Automated report

hubmapconsortium · Apr 3, 2024 · ebcc4f6 · ebcc4f6
1 parent 694ca9c
commit ebcc4f6
Show file tree

Hide file tree

Showing 194 changed files with 16,702 additions and 13,144 deletions.
diff --git a/NOTES.md b/NOTES.md
@@ -27,7 +27,7 @@ Release Notes
 |Liver|v1.3|Revise for April 1, 2024|
 |Lung|v1.5|NA|
 |Lymph_node|v1.4|revise for April 1, 2024|
-|Lymph_vasculature|v1.5|revise for April 1, 2024|
+|Lymph_vasculature|v1.5|March 29, 2024|
 |Main_Bronchus|v1.2|revise for April 1, 2024|
 |Mammary_Gland|v1.0|revise for April 1, 2024|
 |Muscular_System|v1.2|revise for April 1, 2024|

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 (2024-03-27)
+ASCT+B Validation Reports for Anatomical_Systems (2024-04-03)
 =============================================================
 
 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 (2024-03-27)
+ASCT+B Validation Reports for Anatomical_Systems (2024-04-03)
 =============================================================
 
 # 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 (2024-03-27)
+ASCT+B Validation Reports for Blood (2024-04-03)
 ================================================
 
 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 (2024-03-27)
+ASCT+B Validation Reports for Blood (2024-04-03)
 ================================================
 
 # 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 (2024-03-27)
+ASCT+B Validation Reports for Blood_vasculature (2024-04-03)
 ============================================================
 
 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 (2024-03-27)
+ASCT+B Validation Reports for Blood_vasculature (2024-04-03)
 ============================================================
 
 # 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 (2024-03-27)
+ASCT+B Validation Reports for Bone-Marrow (2024-04-03)
 ======================================================
 
 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 (2024-03-27)
+ASCT+B Validation Reports for Bone-Marrow (2024-04-03)
 ======================================================
 
 # 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 (2024-03-27)
+ASCT+B Validation Reports for Brain (2024-04-03)
 ================================================
 
 Table of contents
@@ -56,10 +56,10 @@ If the name/label in the ontology contains *obsolete*, please look into OLS, cli
 
 1. The term _[PCL:0015079](http://purl.obolibrary.org/obo/PCL_0015079)_ has a different name/label in the source ontology in the following 1 row _[736](https://docs.google.com/spreadsheets/d/1_esnpxPeXtZ-XNt2H1-TfEzJidBEt_prlXMsG33z9I8/edit#gid=2056967441&range=736:736)_. The name/label in the **ASCT+B table** is _Oligo L2-6 OPALIN MAP6D1 primary motor cortex oligodendrocyte (Hsap)_ and the one in the **ontology** is _Oligo L2-6 OPALIN MAP6D1 primary motor cortex oligodendrocyte precursor cell (Hsap)_. For reference, the given name/label **by SMEs** is _Oligo L2-6 OPALIN MAP6D1_. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
 
-1. The term _[UBERON:0002705](http://purl.obolibrary.org/obo/UBERON_0002705)_ has a different name/label in the source ontology in the following 1 row _[102](https://docs.google.com/spreadsheets/d/1_esnpxPeXtZ-XNt2H1-TfEzJidBEt_prlXMsG33z9I8/edit#gid=2056967441&range=102:102)_. The name/label in the **ASCT+B table** is _midline nuclear complex_ and the one in the **ontology** is _midline nuclear group_. For reference, the given name/label **by SMEs** is _midline nuclear complex_. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
-
 1. The term _[PCL:0015120](http://purl.obolibrary.org/obo/PCL_0015120)_ has a different name/label in the source ontology in the following 1 row _[738](https://docs.google.com/spreadsheets/d/1_esnpxPeXtZ-XNt2H1-TfEzJidBEt_prlXMsG33z9I8/edit#gid=2056967441&range=738:738)_. The name/label in the **ASCT+B table** is _Oligo L2-6 OPALIN FTH1P3 primary motor cortex oligodendrocyte (Hsap)_ and the one in the **ontology** is _Oligo L2-6 OPALIN FTH1P3 primary motor cortex oligodendrocyte precursor cell (Hsap)_. For reference, the given name/label **by SMEs** is _Oligo L2-6 OPALIN FTH1P3_. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
 
+1. The term _[UBERON:0002705](http://purl.obolibrary.org/obo/UBERON_0002705)_ has a different name/label in the source ontology in the following 1 row _[102](https://docs.google.com/spreadsheets/d/1_esnpxPeXtZ-XNt2H1-TfEzJidBEt_prlXMsG33z9I8/edit#gid=2056967441&range=102:102)_. The name/label in the **ASCT+B table** is _midline nuclear complex_ and the one in the **ontology** is _midline nuclear group_. For reference, the given name/label **by SMEs** is _midline nuclear complex_. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
+
 
 ## Blank ontology ID
 

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 (2024-03-27)
+ASCT+B Validation Reports for Brain (2024-04-03)
 ================================================
 
 # ASCT+B as Graph

diff --git a/docs/Brain/logs_dict.json b/docs/Brain/logs_dict.json
@@ -3035,19 +3035,19 @@
       "user_label": "Oligo L2-6 OPALIN MAP6D1",
       "row_number": 736
     },
-    {
-      "id": "UBERON:0002705",
-      "label": "midline nuclear group",
-      "asct_label": "midline nuclear complex",
-      "user_label": "midline nuclear complex",
-      "row_number": 102
-    },
     {
       "id": "PCL:0015120",
       "label": "Oligo L2-6 OPALIN FTH1P3 primary motor cortex oligodendrocyte precursor cell (Hsap)",
       "asct_label": "Oligo L2-6 OPALIN FTH1P3 primary motor cortex oligodendrocyte (Hsap)",
       "user_label": "Oligo L2-6 OPALIN FTH1P3",
       "row_number": 738
+    },
+    {
+      "id": "UBERON:0002705",
+      "label": "midline nuclear group",
+      "asct_label": "midline nuclear complex",
+      "user_label": "midline nuclear complex",
+      "row_number": 102
     }
   ],
   "no_parent": []

diff --git a/docs/Eye/README.md b/docs/Eye/README.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Eye (2024-03-27)
+ASCT+B Validation Reports for Eye (2024-04-03)
 ==============================================
 
 Table of contents

diff --git a/docs/Eye/assets/ccf_Eye_graph.pdf b/docs/Eye/assets/ccf_Eye_graph.pdf
diff --git a/docs/Eye/graph.md b/docs/Eye/graph.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Eye (2024-03-27)
+ASCT+B Validation Reports for Eye (2024-04-03)
 ==============================================
 
 # ASCT+B as Graph

diff --git a/docs/Fallopian_tube/README.md b/docs/Fallopian_tube/README.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Fallopian_tube (2024-03-27)
+ASCT+B Validation Reports for Fallopian_tube (2024-04-03)
 =========================================================
 
 Table of contents

diff --git a/docs/Fallopian_tube/assets/ccf_Fallopian_tube_graph.pdf b/docs/Fallopian_tube/assets/ccf_Fallopian_tube_graph.pdf
diff --git a/docs/Fallopian_tube/graph.md b/docs/Fallopian_tube/graph.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Fallopian_tube (2024-03-27)
+ASCT+B Validation Reports for Fallopian_tube (2024-04-03)
 =========================================================
 
 # ASCT+B as Graph

diff --git a/docs/Heart/README.md b/docs/Heart/README.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Heart (2024-03-27)
+ASCT+B Validation Reports for Heart (2024-04-03)
 ================================================
 
 Table of contents

diff --git a/docs/Heart/assets/ccf_Heart_graph.pdf b/docs/Heart/assets/ccf_Heart_graph.pdf
diff --git a/docs/Heart/graph.md b/docs/Heart/graph.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Heart (2024-03-27)
+ASCT+B Validation Reports for Heart (2024-04-03)
 ================================================
 
 # ASCT+B as Graph

diff --git a/docs/Kidney/README.md b/docs/Kidney/README.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Kidney (2024-03-27)
+ASCT+B Validation Reports for Kidney (2024-04-03)
 =================================================
 
 Table of contents

diff --git a/docs/Kidney/assets/ccf_Kidney_graph.pdf b/docs/Kidney/assets/ccf_Kidney_graph.pdf
diff --git a/docs/Kidney/graph.md b/docs/Kidney/graph.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Kidney (2024-03-27)
+ASCT+B Validation Reports for Kidney (2024-04-03)
 =================================================
 
 # ASCT+B as Graph

diff --git a/docs/Knee/README.md b/docs/Knee/README.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Knee (2024-03-27)
+ASCT+B Validation Reports for Knee (2024-04-03)
 ===============================================
 
 Table of contents

diff --git a/docs/Knee/assets/ccf_Knee_graph.pdf b/docs/Knee/assets/ccf_Knee_graph.pdf
diff --git a/docs/Knee/graph.md b/docs/Knee/graph.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Knee (2024-03-27)
+ASCT+B Validation Reports for Knee (2024-04-03)
 ===============================================
 
 # ASCT+B as Graph

diff --git a/docs/Large_intestine/README.md b/docs/Large_intestine/README.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Large_intestine (2024-03-27)
+ASCT+B Validation Reports for Large_intestine (2024-04-03)
 ==========================================================
 
 Table of contents

diff --git a/docs/Large_intestine/assets/ccf_Large_intestine_graph.pdf b/docs/Large_intestine/assets/ccf_Large_intestine_graph.pdf
diff --git a/docs/Large_intestine/graph.md b/docs/Large_intestine/graph.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Large_intestine (2024-03-27)
+ASCT+B Validation Reports for Large_intestine (2024-04-03)
 ==========================================================
 
 # ASCT+B as Graph

diff --git a/docs/Liver/README.md b/docs/Liver/README.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Liver (2024-03-27)
+ASCT+B Validation Reports for Liver (2024-04-03)
 ================================================
 
 Table of contents

diff --git a/docs/Liver/assets/ccf_Liver_graph.pdf b/docs/Liver/assets/ccf_Liver_graph.pdf
diff --git a/docs/Liver/graph.md b/docs/Liver/graph.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Liver (2024-03-27)
+ASCT+B Validation Reports for Liver (2024-04-03)
 ================================================
 
 # ASCT+B as Graph

diff --git a/docs/Lung/README.md b/docs/Lung/README.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Lung (2024-03-27)
+ASCT+B Validation Reports for Lung (2024-04-03)
 ===============================================
 
 Table of contents

diff --git a/docs/Lung/assets/ccf_Lung_graph.pdf b/docs/Lung/assets/ccf_Lung_graph.pdf
diff --git a/docs/Lung/graph.md b/docs/Lung/graph.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Lung (2024-03-27)
+ASCT+B Validation Reports for Lung (2024-04-03)
 ===============================================
 
 # ASCT+B as Graph

diff --git a/docs/Lymph_node/README.md b/docs/Lymph_node/README.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Lymph_node (2024-03-27)
+ASCT+B Validation Reports for Lymph_node (2024-04-03)
 =====================================================
 
 Table of contents

diff --git a/docs/Lymph_node/assets/ccf_Lymph_node_graph.pdf b/docs/Lymph_node/assets/ccf_Lymph_node_graph.pdf
diff --git a/docs/Lymph_node/graph.md b/docs/Lymph_node/graph.md
@@ -1,5 +1,5 @@
 
-ASCT+B Validation Reports for Lymph_node (2024-03-27)
+ASCT+B Validation Reports for Lymph_node (2024-04-03)
 =====================================================
 
 # ASCT+B as Graph

diff --git a/docs/Lymph_vasculature/Lymph_vasculature_AS_CT_strict_log.tsv b/docs/Lymph_vasculature/Lymph_vasculature_AS_CT_strict_log.tsv
@@ -1,25 +1,32 @@
 row_number	s	slabel	user_slabel	o	olabel	user_olabel
-17	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
-88	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0035279	supraclavicular lymph node	supraclavicular lymph node
-42	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
-41	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
-40	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
-39	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
-38	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
-37	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0005435	upper part of cisterna chyli	cisterna chyli
-35	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0015881	internal iliac lymph node	internal iliac lymph node
-34	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001543	popliteal lymph node	popliteal lymph node
-33	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0009006	deep inguinal lymph node	deep inguinal lymph node
-32	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0015880	external iliac lymph node	external iliac lymph node
-31	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0015878	common iliac lymph node	common iliac lymph node
-30	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0016386	paraaortic lymph node	paraaortic lymph node
-29	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0016402	mesocolic lymph node	mesocolic lymph node
-28	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0002509	mesenteric lymph node	mesenteric lymph node
-25	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0016378	ileocolic lymph node	ileocolic lymph node
-24	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0002508	celiac lymph node	celiac lymph node
-21	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0005435	upper part of cisterna chyli	cisterna chyli
-20	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0005435	upper part of cisterna chyli	cisterna chyli
-19	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0005435	upper part of cisterna chyli	cisterna chyli
-18	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
-89	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0035279	supraclavicular lymph node	supraclavicular lymph node
-98	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
+20	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
+123	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0035279	supraclavicular lymph node	supraclavicular lymph node
+74	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
+73	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
+72	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
+71	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
+70	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
+67	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
+66	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
+65	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
+64	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
+63	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
+59	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0005435	upper part of cisterna chyli	cisterna chyli
+58	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0005435	upper part of cisterna chyli	cisterna chyli
+124	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0035279	supraclavicular lymph node	supraclavicular lymph node
+56	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0015881	internal iliac lymph node	internal iliac lymph node
+54	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0009006	deep inguinal lymph node	deep inguinal lymph node
+53	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0015880	external iliac lymph node	external iliac lymph node
+52	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0015878	common iliac lymph node	common iliac lymph node
+51	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0016386	paraaortic lymph node	paraaortic lymph node
+49	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0016402	mesocolic lymph node	mesocolic lymph node
+48	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0002509	mesenteric lymph node	mesenteric lymph node
+43	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0016378	ileocolic lymph node	ileocolic lymph node
+42	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0002508	celiac lymph node	celiac lymph node
+38	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0005435	upper part of cisterna chyli	cisterna chyli
+34	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0005435	upper part of cisterna chyli	cisterna chyli
+33	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0005435	upper part of cisterna chyli	cisterna chyli
+32	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
+21	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct
+55	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001543	popliteal lymph node	popliteal lymph node
+132	CL:0002138	endothelial cell of lymphatic vessel	lymphatic endothelial cell	UBERON:0001631	thoracic duct	thoracic duct