortium · Jun 27, 2022 · 7c15064 · 7c15064
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diff --git a/NOTES.md b/NOTES.md
@@ -6,8 +6,8 @@ Release Notes
 
 |Ontology|Version|
 | :---: | :---: |
-|CL|2022-02-16|
 |UBERON|2022-05-17|
+|CL|2022-02-16|
 
 ### ASCT+b Tables
 

diff --git a/graphs/ccf_Blood_graph.pdf b/graphs/ccf_Blood_graph.pdf
diff --git a/graphs/ccf_Blood_vasculature_graph.pdf b/graphs/ccf_Blood_vasculature_graph.pdf
diff --git a/graphs/ccf_Bone-Marrow_graph.pdf b/graphs/ccf_Bone-Marrow_graph.pdf
diff --git a/graphs/ccf_Brain_graph.pdf b/graphs/ccf_Brain_graph.pdf
diff --git a/graphs/ccf_Eye_graph.pdf b/graphs/ccf_Eye_graph.pdf
diff --git a/graphs/ccf_Fallopian_tube_graph.pdf b/graphs/ccf_Fallopian_tube_graph.pdf
diff --git a/graphs/ccf_Heart_graph.pdf b/graphs/ccf_Heart_graph.pdf
diff --git a/graphs/ccf_Kidney_graph.pdf b/graphs/ccf_Kidney_graph.pdf
diff --git a/graphs/ccf_Knee_graph.pdf b/graphs/ccf_Knee_graph.pdf
diff --git a/graphs/ccf_Large_intestine_graph.pdf b/graphs/ccf_Large_intestine_graph.pdf
diff --git a/graphs/ccf_Liver_graph.pdf b/graphs/ccf_Liver_graph.pdf
diff --git a/graphs/ccf_Lung_graph.pdf b/graphs/ccf_Lung_graph.pdf
diff --git a/graphs/ccf_Lymph_node_graph.pdf b/graphs/ccf_Lymph_node_graph.pdf
diff --git a/graphs/ccf_Lymph_vasculature_graph.pdf b/graphs/ccf_Lymph_vasculature_graph.pdf
diff --git a/graphs/ccf_Ovary_graph.pdf b/graphs/ccf_Ovary_graph.pdf
diff --git a/graphs/ccf_Ovary_graph.png b/graphs/ccf_Ovary_graph.png
diff --git a/graphs/ccf_Pancreas_graph.pdf b/graphs/ccf_Pancreas_graph.pdf
diff --git a/graphs/ccf_Pancreas_graph.png b/graphs/ccf_Pancreas_graph.png
diff --git a/graphs/ccf_Peripheral_nervous_system_graph.pdf b/graphs/ccf_Peripheral_nervous_system_graph.pdf
diff --git a/graphs/ccf_Placenta_graph.pdf b/graphs/ccf_Placenta_graph.pdf
diff --git a/graphs/ccf_Prostate_graph.pdf b/graphs/ccf_Prostate_graph.pdf
diff --git a/graphs/ccf_Skin_graph.pdf b/graphs/ccf_Skin_graph.pdf
diff --git a/graphs/ccf_Small_intestine_graph.pdf b/graphs/ccf_Small_intestine_graph.pdf
diff --git a/graphs/ccf_Spinal_Cord_graph.pdf b/graphs/ccf_Spinal_Cord_graph.pdf
diff --git a/graphs/ccf_Spleen_graph.pdf b/graphs/ccf_Spleen_graph.pdf
diff --git a/graphs/ccf_Thymus_graph.pdf b/graphs/ccf_Thymus_graph.pdf
diff --git a/graphs/ccf_Ureter_graph.pdf b/graphs/ccf_Ureter_graph.pdf
diff --git a/graphs/ccf_Urinary_bladder_graph.pdf b/graphs/ccf_Urinary_bladder_graph.pdf
diff --git a/graphs/ccf_Uterus_graph.pdf b/graphs/ccf_Uterus_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Blood_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Blood_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Blood_graph.png b/graphs/last_official_ASCTB_release/ccf_Blood_graph.png
diff --git a/graphs/last_official_ASCTB_release/ccf_Blood_vasculature_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Blood_vasculature_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Bone-Marrow_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Bone-Marrow_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Bone-Marrow_graph.png b/graphs/last_official_ASCTB_release/ccf_Bone-Marrow_graph.png
diff --git a/graphs/last_official_ASCTB_release/ccf_Brain_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Brain_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Eye_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Eye_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Fallopian_tube_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Fallopian_tube_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Heart_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Heart_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Kidney_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Kidney_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Knee_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Knee_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Large_intestine_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Large_intestine_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Liver_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Liver_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Lung_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Lung_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Lymph_node_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Lymph_node_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Lymph_vasculature_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Lymph_vasculature_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Ovary_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Ovary_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Pancreas_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Pancreas_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Peripheral_nervous_system_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Peripheral_nervous_system_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Prostate_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Prostate_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Skin_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Skin_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Small_intestine_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Small_intestine_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Spleen_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Spleen_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Thymus_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Thymus_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Ureter_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Ureter_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Urinary_bladder_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Urinary_bladder_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Uterus_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Uterus_graph.pdf
diff --git a/logs/Pancreas_AS_CT_strict_log.tsv b/logs/Pancreas_AS_CT_strict_log.tsv
@@ -6,9 +6,9 @@ CL:1001433	epithelial cell of exocrine pancreas	epithelial cell of exocrine panc
 CL:0002080	pancreatic centro-acinar cell	pancreatic centro-acinar cell	UBERON:0014726	intercalated duct of pancreas	intercalated duct of pancreas
 CL:1000322	Pancreatic goblet cell	pancreatic goblet cell	UBERON:0014726	intercalated duct of pancreas	intercalated duct of pancreas
 CL:0002204	brush cell	brush cell?	UBERON:0014726	intercalated duct of pancreas	intercalated duct of pancreas
-CL:0000577	type EC enteroendocrine cell	type EC enteroendocrine cell	UBERON:0014726	intercalated duct of pancreas	intercalated duct of pancreas
+CL:0002079	pancreatic ductal cell	pancreatic ductal cell	UBERON:0014726	intercalated duct of pancreas	intercalated duct of pancreas
 CL:0000192	Smooth muscle cell	smooth muscle cell	UBERON:0005429	dorsal pancreatic duct	dorsal pancreatic duct
-CL:1001433	epithelial cell of exocrine pancreas	epithelial cell of exocrine pancreas	UBERON:0001174	Common bile duct	common bile duct
+CL:1001433	epithelial cell of exocrine pancreas	epithelial cell of exocrine pancreas	UBERON:0000017	Exocrine pancreas	exocrine pancreas
 CL:0000236	B cell	B cell	UBERON:0000017	Exocrine pancreas	exocrine pancreas
 CL:0000084	T cell	T cell	UBERON:0000017	Exocrine pancreas	exocrine pancreas
 CL:0000235	Macrophage	macrophage	UBERON:0000017	Exocrine pancreas	exocrine pancreas

diff --git a/logs/class_Pancreas_log.tsv b/logs/class_Pancreas_log.tsv
@@ -19,12 +19,9 @@ CL:1000322	Pancreatic goblet cell	pancreatic goblet cell	CL:0002079	pancreatic d
 CL:1000322	Pancreatic goblet cell	pancreatic goblet cell	UBERON:0014726	intercalated duct of pancreas	intercalated duct of pancreas
 CL:0002204	brush cell	brush cell?	CL:0002079	pancreatic ductal cell	pancreatic ductal cell
 CL:0002204	brush cell	brush cell?	UBERON:0014726	intercalated duct of pancreas	intercalated duct of pancreas
-CL:0000577	type EC enteroendocrine cell	type EC enteroendocrine cell	CL:0002079	pancreatic ductal cell	pancreatic ductal cell
-CL:0000577	type EC enteroendocrine cell	type EC enteroendocrine cell	UBERON:0014726	intercalated duct of pancreas	intercalated duct of pancreas
+CL:0002079	pancreatic ductal cell	pancreatic ductal cell	UBERON:0014726	intercalated duct of pancreas	intercalated duct of pancreas
 UBERON:0005429	dorsal pancreatic duct	dorsal pancreatic duct	UBERON:0005429	dorsal pancreatic duct	Dorsal pancreatic duct
 CL:0000192	Smooth muscle cell	smooth muscle cell	UBERON:0005429	dorsal pancreatic duct	dorsal pancreatic duct
-UBERON:0001174	Common bile duct	common bile duct	UBERON:2005346	Extrapancreatic duct	extrapancreatic duct
-CL:1001433	epithelial cell of exocrine pancreas	epithelial cell of exocrine pancreas	UBERON:0001174	Common bile duct	common bile duct
 CL:0000236	B cell	B cell	UBERON:0000017	Exocrine pancreas	exocrine pancreas
 CL:0000084	T cell	T cell	UBERON:0000017	Exocrine pancreas	exocrine pancreas
 CL:0000235	Macrophage	macrophage	UBERON:0000017	Exocrine pancreas	exocrine pancreas
@@ -47,6 +44,7 @@ UBERON:0010373	Uncinate process of pancreas	uncinate process of pancreas	UBERON:
 UBERON:0007324	pancreatic lobule	pancreatic lobule	UBERON:0010373	Uncinate process of pancreas	uncinate process of pancreas
 UBERON:0007324	pancreatic lobule	pancreatic lobule	UBERON:0009709	Ventral pancreas	ventral pancreas
 UBERON:0009708	Dorsal pancreas	dorsal pancreas	UBERON:0001069	Head of pancreas	head of pancreas
+UBERON:0001174	Common bile duct	common bile duct	UBERON:2005346	Extrapancreatic duct	extrapancreatic duct
 UBERON:0012271	Major duodenal papilla	major duodenal papilla	UBERON:0001174	Common bile duct	common bile duct
 UBERON:0007324	pancreatic lobule	pancreatic lobule	UBERON:0009708	Dorsal pancreas	dorsal pancreas
 UBERON:0007324	pancreatic lobule	pancreatic lobule	UBERON:0001150	Body of pancreas	body of pancreas

diff --git a/logs/error_class_Blood.log b/logs/error_class_Blood.log
@@ -4,22 +4,22 @@ WARNING - No valid ID provided for '', label: CD4 T cell memory, user_label:
 WARNING - No valid ID provided for '', label: CD4 T cell effector memory CD45RA, user_label: 
 WARNING - No valid ID provided for '', label: CD8 T cell memory, user_label: 
 WARNING - No valid ID provided for '', label: mature CD8 T cell, user_label: 
+WARNING - Different labels found for CL:0000900. Uberongraph: naive thymus-derived CD8-positive, alpha-beta T cell ; ASCT+b table: CD8 naive
+WARNING - Different labels found for CL:0001058. Uberongraph: plasmacytoid dendritic cell, human ; ASCT+b table: Plasmacytoid Dendritic Cell (pDC)
+WARNING - Different labels found for CL:0000938. Uberongraph: CD16-negative, CD56-bright natural killer cell, human ; ASCT+b table: CD56 bright Natural killer
+WARNING - Different labels found for CL:0000814. Uberongraph: mature NK T cell ; ASCT+b table: NK lymphocytes
+WARNING - Different labels found for CL:0000818. Uberongraph: transitional stage B cell ; ASCT+b table: transitional B cell
+WARNING - Different labels found for CL:0001050. Uberongraph: effector CD8-positive, alpha-beta T cell ; ASCT+b table: CD8 T cell effector memory
+WARNING - Different labels found for CL:0000945. Uberongraph: lymphocyte of B lineage ; ASCT+b table: B lineage
 WARNING - Different labels found for CL:0000775. Uberongraph: neutrophil ; ASCT+b table: neutrophilic granulocyte
-WARNING - Different labels found for CL:0001054. Uberongraph: CD14-positive monocyte ; ASCT+b table: CD14 monocyte
 WARNING - Different labels found for CL:0000840. Uberongraph: immature conventional dendritic cell ; ASCT+b table: transitional Dendritic Cell (tDC)
-WARNING - Different labels found for CL:0002396. Uberongraph: CD14-low, CD16-positive monocyte ; ASCT+b table: CD16 monocyte
-WARNING - Different labels found for CL:0000818. Uberongraph: transitional stage B cell ; ASCT+b table: transitional B cell
 WARNING - Different labels found for CL:0002394. Uberongraph: CD141-positive myeloid dendritic cell ; ASCT+b table: dendritic cell type 1 (DC1)
 WARNING - Different labels found for CL:0000824. Uberongraph: mature natural killer cell ; ASCT+b table: mature Natural killer
-WARNING - Different labels found for CL:0000938. Uberongraph: CD16-negative, CD56-bright natural killer cell, human ; ASCT+b table: CD56 bright Natural killer
-WARNING - Different labels found for CL:0001056. Uberongraph: dendritic cell, human ; ASCT+b table: dendritic cell (DC)
-WARNING - Different labels found for CL:0000084. Uberongraph: T cell ; ASCT+b table: T lymphocytes
-WARNING - Different labels found for CL:0001058. Uberongraph: plasmacytoid dendritic cell, human ; ASCT+b table: Plasmacytoid Dendritic Cell (pDC)
-WARNING - Different labels found for CL:0000945. Uberongraph: lymphocyte of B lineage ; ASCT+b table: B lineage
-WARNING - Different labels found for CL:0001050. Uberongraph: effector CD8-positive, alpha-beta T cell ; ASCT+b table: CD8 T cell effector memory
-WARNING - Different labels found for CL:0000895. Uberongraph: naive thymus-derived CD4-positive, alpha-beta T cell ; ASCT+b table: CD4 naive
 WARNING - Different labels found for CL:0002399. Uberongraph: CD1c-positive myeloid dendritic cell ; ASCT+b table: dendritic cell type 2 (DC2)
-WARNING - Different labels found for CL:0001062. Uberongraph: effector memory CD8-positive, alpha-beta T cell, terminally differentiated ; ASCT+b table: CD8 T cell effector memory CD45RA
-WARNING - Different labels found for CL:0000814. Uberongraph: mature NK T cell ; ASCT+b table: NK lymphocytes
+WARNING - Different labels found for CL:0000895. Uberongraph: naive thymus-derived CD4-positive, alpha-beta T cell ; ASCT+b table: CD4 naive
 WARNING - Different labels found for CL:0000815. Uberongraph: regulatory T cell ; ASCT+b table: T regulatory
-WARNING - Different labels found for CL:0000900. Uberongraph: naive thymus-derived CD8-positive, alpha-beta T cell ; ASCT+b table: CD8 naive
+WARNING - Different labels found for CL:0001062. Uberongraph: effector memory CD8-positive, alpha-beta T cell, terminally differentiated ; ASCT+b table: CD8 T cell effector memory CD45RA
+WARNING - Different labels found for CL:0001054. Uberongraph: CD14-positive monocyte ; ASCT+b table: CD14 monocyte
+WARNING - Different labels found for CL:0001056. Uberongraph: dendritic cell, human ; ASCT+b table: dendritic cell (DC)
+WARNING - Different labels found for CL:0000084. Uberongraph: T cell ; ASCT+b table: T lymphocytes
+WARNING - Different labels found for CL:0002396. Uberongraph: CD14-low, CD16-positive monocyte ; ASCT+b table: CD16 monocyte