Skip to content

Commit

Permalink
Automated report
Browse files Browse the repository at this point in the history
  • Loading branch information
anitacaron committed Dec 11, 2024
1 parent b5838c6 commit 5b725a0
Show file tree
Hide file tree
Showing 207 changed files with 16,448 additions and 22,229 deletions.
20 changes: 10 additions & 10 deletions NOTES.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,26 +6,26 @@ Release Notes

|Ontology|Version|
| :---: | :---: |
|CL|2024-09-26|
|PCL|2024-07-11|
|CL|2024-09-26|
|UBERON|2024-11-25|

### ASCT+b Tables

|Organ|Version|Date|
| :---: | :---: | :---: |
|Anatomical_Systems|v1.1|June 15, 2024|
|Anatomical_Systems|v1.1|December 15, 2024|
|Blood|v1.5|NA|
|Bone-Marrow|v1.6|NA|
|Brain|v1.7|NA|
|Eye|v1.4|revise for October 1, 2024|
|Fallopian_tube|v1.4|prepare for October 1, 2024|
|Heart|v1.5|NA|
|Kidney|v1.6|revise for October 1, 2024|
|Brain|v1.7|December 15, 2024|
|Eye|v1.4|December 15, 2024|
|Fallopian_tube|v1.4|December 15, 2024|
|Heart|v1.5|December 15, 2024|
|Kidney|v1.6|December 15, 2024|
|Knee|v1.3|revise for October 1, 2024|
|Large_intestine|v1.4|revise for October 1, 2024|
|Liver|v1.4|NA|
|Lung|v1.6|December 15, 2024|
|Lung|v1.6|prepare for April 1, 2025|
|Lymph_node|v1.5|revise for October 1, 2024|
|Lymph_vasculature|v1.5|revise for October 1, 2024|
|Main_Bronchus|v1.3|NA|
Expand All @@ -40,11 +40,11 @@ Release Notes
|Skeleton|v1.3|revise for October 1, 2024|
|Skin|v1.4|Revise for October 1, 2024|
|Small_intestine|v1.2|revise for October 1, 2024|
|Spinal_Cord|v1.0|revise for April 1, 2024|
|Spinal_Cord|v1.1|December 15, 2024|
|Spleen|v1.4|revise for April 1, 2024|
|Thymus|v1.5|revise for April 1, 2024|
|Trachea|v1.1|revise for October 1|
|Ureter|NA|revise for April 2023|
|Urinary_bladder|v1.1|revise for April 2024|
|Uterus|v1.2|revise for April 1, 2024|
|Blood_vasculature|v1.7|September 24, 2024|
|Blood_vasculature|v1.7|December 15, 2024|
10 changes: 5 additions & 5 deletions docs/Anatomical_Systems/README.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@

ASCT+B Validation Reports for Anatomical_Systems (2024-12-04)
ASCT+B Validation Reports for Anatomical_Systems (2024-12-11)
=============================================================

Table of contents
Expand Down Expand Up @@ -52,7 +52,7 @@ If the term's name/label and the name/label given by SME are too different, plea

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 _[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.
- No issues found.


## Blank ontology ID
Expand Down Expand Up @@ -126,9 +126,9 @@ This table contains terms for anatomical structures that are related to each oth

| | s | slabel | user_slabel | o | olabel | user_olabel | row_number | deltaIC |
|----|-----------------------------------------------------------------|--------------------|--------------------|-----------------------------------------------------------------|----------------------------|----------------------------|---------------------------------------------------------------------------------------------------------------------------|-----------|
| 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 |
| 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 | [28](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=28:28) | 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 | [47](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=47:47) | 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 | [48](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=48:48) | nan |



Expand Down
Binary file modified docs/Anatomical_Systems/assets/ccf_Anatomical_Systems_graph.pdf
Binary file not shown.
Binary file modified docs/Anatomical_Systems/assets/ccf_Anatomical_Systems_graph.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
33 changes: 14 additions & 19 deletions docs/Anatomical_Systems/class_Anatomical_Systems_indirect_log.tsv
Original file line number Diff line number Diff line change
@@ -1,25 +1,20 @@
s slabel user_slabel o olabel user_olabel row_number
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:0000017 exocrine pancreas exocrine pancreas UBERON:0002330 exocrine system exocrine system 29
UBERON:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 39
UBERON:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 38
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:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 41
UBERON:0000992 ovary ovary UBERON:0000474 female reproductive system female reproductive system 46
UBERON:0001911 mammary gland mammary gland UBERON:0002416 integumental system integumental system 37
UBERON:0002048 lung lung UBERON:0000170 pair of lungs pair of lungs 39
UBERON:0002106 spleen spleen UBERON:0002390 hematopoietic system hematopoietic system 32
UBERON:0002107 liver liver UBERON:0001007 digestive system digestive system 15
UBERON:0002370 thymus thymus UBERON:0002390 hematopoietic system hematopoietic system 35
UBERON:0003729 mouth mucosa mouth mucosa UBERON:0000165 mouth mouth 21
UBERON:0002370 thymus thymus UBERON:0002390 hematopoietic system hematopoietic system 33
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:0003729 mouth mucosa mouth mucosa UBERON:0000165 mouth mouth 21
UBERON:0003889 fallopian tube fallopian tube UBERON:0003975 internal female genitalia internal female genitalia 47
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 52
UBERON:0011143 upper urinary tract upper urinary tract UBERON:0001008 renal system renal system 46
UBERON:0010147 male accessory sex gland male accessory sex gland UBERON:0000079 male reproductive system male reproductive system 50
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
UBERON:0011143 upper urinary tract upper urinary tract UBERON:0001008 renal system renal system 42
UBERON:0011143 upper urinary tract upper urinary tract UBERON:0001008 renal system renal system 43
6 changes: 3 additions & 3 deletions docs/Anatomical_Systems/class_Anatomical_Systems_log.tsv
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
s slabel user_slabel o olabel user_olabel row_number deltaIC
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
UBERON:0001033 gustatory system gustatory system UBERON:0001007 digestive system digestive system 28
UBERON:0004175 internal genitalia internal genitalia UBERON:0000474 female reproductive system female reproductive system 47
UBERON:0004175 internal genitalia internal genitalia UBERON:0000474 female reproductive system female reproductive system 48
2 changes: 1 addition & 1 deletion docs/Anatomical_Systems/graph.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@

ASCT+B Validation Reports for Anatomical_Systems (2024-12-04)
ASCT+B Validation Reports for Anatomical_Systems (2024-12-11)
=============================================================

# ASCT+B as Graph
Expand Down
17 changes: 1 addition & 16 deletions docs/Anatomical_Systems/logs_dict.json
Original file line number Diff line number Diff line change
@@ -1,21 +1,6 @@
{
"no_valid_id": [],
"no_found_id": [],
"diff_label": [
{
"id": "UBERON:0011143",
"label": "upper urinary tract",
"asct_label": "kidney",
"user_label": "kidney",
"row_number": 44
},
{
"id": "UBERON:0011143",
"label": "upper urinary tract",
"asct_label": "kidney",
"user_label": "kidney",
"row_number": 44
}
],
"diff_label": [],
"no_parent": []
}
2 changes: 1 addition & 1 deletion docs/Blood/README.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@

ASCT+B Validation Reports for Blood (2024-12-04)
ASCT+B Validation Reports for Blood (2024-12-11)
================================================

Table of contents
Expand Down
Binary file modified docs/Blood/assets/ccf_Blood_graph.pdf
Binary file not shown.
2 changes: 1 addition & 1 deletion docs/Blood/graph.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@

ASCT+B Validation Reports for Blood (2024-12-04)
ASCT+B Validation Reports for Blood (2024-12-11)
================================================

# ASCT+B as Graph
Expand Down
10 changes: 3 additions & 7 deletions docs/Blood_vasculature/README.md

Large diffs are not rendered by default.

Binary file modified docs/Blood_vasculature/assets/ccf_Blood_vasculature_graph.pdf
Binary file not shown.
2 changes: 1 addition & 1 deletion docs/Blood_vasculature/graph.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@

ASCT+B Validation Reports for Blood_vasculature (2024-12-04)
ASCT+B Validation Reports for Blood_vasculature (2024-12-11)
============================================================

# ASCT+B as Graph
Expand Down
Loading

0 comments on commit 5b725a0

Please sign in to comment.