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‎NOTES.md

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|Ontology|Version|
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| :---: | :---: |
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|PCL|2024-07-11|
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|UBERON|2024-09-03|
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|CL|2024-09-26|
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|PCL|2024-07-11|
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### ASCT+b Tables
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‎docs/Anatomical_Systems/README.md

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=============================================================
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Table of contents
@@ -52,7 +52,7 @@ If the term's name/label and the name/label given by SME are too different, plea
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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.
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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 _[40](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=40:40)_, _[40](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=40:40)_. 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.
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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.
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## Blank ontology ID
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| | s | slabel | user_slabel | o | olabel | user_olabel | row_number | deltaIC |
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|----|-----------------------------------------------------------------|--------------------|--------------------|-----------------------------------------------------------------|----------------------------|----------------------------|---------------------------------------------------------------------------------------------------------------------------|-----------|
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| 0 | [UBERON:0002106](http://purl.obolibrary.org/obo/UBERON_0002106) | spleen | spleen | [UBERON:0001007](http://purl.obolibrary.org/obo/UBERON_0001007) | digestive system | digestive system | [19](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=19:19) | nan |
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| 1 | [UBERON:0002405](http://purl.obolibrary.org/obo/UBERON_0002405) | immune system | immune system | [UBERON:0000467](http://purl.obolibrary.org/obo/UBERON_0000467) | anatomical system | anatomical system | [24](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=24:24) | nan |
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| 2 | [UBERON:0002405](http://purl.obolibrary.org/obo/UBERON_0002405) | immune system | immune system | [UBERON:0000467](http://purl.obolibrary.org/obo/UBERON_0000467) | anatomical system | anatomical system | [25](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=25:25) | nan |
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| 3 | [UBERON:0002405](http://purl.obolibrary.org/obo/UBERON_0002405) | immune system | immune system | [UBERON:0000467](http://purl.obolibrary.org/obo/UBERON_0000467) | anatomical system | anatomical system | [26](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=26:26) | nan |
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| 4 | [UBERON:0002405](http://purl.obolibrary.org/obo/UBERON_0002405) | immune system | immune system | [UBERON:0000467](http://purl.obolibrary.org/obo/UBERON_0000467) | anatomical system | anatomical system | [27](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=27:27) | nan |
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| 5 | [UBERON:0002405](http://purl.obolibrary.org/obo/UBERON_0002405) | immune system | immune system | [UBERON:0000467](http://purl.obolibrary.org/obo/UBERON_0000467) | anatomical system | anatomical system | [28](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=28:28) | nan |
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| 6 | [UBERON:0002405](http://purl.obolibrary.org/obo/UBERON_0002405) | immune system | immune system | [UBERON:0000467](http://purl.obolibrary.org/obo/UBERON_0000467) | anatomical system | anatomical system | [29](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=29:29) | nan |
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| 7 | [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 | [45](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=45:45) | nan |
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| 8 | [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 | [46](https://docs.google.com/spreadsheets/d/13qyyCHS4lxgIfVtQJ_aVxB-aWch7oJG-psrZn4ZoFEM/edit#gid=2028977062&range=46:46) | nan |
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| 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 |
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| 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 |
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‎docs/Anatomical_Systems/assets/ccf_Anatomical_Systems_graph.pdf

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‎docs/Anatomical_Systems/class_Anatomical_Systems_indirect_log.tsv

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s slabel user_slabel o olabel user_olabel row_number
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UBERON:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 36
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UBERON:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 37
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UBERON:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 38
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UBERON:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 39
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UBERON:0000992 ovary ovary UBERON:0000474 female reproductive system female reproductive system 44
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UBERON:0001224 renal pelvis renal pelvis UBERON:0011143 upper urinary tract kidney 40
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UBERON:0001557 upper respiratory tract upper respiratory tract UBERON:0000065 respiratory tract respiratory tract 36
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UBERON:0001558 lower respiratory tract lower respiratory tract UBERON:0000065 respiratory tract respiratory tract 37
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UBERON:0001558 lower respiratory tract lower respiratory tract UBERON:0000065 respiratory tract respiratory tract 39
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UBERON:0001558 lower respiratory tract lower respiratory tract UBERON:0000065 respiratory tract respiratory tract 38
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UBERON:0001911 mammary gland mammary gland UBERON:0002416 integumental system integumental system 31
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UBERON:0002048 lung lung UBERON:0000170 pair of lungs pair of lungs 37
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UBERON:0002106 spleen spleen UBERON:0002405 immune system immune system 25
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UBERON:0002106 spleen spleen UBERON:0002390 hematopoietic system hematopoietic system 34
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UBERON:0002107 liver liver UBERON:0001007 digestive system digestive system 18
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UBERON:0002370 thymus thymus UBERON:0002390 hematopoietic system hematopoietic system 35
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UBERON:0002370 thymus thymus UBERON:0002405 immune system immune system 26
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UBERON:0003889 fallopian tube fallopian tube UBERON:0003975 internal female genitalia internal female genitalia 45
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UBERON:0010147 male accessory sex gland male accessory sex gland UBERON:0000079 male reproductive system male reproductive system 48
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UBERON:0011143 upper urinary tract upper urinary tract UBERON:0001008 renal system renal system 40
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UBERON:0011143 upper urinary tract upper urinary tract UBERON:0001008 renal system renal system 41
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UBERON:0011143 upper urinary tract upper urinary tract UBERON:0001008 renal system renal system 42
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UBERON:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 31
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UBERON:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 29
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UBERON:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 30
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UBERON:0000065 respiratory tract respiratory tract UBERON:0001004 respiratory system respiratory system 32
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UBERON:0000992 ovary ovary UBERON:0000474 female reproductive system female reproductive system 37
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UBERON:0001224 renal pelvis renal pelvis UBERON:0011143 upper urinary tract kidney 33
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UBERON:0001557 upper respiratory tract upper respiratory tract UBERON:0000065 respiratory tract respiratory tract 29
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UBERON:0001558 lower respiratory tract lower respiratory tract UBERON:0000065 respiratory tract respiratory tract 30
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UBERON:0001558 lower respiratory tract lower respiratory tract UBERON:0000065 respiratory tract respiratory tract 31
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UBERON:0001558 lower respiratory tract lower respiratory tract UBERON:0000065 respiratory tract respiratory tract 32
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UBERON:0001911 mammary gland mammary gland UBERON:0002416 integumental system integumental system 28
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UBERON:0002048 lung lung UBERON:0000170 pair of lungs pair of lungs 30
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UBERON:0002106 spleen spleen UBERON:0002390 hematopoietic system hematopoietic system 23
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UBERON:0002107 liver liver UBERON:0001007 digestive system digestive system 15
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UBERON:0002370 thymus thymus UBERON:0002390 hematopoietic system hematopoietic system 24
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UBERON:0003889 fallopian tube fallopian tube UBERON:0003975 internal female genitalia internal female genitalia 38
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UBERON:0004537 blood vasculature blood vasculature UBERON:0004535 cardiovascular system cardiovascular system 14
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UBERON:0010147 male accessory sex gland male accessory sex gland UBERON:0000079 male reproductive system male reproductive system 41
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UBERON:0011143 upper urinary tract upper urinary tract UBERON:0001008 renal system renal system 35
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UBERON:0011143 upper urinary tract upper urinary tract UBERON:0001008 renal system renal system 33
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UBERON:0011143 upper urinary tract upper urinary tract UBERON:0001008 renal system renal system 34

‎docs/Anatomical_Systems/class_Anatomical_Systems_log.tsv

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s slabel user_slabel o olabel user_olabel row_number deltaIC
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UBERON:0002106 spleen spleen UBERON:0001007 digestive system digestive system 19
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UBERON:0002405 immune system immune system UBERON:0000467 anatomical system anatomical system 24
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UBERON:0002405 immune system immune system UBERON:0000467 anatomical system anatomical system 25
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UBERON:0002405 immune system immune system UBERON:0000467 anatomical system anatomical system 26
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UBERON:0002405 immune system immune system UBERON:0000467 anatomical system anatomical system 27
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UBERON:0002405 immune system immune system UBERON:0000467 anatomical system anatomical system 28
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UBERON:0002405 immune system immune system UBERON:0000467 anatomical system anatomical system 29
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UBERON:0004175 internal genitalia internal genitalia UBERON:0000474 female reproductive system female reproductive system 45
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UBERON:0004175 internal genitalia internal genitalia UBERON:0000474 female reproductive system female reproductive system 46
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UBERON:0004175 internal genitalia internal genitalia UBERON:0000474 female reproductive system female reproductive system 38
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UBERON:0004175 internal genitalia internal genitalia UBERON:0000474 female reproductive system female reproductive system 39

‎docs/Anatomical_Systems/graph.md

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# ASCT+B as Graph

‎docs/Anatomical_Systems/logs_dict.json

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"label": "upper urinary tract",
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"row_number": 40
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"row_number": 33
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"row_number": 33
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"no_parent": []

‎docs/Blood/README.md

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‎docs/Blood/graph.md

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# ASCT+B as Graph

‎docs/Blood_vasculature/README.md

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‎docs/Bone-Marrow/README.md

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‎docs/Bone-Marrow/assets/ccf_Bone-Marrow_graph.pdf

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‎docs/Bone-Marrow/graph.md

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# ASCT+B as Graph

‎docs/Brain/README.md

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‎docs/Brain/assets/ccf_Brain_graph.pdf

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‎docs/Brain/graph.md

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# ASCT+B as Graph

‎docs/Eye/README.md

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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.
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1. The term _[UBERON:0004904](http://purl.obolibrary.org/obo/UBERON_0004904)_ has a different name/label in the source ontology in the following 2 rows _[70](https://docs.google.com/spreadsheets/d/1tNNPZXL0ycw5gNksDUKHZJpRkKgRdVAUh9AZ6ohpgOA/edit#gid=695483621&range=70:70)_, _[70](https://docs.google.com/spreadsheets/d/1tNNPZXL0ycw5gNksDUKHZJpRkKgRdVAUh9AZ6ohpgOA/edit#gid=695483621&range=70:70)_. The name/label in the **ASCT+B table** is _optic nerve_ and the one in the **ontology** is _neuron projection bundle connecting eye with brain_. For reference, the given name/label **by SMEs** is _neuron projection bundle connecting eye with brain_. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
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1. The term _[UBERON:0000965](http://purl.obolibrary.org/obo/UBERON_0000965)_ has a different name/label in the source ontology in the following 2 rows _[59](https://docs.google.com/spreadsheets/d/1tNNPZXL0ycw5gNksDUKHZJpRkKgRdVAUh9AZ6ohpgOA/edit#gid=695483621&range=59:59)_, _[59](https://docs.google.com/spreadsheets/d/1tNNPZXL0ycw5gNksDUKHZJpRkKgRdVAUh9AZ6ohpgOA/edit#gid=695483621&range=59:59)_. The name/label in the **ASCT+B table** is _lens_ and the one in the **ontology** is _lens of camera-type eye_. For reference, the given name/label **by SMEs** is _lens_. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
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1. The term _[UBERON:0004904](http://purl.obolibrary.org/obo/UBERON_0004904)_ has a different name/label in the source ontology in the following 2 rows _[70](https://docs.google.com/spreadsheets/d/1tNNPZXL0ycw5gNksDUKHZJpRkKgRdVAUh9AZ6ohpgOA/edit#gid=695483621&range=70:70)_, _[70](https://docs.google.com/spreadsheets/d/1tNNPZXL0ycw5gNksDUKHZJpRkKgRdVAUh9AZ6ohpgOA/edit#gid=695483621&range=70:70)_. The name/label in the **ASCT+B table** is _optic nerve_ and the one in the **ontology** is _neuron projection bundle connecting eye with brain_. For reference, the given name/label **by SMEs** is _neuron projection bundle connecting eye with brain_. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
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## Blank ontology ID
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‎docs/Eye/assets/ccf_Eye_graph.pdf

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‎docs/Eye/graph.md

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# ASCT+B as Graph

‎docs/Eye/logs_dict.json

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],
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"no_found_id": [],
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"diff_label": [
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{
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"id": "UBERON:0004904",
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"label": "neuron projection bundle connecting eye with brain",
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"asct_label": "optic nerve",
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"user_label": "neuron projection bundle connecting eye with brain",
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"row_number": 70
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},
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{
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"id": "UBERON:0004904",
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"label": "neuron projection bundle connecting eye with brain",
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"asct_label": "optic nerve",
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"user_label": "neuron projection bundle connecting eye with brain",
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},
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"user_label": "lens",
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},
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{
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"id": "UBERON:0004904",
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"label": "neuron projection bundle connecting eye with brain",
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"asct_label": "optic nerve",
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"user_label": "neuron projection bundle connecting eye with brain",
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"row_number": 70
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},
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{
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"id": "UBERON:0004904",
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"label": "neuron projection bundle connecting eye with brain",
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"asct_label": "optic nerve",
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"user_label": "neuron projection bundle connecting eye with brain",
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"row_number": 70
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}
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],
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"no_parent": [

‎docs/Fallopian_tube/README.md

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‎docs/Fallopian_tube/graph.md

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# ASCT+B as Graph

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