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8 changes: 4 additions & 4 deletions NOTES.md
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Expand Up @@ -6,9 +6,9 @@ Release Notes

|Ontology|Version|
| :---: | :---: |
|PCL|2023-02-27|
|CL|2023-08-24|
|UBERON|2023-09-05|
|CL|2023-08-24|
|PCL|2023-02-27|

### ASCT+b Tables

Expand All @@ -34,8 +34,8 @@ Release Notes
|Ovary|v1.3|revise for April 1, 2023|
|Pancreas|v1.3|revise for April 1, 2023|
|Palatine_Tonsil|V1.0|June 15, 2023|
|Peripheral_nervous_system|v1.1|revise for Oct 1, 2022|
|Placenta|V1.1|revise for October 1, 2023|
|Peripheral_nervous_system|v1.1|revise for Oct 1, 2023|
|Placenta|1.1|10/1/23|
|Prostate|v1.1|revise for Oct 1, 2023|
|Skeleton|v1.1|September 27, 2023|
|Skin|v1.3|revise for October 1, 2023|
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2 changes: 1 addition & 1 deletion docs/Anatomical_Systems/README.md
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ASCT+B Validation Reports for Anatomical_Systems (2023-10-02)
ASCT+B Validation Reports for Anatomical_Systems (2023-10-03)
=============================================================

Table of contents
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ASCT+B Validation Reports for Anatomical_Systems (2023-10-02)
ASCT+B Validation Reports for Anatomical_Systems (2023-10-03)
=============================================================

# ASCT+B as Graph
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2 changes: 1 addition & 1 deletion docs/Blood/README.md
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ASCT+B Validation Reports for Blood (2023-10-02)
ASCT+B Validation Reports for Blood (2023-10-03)
================================================

Table of contents
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ASCT+B Validation Reports for Blood (2023-10-02)
ASCT+B Validation Reports for Blood (2023-10-03)
================================================

# ASCT+B as Graph
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2 changes: 1 addition & 1 deletion docs/Blood_vasculature/README.md
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ASCT+B Validation Reports for Blood_vasculature (2023-10-02)
ASCT+B Validation Reports for Blood_vasculature (2023-10-03)
============================================================

Table of contents
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ASCT+B Validation Reports for Blood_vasculature (2023-10-02)
ASCT+B Validation Reports for Blood_vasculature (2023-10-03)
============================================================

# ASCT+B as Graph
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8 changes: 4 additions & 4 deletions docs/Blood_vasculature/report_images_Blood_vasculature.tsv
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Expand Up @@ -10,8 +10,8 @@ UBERON:0001138 http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png
UBERON:0001139 https://upload.wikimedia.org/wikipedia/commons/6/65/Iliac_veins.gif
UBERON:0001140 http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png
UBERON:0001142 http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png
UBERON:0001182 http://upload.wikimedia.org/wikipedia/commons/c/c0/Superior_mesenteric_a.gif
UBERON:0001182 http://upload.wikimedia.org/wikipedia/commons/6/68/Gray1099.png
UBERON:0001182 http://upload.wikimedia.org/wikipedia/commons/c/c0/Superior_mesenteric_a.gif
UBERON:0001183 http://upload.wikimedia.org/wikipedia/commons/e/e4/Gray538.png
UBERON:0001184 http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png
UBERON:0001185 http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png
Expand Down Expand Up @@ -117,8 +117,8 @@ UBERON:0001641 https://upload.wikimedia.org/wikipedia/commons/b/bd/Gray488_blue.
UBERON:0001642 https://upload.wikimedia.org/wikipedia/commons/b/bd/Gray488_blue.gif
UBERON:0001651 https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png
UBERON:0001651 http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png
UBERON:0001652 http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png
UBERON:0001652 https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png
UBERON:0001652 http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png
UBERON:0001653 http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png
UBERON:0001654 http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png
UBERON:0001656 http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png
Expand All @@ -145,8 +145,8 @@ UBERON:0002460 http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png
UBERON:0002493 http://upload.wikimedia.org/wikipedia/commons/a/ae/Gray1170.png
UBERON:0003478 http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png
UBERON:0003711 http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png
UBERON:0003713 http://upload.wikimedia.org/wikipedia/commons/5/5b/Gray1189.png
UBERON:0003713 http://upload.wikimedia.org/wikipedia/commons/e/e4/Bilebladder.png
UBERON:0003713 http://upload.wikimedia.org/wikipedia/commons/5/5b/Gray1189.png
UBERON:0004639 http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png
UBERON:0004640 http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png
UBERON:0004646 http://upload.wikimedia.org/wikipedia/commons/a/aa/Gray511.png
Expand Down Expand Up @@ -179,8 +179,8 @@ UBERON:0007317 http://upload.wikimedia.org/wikipedia/commons/4/43/Gray549.png
UBERON:0008321 http://upload.wikimedia.org/wikipedia/commons/2/2b/Gray543.png
UBERON:0008783 http://upload.wikimedia.org/wikipedia/commons/4/4e/Gray581.png
UBERON:0008889 http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png
UBERON:0009040 http://upload.wikimedia.org/wikipedia/commons/0/07/Gray586.png
UBERON:0009040 http://upload.wikimedia.org/wikipedia/commons/7/74/Gray586.png
UBERON:0009040 http://upload.wikimedia.org/wikipedia/commons/0/07/Gray586.png
UBERON:0009041 http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray548.png
UBERON:0009042 http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png
UBERON:0009885 https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png
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2 changes: 1 addition & 1 deletion docs/Bone-Marrow/README.md
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ASCT+B Validation Reports for Bone-Marrow (2023-10-02)
ASCT+B Validation Reports for Bone-Marrow (2023-10-03)
======================================================

Table of contents
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ASCT+B Validation Reports for Bone-Marrow (2023-10-02)
ASCT+B Validation Reports for Bone-Marrow (2023-10-03)
======================================================

# ASCT+B as Graph
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10 changes: 5 additions & 5 deletions docs/Brain/README.md
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ASCT+B Validation Reports for Brain (2023-10-02)
ASCT+B Validation Reports for Brain (2023-10-03)
================================================

Table of contents
Expand Down Expand Up @@ -52,13 +52,13 @@ 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. In row _[736](https://docs.google.com/spreadsheets/d/1DrsZo9QUgnye6qX9hGKQoXVruRbM3LZPT2tzUy-SixI/edit#gid=2056967441&range=736:736)_, the term _[PCL:0015079](Phttp://purl.obolibrary.org/obo/CL_0015079)_ has different name/label in the source ontology. 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. In row _[737](https://docs.google.com/spreadsheets/d/1DrsZo9QUgnye6qX9hGKQoXVruRbM3LZPT2tzUy-SixI/edit#gid=2056967441&range=737:737)_, the term _[PCL:0015119](Phttp://purl.obolibrary.org/obo/CL_0015119)_ has different name/label in the source ontology. The name/label in the **ASCT+B table** is _Oligo L3-6 OPALIN-like ENPP6 primary motor cortex oligodendrocyte (Hsap)_ and the one in the **ontology** is _Oligo L3-6 OPALIN-like ENPP6 primary motor cortex oligodendrocyte precursor cell (Hsap)_. For reference, the given name/label **by SMEs** is _Oligo L3-6 OPALIN ENPP6_. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
1. In row _[234](https://docs.google.com/spreadsheets/d/1DrsZo9QUgnye6qX9hGKQoXVruRbM3LZPT2tzUy-SixI/edit#gid=2056967441&range=234:234)_, the term _[CL:4023073](http://purl.obolibrary.org/obo/CL_4023073)_ has different name/label in the source ontology. The name/label in the **ASCT+B table** is _choroid plexus cell_ and the one in the **ontology** is _obsolete choroid plexus cell_. For reference, the given name/label **by SMEs** is _choroid plexus cell_. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

1. In row _[738](https://docs.google.com/spreadsheets/d/1DrsZo9QUgnye6qX9hGKQoXVruRbM3LZPT2tzUy-SixI/edit#gid=2056967441&range=738:738)_, the term _[PCL:0015120](Phttp://purl.obolibrary.org/obo/CL_0015120)_ has different name/label in the source ontology. 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. In row _[234](https://docs.google.com/spreadsheets/d/1DrsZo9QUgnye6qX9hGKQoXVruRbM3LZPT2tzUy-SixI/edit#gid=2056967441&range=234:234)_, the term _[CL:4023073](http://purl.obolibrary.org/obo/CL_4023073)_ has different name/label in the source ontology. The name/label in the **ASCT+B table** is _choroid plexus cell_ and the one in the **ontology** is _obsolete choroid plexus cell_. For reference, the given name/label **by SMEs** is _choroid plexus cell_. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
1. In row _[737](https://docs.google.com/spreadsheets/d/1DrsZo9QUgnye6qX9hGKQoXVruRbM3LZPT2tzUy-SixI/edit#gid=2056967441&range=737:737)_, the term _[PCL:0015119](Phttp://purl.obolibrary.org/obo/CL_0015119)_ has different name/label in the source ontology. The name/label in the **ASCT+B table** is _Oligo L3-6 OPALIN-like ENPP6 primary motor cortex oligodendrocyte (Hsap)_ and the one in the **ontology** is _Oligo L3-6 OPALIN-like ENPP6 primary motor cortex oligodendrocyte precursor cell (Hsap)_. For reference, the given name/label **by SMEs** is _Oligo L3-6 OPALIN ENPP6_. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

1. In row _[736](https://docs.google.com/spreadsheets/d/1DrsZo9QUgnye6qX9hGKQoXVruRbM3LZPT2tzUy-SixI/edit#gid=2056967441&range=736:736)_, the term _[PCL:0015079](Phttp://purl.obolibrary.org/obo/CL_0015079)_ has different name/label in the source ontology. 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.


## Blank ontology ID
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ASCT+B Validation Reports for Brain (2023-10-02)
ASCT+B Validation Reports for Brain (2023-10-03)
================================================

# ASCT+B as Graph
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34 changes: 17 additions & 17 deletions docs/Brain/logs_dict.json
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Expand Up @@ -3766,18 +3766,11 @@
"no_found_id": [],
"diff_label": [
{
"id": "PCL:0015079",
"label": "Oligo L2-6 OPALIN MAP6D1 primary motor cortex oligodendrocyte precursor cell (Hsap)",
"asct_label": "Oligo L2-6 OPALIN MAP6D1 primary motor cortex oligodendrocyte (Hsap)",
"user_label": "Oligo L2-6 OPALIN MAP6D1",
"rowNumber": 736
},
{
"id": "PCL:0015119",
"label": "Oligo L3-6 OPALIN-like ENPP6 primary motor cortex oligodendrocyte precursor cell (Hsap)",
"asct_label": "Oligo L3-6 OPALIN-like ENPP6 primary motor cortex oligodendrocyte (Hsap)",
"user_label": "Oligo L3-6 OPALIN ENPP6",
"rowNumber": 737
"id": "CL:4023073",
"label": "obsolete choroid plexus cell",
"asct_label": "choroid plexus cell",
"user_label": "choroid plexus cell",
"rowNumber": 234
},
{
"id": "PCL:0015120",
Expand All @@ -3787,11 +3780,18 @@
"rowNumber": 738
},
{
"id": "CL:4023073",
"label": "obsolete choroid plexus cell",
"asct_label": "choroid plexus cell",
"user_label": "choroid plexus cell",
"rowNumber": 234
"id": "PCL:0015119",
"label": "Oligo L3-6 OPALIN-like ENPP6 primary motor cortex oligodendrocyte precursor cell (Hsap)",
"asct_label": "Oligo L3-6 OPALIN-like ENPP6 primary motor cortex oligodendrocyte (Hsap)",
"user_label": "Oligo L3-6 OPALIN ENPP6",
"rowNumber": 737
},
{
"id": "PCL:0015079",
"label": "Oligo L2-6 OPALIN MAP6D1 primary motor cortex oligodendrocyte precursor cell (Hsap)",
"asct_label": "Oligo L2-6 OPALIN MAP6D1 primary motor cortex oligodendrocyte (Hsap)",
"user_label": "Oligo L2-6 OPALIN MAP6D1",
"rowNumber": 736
}
],
"no_parent": []
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2 changes: 1 addition & 1 deletion docs/Brain/report_images_Brain.tsv
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Expand Up @@ -33,8 +33,8 @@ UBERON:0002150 http://upload.wikimedia.org/wikipedia/commons/9/97/Gray704.png
UBERON:0002151 http://upload.wikimedia.org/wikipedia/commons/d/dc/Lower_pons_horizontal_KB.svg
UBERON:0002152 http://upload.wikimedia.org/wikipedia/commons/2/2b/Gray705.png
UBERON:0002163 http://upload.wikimedia.org/wikipedia/commons/f/fc/Gray677.png
UBERON:0002264 http://upload.wikimedia.org/wikipedia/commons/d/d2/1543%2CVesalius%27OlfactoryBulbs.jpg
UBERON:0002264 http://upload.wikimedia.org/wikipedia/commons/f/f9/1543,Vesalius%27OlfactoryBulbs.jpg
UBERON:0002264 http://upload.wikimedia.org/wikipedia/commons/d/d2/1543%2CVesalius%27OlfactoryBulbs.jpg
UBERON:0002265 http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray732.png
UBERON:0002285 http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png
UBERON:0002289 http://upload.wikimedia.org/wikipedia/commons/d/da/Cn3nucleus.png
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8 changes: 1 addition & 7 deletions docs/Eye/README.md
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ASCT+B Validation Reports for Eye (2023-10-02)
ASCT+B Validation Reports for Eye (2023-10-03)
==============================================

Table of contents
Expand Down Expand Up @@ -92,16 +92,10 @@ This report provides a list of blank spreadsheet cells that often mean no ontolo

This report provides a list of CT terms with blank ontology ID without an upper term from [Cell Ontology](https://www.ebi.ac.uk/ols4/ontologies/cl). Please, create an upper level in the ASCT+B table and add an upper term for them. Please, make sure the term without ontology ID _doesn't exist_ in the ontology.

1. In row _[16](https://docs.google.com/spreadsheets/d/1tNNPZXL0ycw5gNksDUKHZJpRkKgRdVAUh9AZ6ohpgOA/edit#gid=695483621&range=16:16)_, the term _polyaxonal amacrine cell_ without ontology ID has no parent that is from the CL ontology.

1. In row _[16](https://docs.google.com/spreadsheets/d/1tNNPZXL0ycw5gNksDUKHZJpRkKgRdVAUh9AZ6ohpgOA/edit#gid=695483621&range=16:16)_, the term _semilunar type 1 cell_ without ontology ID has no parent that is from the CL ontology.

1. In row _[17](https://docs.google.com/spreadsheets/d/1tNNPZXL0ycw5gNksDUKHZJpRkKgRdVAUh9AZ6ohpgOA/edit#gid=695483621&range=17:17)_, the term _polyaxonal amacrine cell_ without ontology ID has no parent that is from the CL ontology.

1. In row _[17](https://docs.google.com/spreadsheets/d/1tNNPZXL0ycw5gNksDUKHZJpRkKgRdVAUh9AZ6ohpgOA/edit#gid=695483621&range=17:17)_, the term _semilunar type 3 cell_ without ontology ID has no parent that is from the CL ontology.

1. In row _[18](https://docs.google.com/spreadsheets/d/1tNNPZXL0ycw5gNksDUKHZJpRkKgRdVAUh9AZ6ohpgOA/edit#gid=695483621&range=18:18)_, the term _polyaxonal amacrine cell_ without ontology ID has no parent that is from the CL ontology.


## Terms from another ontology

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ASCT+B Validation Reports for Eye (2023-10-02)
ASCT+B Validation Reports for Eye (2023-10-03)
==============================================

# ASCT+B as Graph
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18 changes: 0 additions & 18 deletions docs/Eye/logs_dict.json
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Expand Up @@ -90,35 +90,17 @@
}
],
"no_parent": [
{
"id": "",
"label": "",
"user_label": "polyaxonal amacrine cell",
"row_number": 16
},
{
"id": "",
"label": "",
"user_label": "semilunar type 1 cell",
"row_number": 16
},
{
"id": "",
"label": "",
"user_label": "polyaxonal amacrine cell",
"row_number": 17
},
{
"id": "",
"label": "",
"user_label": "semilunar type 3 cell",
"row_number": 17
},
{
"id": "",
"label": "",
"user_label": "polyaxonal amacrine cell",
"row_number": 18
}
]
}
2 changes: 1 addition & 1 deletion docs/Fallopian_tube/README.md
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ASCT+B Validation Reports for Fallopian_tube (2023-10-02)
ASCT+B Validation Reports for Fallopian_tube (2023-10-03)
=========================================================

Table of contents
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ASCT+B Validation Reports for Fallopian_tube (2023-10-02)
ASCT+B Validation Reports for Fallopian_tube (2023-10-03)
=========================================================

# ASCT+B as Graph
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2 changes: 1 addition & 1 deletion docs/Heart/README.md
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ASCT+B Validation Reports for Heart (2023-10-02)
ASCT+B Validation Reports for Heart (2023-10-03)
================================================

Table of contents
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ASCT+B Validation Reports for Heart (2023-10-02)
ASCT+B Validation Reports for Heart (2023-10-03)
================================================

# ASCT+B as Graph
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2 changes: 1 addition & 1 deletion docs/Kidney/README.md
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ASCT+B Validation Reports for Kidney (2023-10-02)
ASCT+B Validation Reports for Kidney (2023-10-03)
=================================================

Table of contents
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ASCT+B Validation Reports for Kidney (2023-10-02)
ASCT+B Validation Reports for Kidney (2023-10-03)
=================================================

# ASCT+B as Graph
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6 changes: 3 additions & 3 deletions docs/Knee/README.md
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@@ -1,5 +1,5 @@

ASCT+B Validation Reports for Knee (2023-10-02)
ASCT+B Validation Reports for Knee (2023-10-03)
===============================================

Table of contents
Expand Down Expand Up @@ -52,12 +52,12 @@ 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. In row _[21](https://docs.google.com/spreadsheets/d/1v3BfUp55Ty8Bl9ufHursLN9hXmyRcj0MHDbEpPwgFZc/edit#gid=1815525900&range=21:21)_, the term _[CL:0000743](http://purl.obolibrary.org/obo/CL_0000743)_ has different name/label in the source ontology. The name/label in the **ASCT+B table** is __ and the one in the **ontology** is _hypertrophic chondrocyte_. For reference, the given name/label **by SMEs** is _Hypertrophic Chondrocyte_. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

1. In row _[12](https://docs.google.com/spreadsheets/d/1v3BfUp55Ty8Bl9ufHursLN9hXmyRcj0MHDbEpPwgFZc/edit#gid=1815525900&range=12:12)_, the term _[CL:1001607](http://purl.obolibrary.org/obo/CL_1001607)_ has different name/label in the source ontology. The name/label in the **ASCT+B table** is _articular chondrocyte of the femur_ and the one in the **ontology** is _articular chondrocyte_. For reference, the given name/label **by SMEs** is _articular chondrocyte_. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

1. In row _[12](https://docs.google.com/spreadsheets/d/1v3BfUp55Ty8Bl9ufHursLN9hXmyRcj0MHDbEpPwgFZc/edit#gid=1815525900&range=12:12)_, the term _[UBERON:0010996](http://purl.obolibrary.org/obo/UBERON_0010996)_ has different name/label in the source ontology. The name/label in the **ASCT+B table** is _Articular Cartilage of femur_ and the one in the **ontology** is _articular cartilage of joint_. For reference, the given name/label **by SMEs** is _Articular cartilage of a joint_. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

1. In row _[21](https://docs.google.com/spreadsheets/d/1v3BfUp55Ty8Bl9ufHursLN9hXmyRcj0MHDbEpPwgFZc/edit#gid=1815525900&range=21:21)_, the term _[CL:0000743](http://purl.obolibrary.org/obo/CL_0000743)_ has different name/label in the source ontology. The name/label in the **ASCT+B table** is __ and the one in the **ontology** is _hypertrophic chondrocyte_. For reference, the given name/label **by SMEs** is _Hypertrophic Chondrocyte_. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.


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ASCT+B Validation Reports for Knee (2023-10-02)
ASCT+B Validation Reports for Knee (2023-10-03)
===============================================

# ASCT+B as Graph
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