Automated report

hubmapconsortium · Nov 27, 2024 · f4f5990 · f4f5990
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diff --git a/NOTES.md b/NOTES.md
@@ -6,9 +6,9 @@ Release Notes
 
 |Ontology|Version|
 | :---: | :---: |
-|UBERON|2024-09-03|
-|PCL|2024-07-11|
 |CL|2024-09-26|
+|PCL|2024-07-11|
+|UBERON|2024-09-03|
 
 ### ASCT+b Tables
 
@@ -25,7 +25,7 @@ Release Notes
 |Knee|v1.3|revise for October 1, 2024|
 |Large_intestine|v1.4|revise for October 1, 2024|
 |Liver|v1.4|NA|
-|Lung|v1.6|revise for October 1, 2024|
+|Lung|v1.6|December 15, 2024|
 |Lymph_node|v1.5|revise for October 1, 2024|
 |Lymph_vasculature|v1.5|revise for October 1, 2024|
 |Main_Bronchus|v1.3|NA|

diff --git a/docs/Anatomical_Systems/README.md b/docs/Anatomical_Systems/README.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Anatomical_Systems (2024-11-20)
+ASCT+B Validation Reports for Anatomical_Systems (2024-11-27)
 =============================================================
 
 Table of contents

diff --git a/docs/Anatomical_Systems/assets/ccf_Anatomical_Systems_graph.pdf b/docs/Anatomical_Systems/assets/ccf_Anatomical_Systems_graph.pdf
diff --git a/docs/Anatomical_Systems/graph.md b/docs/Anatomical_Systems/graph.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Anatomical_Systems (2024-11-20)
+ASCT+B Validation Reports for Anatomical_Systems (2024-11-27)
 =============================================================
 
 # ASCT+B as Graph

diff --git a/docs/Blood/README.md b/docs/Blood/README.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Blood (2024-11-20)
+ASCT+B Validation Reports for Blood (2024-11-27)
 ================================================
 
 Table of contents

diff --git a/docs/Blood/assets/ccf_Blood_graph.pdf b/docs/Blood/assets/ccf_Blood_graph.pdf
diff --git a/docs/Blood/graph.md b/docs/Blood/graph.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Blood (2024-11-20)
+ASCT+B Validation Reports for Blood (2024-11-27)
 ================================================
 
 # ASCT+B as Graph

diff --git a/docs/Blood_vasculature/README.md b/docs/Blood_vasculature/README.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Blood_vasculature (2024-11-20)
+ASCT+B Validation Reports for Blood_vasculature (2024-11-27)
 ============================================================
 
 Table of contents

diff --git a/docs/Blood_vasculature/assets/ccf_Blood_vasculature_graph.pdf b/docs/Blood_vasculature/assets/ccf_Blood_vasculature_graph.pdf
diff --git a/docs/Blood_vasculature/graph.md b/docs/Blood_vasculature/graph.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Blood_vasculature (2024-11-20)
+ASCT+B Validation Reports for Blood_vasculature (2024-11-27)
 ============================================================
 
 # ASCT+B as Graph

diff --git a/docs/Bone-Marrow/README.md b/docs/Bone-Marrow/README.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Bone-Marrow (2024-11-20)
+ASCT+B Validation Reports for Bone-Marrow (2024-11-27)
 ======================================================
 
 Table of contents

diff --git a/docs/Bone-Marrow/assets/ccf_Bone-Marrow_graph.pdf b/docs/Bone-Marrow/assets/ccf_Bone-Marrow_graph.pdf
diff --git a/docs/Bone-Marrow/graph.md b/docs/Bone-Marrow/graph.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Bone-Marrow (2024-11-20)
+ASCT+B Validation Reports for Bone-Marrow (2024-11-27)
 ======================================================
 
 # ASCT+B as Graph

diff --git a/docs/Brain/README.md b/docs/Brain/README.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Brain (2024-11-20)
+ASCT+B Validation Reports for Brain (2024-11-27)
 ================================================
 
 Table of contents

diff --git a/docs/Brain/assets/ccf_Brain_graph.pdf b/docs/Brain/assets/ccf_Brain_graph.pdf
diff --git a/docs/Brain/graph.md b/docs/Brain/graph.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Brain (2024-11-20)
+ASCT+B Validation Reports for Brain (2024-11-27)
 ================================================
 
 # ASCT+B as Graph

diff --git a/docs/Eye/Eye_AS_CT_strict_log.tsv b/docs/Eye/Eye_AS_CT_strict_log.tsv
@@ -3,9 +3,16 @@ CL:0000036	epithelial fate stem cell	epithelial fate stem cell	UBERON:0000482	ba
 CL:0000066	epithelial cell	epithelial cell	UBERON:0002506	iris epithelium	iris epithelium	61
 CL:0000125	glial cell	glial cell	UBERON:0018107	foveola of retina	foveola of retina	75
 CL:0000125	glial cell	glial cell	UBERON:0035966	scleral lamina cribrosa	scleral lamina cribrosa	65
-CL:0000125	glial cell	glial cell	UBERON:0004904	neuron projection bundle connecting eye with brain	optic nerve	64
+CL:0000125	glial cell	glial cell	UBERON:0000941	cranial nerve II	optic nerve	64
 CL:0000129	microglial cell	microglial cell	UBERON:0000966	retina	retina	48
+CL:0000561	Amacrine Cell	Amacrine cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	19
 CL:0000561	Amacrine Cell	Amacrine Cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	12
+CL:0000561	Amacrine Cell	Amacrine cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	16
+CL:0000561	Amacrine Cell	Amacrine cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	13
+CL:0000561	Amacrine Cell	Amacrine cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	14
+CL:0000561	Amacrine Cell	Amacrine cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	15
+CL:0000561	Amacrine Cell	Amacrine cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	18
+CL:0000561	Amacrine Cell	Amacrine cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	17
 CL:0000573	retinal cone cell	retinal cone cell	UBERON:0001789	outer nuclear layer of retina	outer nuclear layer	33
 CL:0000604	retinal rod cell	retinal rod cell	UBERON:0001789	outer nuclear layer of retina	outer nuclear layer	51
 CL:0000636	Mueller cell	Muller glia	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	49
@@ -17,16 +24,11 @@ CL:0002225	secondary lens fiber	mature fiber cell	UBERON:0000390	lens nucleus	Fe
 CL:0002228	primary lens fiber	primary lens fiber	UBERON:0002444	lens fiber	lens Fibers	38
 CL:0002363	keratocyte	keratocyte	UBERON:0003952	anterior stroma of cornea	anterior stroma of cornea	56
 CL:0002585	retinal blood vessel endothelial cell	Endothelial Cell	UBERON:0004864	vasculature of retina	vasculature	34
-CL:0004219	A2 amacrine cell	A2 cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	18
-CL:0004232	starburst amacrine cell	starburst amacrine cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	19
-CL:0004253	wide field retinal amacrine cell	wide field cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	15
 CL:0011004	lens fiber cell	lens fiber cell	UBERON:0000389	lens cortex	cortex	46
-CL:0011004	lens fiber cell	lens fiber cell	UBERON:0002444	lens fiber	lens Fibers	41
+CL:0011004	lens fiber cell	lens fiber cell	UBERON:0000390	lens nucleus	Adult nucleus	45
 CL:0011004	lens fiber cell	lens fiber cell	UBERON:0002444	lens Fiber	lens Fiber	53
 CL:0011004	lens fiber cell	lens fiber cell	UBERON:0000389	lens cortex	cortex	47
-CL:0011004	lens fiber cell	lens fiber cell	UBERON:0000390	lens nucleus	Adult nucleus	45
-CL:0011005	GABAergic interneuron	GABAergic interneuron	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	13
+CL:0011004	lens fiber cell	lens fiber cell	UBERON:0002444	lens fiber	lens Fibers	41
 CL:0017004	telocyte	telocyte	UBERON:0003952	anterior stroma of cornea	anterior stroma of cornea	57
 CL:4023188	Midget ganglion cell of retina	Midget cell	UBERON:0001792	ganglionic layer of retina	retinal ganglion cell layer	35
 CL:4023189	Parasol ganglion cell of retina	Parasol cell	UBERON:0001792	ganglionic layer of retina	retinal ganglion cell layer	36
-CL:4030028	glycinergic amacrine cell	Glycinergic Amacrine Cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	14
diff --git a/docs/Eye/Eye_AS_has_part_CT_log.tsv b/docs/Eye/Eye_AS_has_part_CT_log.tsv
@@ -1,9 +1,15 @@
 s	slabel	user_slabel	o	olabel	user_olabel	row_number
 CL:0000066	epithelial cell	epithelial cell	UBERON:0002506	iris epithelium	iris epithelium	61
 CL:0000561	Amacrine Cell	Amacrine Cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	12
+CL:0000561	Amacrine Cell	Amacrine cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	13
+CL:0000561	Amacrine Cell	Amacrine cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	14
+CL:0000561	Amacrine Cell	Amacrine cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	15
+CL:0000561	Amacrine Cell	Amacrine cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	16
+CL:0000561	Amacrine Cell	Amacrine cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	17
+CL:0000561	Amacrine Cell	Amacrine cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	18
+CL:0000561	Amacrine Cell	Amacrine cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	19
 CL:0000740	retinal ganglion cell	Ganglion cell	UBERON:0001792	ganglionic layer of retina	retinal ganglion cell layer	37
 CL:0000740	retinal ganglion cell	Ganglion cell	UBERON:0001792	ganglionic layer of retina	retinal ganglion cell layer	69
 CL:0000745	retina horizontal cell	Horizontal Cell	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	39
 CL:0011004	lens fiber cell	lens fiber cell	UBERON:0002444	lens fiber	lens Fibers	41
 CL:0011004	lens fiber cell	lens fiber cell	UBERON:0002444	lens Fiber	lens Fiber	53
-CL:0011005	GABAergic interneuron	GABAergic interneuron	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	13