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anitacaron committed Dec 4, 2024
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2 changes: 1 addition & 1 deletion NOTES.md
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| :---: | :---: |
|CL|2024-09-26|
|PCL|2024-07-11|
|UBERON|2024-09-03|
|UBERON|2024-11-25|

### ASCT+b Tables

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9 changes: 5 additions & 4 deletions docs/Anatomical_Systems/README.md
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ASCT+B Validation Reports for Anatomical_Systems (2024-11-27)
ASCT+B Validation Reports for Anatomical_Systems (2024-12-04)
=============================================================

Table of contents
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If the name/label in the ontology contains *obsolete*, please look into OLS, clicking on the term ID, for its replacement.

1. The term _[UBERON:0011143](http://purl.obolibrary.org/obo/UBERON_0011143)_ has a different name/label in the source ontology in the following 2 rows _[33](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=33:33)_, _[33](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=33:33)_. The name/label in the **ASCT+B table** is _kidney_ and the one in the **ontology** is _upper urinary tract_. For reference, the given name/label **by SMEs** is _kidney_. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
1. The term _[UBERON:0011143](http://purl.obolibrary.org/obo/UBERON_0011143)_ has a different name/label in the source ontology in the following 2 rows _[44](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=44:44)_, _[44](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=44:44)_. The name/label in the **ASCT+B table** is _kidney_ and the one in the **ontology** is _upper urinary tract_. For reference, the given name/label **by SMEs** is _kidney_. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.


## Blank ontology ID
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| | s | slabel | user_slabel | o | olabel | user_olabel | row_number | deltaIC |
|----|-----------------------------------------------------------------|--------------------|--------------------|-----------------------------------------------------------------|----------------------------|----------------------------|---------------------------------------------------------------------------------------------------------------------------|-----------|
| 0 | [UBERON:0004175](http://purl.obolibrary.org/obo/UBERON_0004175) | internal genitalia | internal genitalia | [UBERON:0000474](http://purl.obolibrary.org/obo/UBERON_0000474) | female reproductive system | female reproductive system | [38](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=38:38) | nan |
| 1 | [UBERON:0004175](http://purl.obolibrary.org/obo/UBERON_0004175) | internal genitalia | internal genitalia | [UBERON:0000474](http://purl.obolibrary.org/obo/UBERON_0000474) | female reproductive system | female reproductive system | [39](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=39:39) | nan |
| 0 | [UBERON:0001033](http://purl.obolibrary.org/obo/UBERON_0001033) | gustatory system | gustatory system | [UBERON:0001007](http://purl.obolibrary.org/obo/UBERON_0001007) | digestive system | digestive system | [30](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=30:30) | nan |
| 1 | [UBERON:0004175](http://purl.obolibrary.org/obo/UBERON_0004175) | internal genitalia | internal genitalia | [UBERON:0000474](http://purl.obolibrary.org/obo/UBERON_0000474) | female reproductive system | female reproductive system | [49](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=49:49) | nan |
| 2 | [UBERON:0004175](http://purl.obolibrary.org/obo/UBERON_0004175) | internal genitalia | internal genitalia | [UBERON:0000474](http://purl.obolibrary.org/obo/UBERON_0000474) | female reproductive system | female reproductive system | [50](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=50:50) | nan |



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41 changes: 22 additions & 19 deletions docs/Anatomical_Systems/class_Anatomical_Systems_indirect_log.tsv
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s slabel user_slabel o olabel user_olabel row_number
UBERON:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 31
UBERON:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 29
UBERON:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 30
UBERON:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 32
UBERON:0000992 ovary ovary UBERON:0000474 female reproductive system female reproductive system 37
UBERON:0001224 renal pelvis renal pelvis UBERON:0011143 upper urinary tract kidney 33
UBERON:0001557 upper respiratory tract upper respiratory tract UBERON:0000065 respiratory tract respiratory tract 29
UBERON:0001558 lower respiratory tract lower respiratory tract UBERON:0000065 respiratory tract respiratory tract 30
UBERON:0001558 lower respiratory tract lower respiratory tract UBERON:0000065 respiratory tract respiratory tract 31
UBERON:0001558 lower respiratory tract lower respiratory tract UBERON:0000065 respiratory tract respiratory tract 32
UBERON:0001911 mammary gland mammary gland UBERON:0002416 integumental system integumental system 28
UBERON:0002048 lung lung UBERON:0000170 pair of lungs pair of lungs 30
UBERON:0002106 spleen spleen UBERON:0002390 hematopoietic system hematopoietic system 23
UBERON:0000017 exocrine pancreas exocrine pancreas UBERON:0002330 exocrine system exocrine system 31
UBERON:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 43
UBERON:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 42
UBERON:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 41
UBERON:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 40
UBERON:0000992 ovary ovary UBERON:0000474 female reproductive system female reproductive system 48
UBERON:0001224 renal pelvis renal pelvis UBERON:0011143 upper urinary tract kidney 44
UBERON:0001557 upper respiratory tract upper respiratory tract UBERON:0000065 respiratory tract respiratory tract 40
UBERON:0001558 lower respiratory tract lower respiratory tract UBERON:0000065 respiratory tract respiratory tract 42
UBERON:0001558 lower respiratory tract lower respiratory tract UBERON:0000065 respiratory tract respiratory tract 43
UBERON:0001558 lower respiratory tract lower respiratory tract UBERON:0000065 respiratory tract respiratory tract 41
UBERON:0001911 mammary gland mammary gland UBERON:0002416 integumental system integumental system 39
UBERON:0002048 lung lung UBERON:0000170 pair of lungs pair of lungs 41
UBERON:0002106 spleen spleen UBERON:0002390 hematopoietic system hematopoietic system 34
UBERON:0002107 liver liver UBERON:0001007 digestive system digestive system 15
UBERON:0002370 thymus thymus UBERON:0002390 hematopoietic system hematopoietic system 24
UBERON:0003889 fallopian tube fallopian tube UBERON:0003975 internal female genitalia internal female genitalia 38
UBERON:0002370 thymus thymus UBERON:0002390 hematopoietic system hematopoietic system 35
UBERON:0003729 mouth mucosa mouth mucosa UBERON:0000165 mouth mouth 21
UBERON:0003729 mouth mucosa mouth mucosa UBERON:0000165 mouth mouth 20
UBERON:0003889 fallopian tube fallopian tube UBERON:0003975 internal female genitalia internal female genitalia 49
UBERON:0004537 blood vasculature blood vasculature UBERON:0004535 cardiovascular system cardiovascular system 14
UBERON:0010147 male accessory sex gland male accessory sex gland UBERON:0000079 male reproductive system male reproductive system 41
UBERON:0011143 upper urinary tract upper urinary tract UBERON:0001008 renal system renal system 35
UBERON:0011143 upper urinary tract upper urinary tract UBERON:0001008 renal system renal system 33
UBERON:0011143 upper urinary tract upper urinary tract UBERON:0001008 renal system renal system 34
UBERON:0010147 male accessory sex gland male accessory sex gland UBERON:0000079 male reproductive system male reproductive system 52
UBERON:0011143 upper urinary tract upper urinary tract UBERON:0001008 renal system renal system 46
UBERON:0011143 upper urinary tract upper urinary tract UBERON:0001008 renal system renal system 44
UBERON:0011143 upper urinary tract upper urinary tract UBERON:0001008 renal system renal system 45
5 changes: 3 additions & 2 deletions docs/Anatomical_Systems/class_Anatomical_Systems_log.tsv
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s slabel user_slabel o olabel user_olabel row_number deltaIC
UBERON:0004175 internal genitalia internal genitalia UBERON:0000474 female reproductive system female reproductive system 38
UBERON:0004175 internal genitalia internal genitalia UBERON:0000474 female reproductive system female reproductive system 39
UBERON:0001033 gustatory system gustatory system UBERON:0001007 digestive system digestive system 30
UBERON:0004175 internal genitalia internal genitalia UBERON:0000474 female reproductive system female reproductive system 49
UBERON:0004175 internal genitalia internal genitalia UBERON:0000474 female reproductive system female reproductive system 50
2 changes: 1 addition & 1 deletion docs/Anatomical_Systems/graph.md
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ASCT+B Validation Reports for Anatomical_Systems (2024-11-27)
ASCT+B Validation Reports for Anatomical_Systems (2024-12-04)
=============================================================

# ASCT+B as Graph
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4 changes: 2 additions & 2 deletions docs/Anatomical_Systems/logs_dict.json
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"label": "upper urinary tract",
"asct_label": "kidney",
"user_label": "kidney",
"row_number": 33
"row_number": 44
},
{
"id": "UBERON:0011143",
"label": "upper urinary tract",
"asct_label": "kidney",
"user_label": "kidney",
"row_number": 33
"row_number": 44
}
],
"no_parent": []
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4 changes: 2 additions & 2 deletions docs/Blood/README.md
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ASCT+B Validation Reports for Blood (2024-11-27)
ASCT+B Validation Reports for Blood (2024-12-04)
================================================

Table of contents
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| | row_number | s | slabel | user_slabel | o | olabel | user_olabel | deltaIC |
|----|--------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------|-------------------------------------------------------|-----------------------------------|---------------------------------------------------------|-----------------------|--------------------------|-----------|
| 0 | [20](https://docs.google.com/spreadsheets/d/1dlQhZqTwP84U5zuNu8uo_xQ6C-hB9onUQJMWFn25oV8/edit#gid=939446662&range=20:20) | [CL:0000840](http://purl.obolibrary.org/obo/CL_0000840) | immature conventional dendritic cell | transitional Dendritic Cell (tDC) | [CL:0001056](http://purl.obolibrary.org/obo/CL_0001056) | dendritic cell, human | dendritic cell (DC) | 11.2345 |
| 0 | [20](https://docs.google.com/spreadsheets/d/1dlQhZqTwP84U5zuNu8uo_xQ6C-hB9onUQJMWFn25oV8/edit#gid=939446662&range=20:20) | [CL:0000840](http://purl.obolibrary.org/obo/CL_0000840) | immature conventional dendritic cell | transitional Dendritic Cell (tDC) | [CL:0001056](http://purl.obolibrary.org/obo/CL_0001056) | dendritic cell, human | dendritic cell (DC) | 11.2307 |
| 5 | [16](https://docs.google.com/spreadsheets/d/1dlQhZqTwP84U5zuNu8uo_xQ6C-hB9onUQJMWFn25oV8/edit#gid=939446662&range=16:16) | [CL:0002394](http://purl.obolibrary.org/obo/CL_0002394) | CD141-positive myeloid dendritic cell | dendritic cell type 1 (DC1) | [CL:0001056](http://purl.obolibrary.org/obo/CL_0001056) | dendritic cell, human | dendritic cell (DC) | nan |
| 7 | [17](https://docs.google.com/spreadsheets/d/1dlQhZqTwP84U5zuNu8uo_xQ6C-hB9onUQJMWFn25oV8/edit#gid=939446662&range=17:17) | [CL:0002399](http://purl.obolibrary.org/obo/CL_0002399) | CD1c-positive myeloid dendritic cell | dendritic cell type 2 (DC2) | [CL:0001056](http://purl.obolibrary.org/obo/CL_0001056) | dendritic cell, human | dendritic cell (DC) | nan |
| 9 | [18](https://docs.google.com/spreadsheets/d/1dlQhZqTwP84U5zuNu8uo_xQ6C-hB9onUQJMWFn25oV8/edit#gid=939446662&range=18:18) | [CL:0002399](http://purl.obolibrary.org/obo/CL_0002399) | CD1c-positive myeloid dendritic cell | dendritic cell type 3 (DC3) | [CL:0001056](http://purl.obolibrary.org/obo/CL_0001056) | dendritic cell, human | dendritic cell (DC) | nan |
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row_number s slabel user_slabel o olabel user_olabel deltaIC
20 CL:0000840 immature conventional dendritic cell transitional Dendritic Cell (tDC) CL:0001056 dendritic cell, human dendritic cell (DC) 11.234501765212997
20 CL:0000840 immature conventional dendritic cell transitional Dendritic Cell (tDC) CL:0001056 dendritic cell, human dendritic cell (DC) 11.230714420680016
12 CL:0000816 immature B cell immature B cell UBERON:0000178 Blood Blood
13 CL:0000787 memory B cell memory B cell UBERON:0000178 Blood Blood
14 CL:0000788 naive B cell naive B cell UBERON:0000178 Blood Blood
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2 changes: 1 addition & 1 deletion docs/Blood/graph.md
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ASCT+B Validation Reports for Blood (2024-11-27)
ASCT+B Validation Reports for Blood (2024-12-04)
================================================

# ASCT+B as Graph
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8 changes: 4 additions & 4 deletions docs/Blood_vasculature/Blood_vasculature_AS_CT_strict_log.tsv
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Expand Up @@ -866,7 +866,7 @@ CL:0000071 blood vessel endothelial cell blood vessel endothelial cell UBERON:86
CL:0000071 blood vessel endothelial cell blood vessel endothelial cell UBERON:0003471 artery of lower lip inferior labial artery 136
CL:0000071 blood vessel endothelial cell blood vessel endothelial cell UBERON:0035273 superior thoracic artery superior thoracic artery 2227
CL:0000071 blood vessel endothelial cell blood vessel endothelial cell UBERON:0003470 artery of upper lip superior labial artery 148
CL:0000071 blood vessel endothelial cell blood vessel endothelial cell UBERON:0009202 vasa recta descending limb descending vasa recta of kidney 1631
CL:0000071 blood vessel endothelial cell blood vessel endothelial cell UBERON:0009202 descending vasa recta descending vasa recta of kidney 1631
CL:0000071 blood vessel endothelial cell blood vessel endothelial cell UBERON:8600075 transverse cervical vein transverse cervical vein 3294
CL:0000071 blood vessel endothelial cell blood vessel endothelial cell UBERON:0004726 vasa recta vasa recta of kidney 1633
CL:0000071 blood vessel endothelial cell blood vessel endothelial cell UBERON:0002011 thoracodorsal artery thoracodorsal artery 2223
Expand Down Expand Up @@ -1042,7 +1042,7 @@ CL:0000071 blood vessel endothelial cell blood vessel endothelial cell UBERON:00
CL:0000071 blood vessel endothelial cell blood vessel endothelial cell UBERON:0011956 right hepatic vein right hepatic vein 2949
CL:0000071 blood vessel endothelial cell blood vessel endothelial cell UBERON:0035222 posterior parietal artery posterior parietal artery 514
CL:0000071 blood vessel endothelial cell blood vessel endothelial cell UBERON:0001072 inferior vena cava inferior vena cava 2947
CL:0000071 blood vessel endothelial cell blood vessel endothelial cell UBERON:0009091 vasa recta ascending limb ascending vasa recta of kidney 2945
CL:0000071 blood vessel endothelial cell blood vessel endothelial cell UBERON:0009091 ascending vasa recta ascending vasa recta of kidney 2945
CL:0000071 blood vessel endothelial cell blood vessel endothelial cell UBERON:0001627 middle cerebral artery middle cerebral artery 518
CL:0000071 blood vessel endothelial cell blood vessel endothelial cell UBERON:0010181 straight venules of kidney straight venule of kidney 2943
CL:0000071 blood vessel endothelial cell blood vessel endothelial cell UBERON:0001594 azygos vein azygos vein 3021
Expand Down Expand Up @@ -1825,12 +1825,12 @@ CL:0000359 vascular associated smooth muscle cell vascular smooth muscle cell UB
CL:0002144 capillary endothelial cell capillary endothelial cell UBERON:8600061 intra-acinar venule intra-acinar venule 30
CL:0002144 capillary endothelial cell capillary endothelial cell UBERON:0013132 penicillar arteriole penicillar arteriole of spleen 818
CL:0002144 capillary endothelial cell capillary endothelial cell UBERON:0016405 pulmonary capillary pulmonary capillary 3412
CL:0002144 capillary endothelial cell capillary endothelial cell UBERON:0009091 vasa recta ascending limb ascending vasa recta of kidney 2946
CL:0002144 capillary endothelial cell capillary endothelial cell UBERON:0009091 ascending vasa recta ascending vasa recta of kidney 2946
CL:0002144 capillary endothelial cell capillary endothelial cell UBERON:0035492 inferior hypophysial artery inferior hypophyseal artery 473
CL:0002144 capillary endothelial cell capillary endothelial cell UBERON:0005272 peritubular capillary peritubular capillary 1636
CL:0002144 capillary endothelial cell capillary endothelial cell UBERON:0004726 vasa recta vasa recta of kidney 1634
CL:0002144 capillary endothelial cell capillary endothelial cell UBERON:0035404 superior hypophysial artery superior hypophyseal artery 609
CL:0002144 capillary endothelial cell capillary endothelial cell UBERON:0009202 vasa recta descending limb descending vasa recta of kidney 1632
CL:0002144 capillary endothelial cell capillary endothelial cell UBERON:0009202 descending vasa recta descending vasa recta of kidney 1632
CL:0002144 capillary endothelial cell capillary endothelial cell UBERON:0004212 glomerular capillary glomerular capillary 1626
CL:0002144 capillary endothelial cell capillary endothelial cell UBERON:0003910 splenic sinusoid splenic venous sinusoid 2811
CL:0002144 capillary endothelial cell capillary endothelial cell UBERON:0005336 capillary layer of choroid capillary layer of choroid 591
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