ccf-validation-tools/Prostate/comments/

[giscus[bot]]

ccf-validation-tools/Prostate/comments/

https://hubmapconsortium.github.io/ccf-validation-tools/Prostate/comments/

[emquardokus]

Prostate_v1.1_DRAFT
https://docs.google.com/spreadsheets/d/1hlSptGNXzyM7vxsH930YMf6gZkHVgHUE-Qc_4uFAmoU/edit#gid=1239199370

Blank ontology ID missing parent
ADDED CT/1 as basal cell of urothelium CL:1000486 In row 25, the term basal cell of prostatic urethra without ontology ID has no parent that is from the CL ontology.

[emquardokus]

Prostate_v1.1_DRAFT
https://docs.google.com/spreadsheets/d/1hlSptGNXzyM7vxsH930YMf6gZkHVgHUE-Qc_4uFAmoU/edit#gid=1239199370

Some substantial changes were made by author Doug Strand, need to inquire intent on the blood vasculature work, this new area seems problematic; seems like there was a copy paste column shift too.

Different labels

1. ADDED: Label was vascular system, added blood vasculature UBERON:0004537 instead of the uberon in this issue In row 19, the term UBERON:0001085 has different name/label in the source ontology. The name/label in the ASCT+B table is vascular system and the one in the ontology is skin of trunk. For reference, the given name/label by SMEs is vascular system. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

2. Removed because misalgined In row 24, the term UBERON:0002441 has different name/label in the source ontology. The name/label in the ASCT+B table is pericyte and the one in the ontology is cervicothoracic ganglion. For reference, the given name/label by SMEs is pericyte. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

3. ADDED: body proper UBERON:0013702 since this is what we use in the HRA for body In row 19, the term UBERON:0001489 has different name/label in the source ontology. The name/label in the ASCT+B table is whole body and the one in the ontology is manus joint. For reference, the given name/label by SMEs is whole body. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

4. ADDED blood vessel smooth muscle In row 23, the term UBERON:0001431 has different name/label in the source ontology. The name/label in the ASCT+B table is vascular smooth muscle and the one in the ontology is distal carpal bone 2. For reference, the given name/label by SMEs is vascular smooth muscle. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

5. ADDED correct uberon ID rows 19, 20, 21, 23, 24 blood vessel UBERON:0001981 In row 19, the term UBERON:0001102 has different name/label in the source ontology. The name/label in the ASCT+B table is blood vessel and the one in the ontology is cartilage of main bronchus. For reference, the given name/label by SMEs is blood vessel. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

6. ADDED correct lymphatic vessel UBERON:0001473 In row 22, the term UBERON:0004167 has different name/label in the source ontology. The name/label in the ASCT+B table is lymphatic endothelial cell and the one in the ontology is orbitofrontal cortex. For reference, the given name/label by SMEs is lymphatic endothelial cell. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

7. ADDED club-like cell of the urethral epithelium In row 26, the term CL:4032000 has different name/label in the source ontology. The name/label in the ASCT+B table is club cell of prostatic urethral epithelium and the one in the ontology is club-like cell of the urethral epithelium. For reference, the given name/label by SMEs is club epithelia. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

Blank ontology ID

1. ADDED ionocyte CL:0005006 In row 15, no term id was found for the name/label ionocyte epithelia.

2. Misaligned columns; fixed In row 19, no term id was found for the name/label endothelial cell of artery.

3. Misaligned columns; fixed In row 20, no term id was found for the name/label capillary endothelial cell.

4. Misaligned columns; fixed In row 21, no term id was found for the name/label vein endothelial cell.

5. Misaligned columns; fixed In row 22, no term id was found for the name/label lymph node lymphatic vessel endothelial cell.

[emquardokus]

Prostate_v1.1
https://docs.google.com/spreadsheets/d/1hlSptGNXzyM7vxsH930YMf6gZkHVgHUE-Qc_4uFAmoU/edit#gid=1239199370

Terms not found
Corrected: The term used in table was: hematopoietic system UBERON:000570, which should be UBERON:0002390

===
Corrected: The term used in table was blood vessel endothelium UBERON:0000766 , which should be UBERON:0004638

Typos or punctuation mistakes
FIXED:
It might have a typo in the term NEED in the following 2 rows 17, 18. The term id should have this pattern: UBERON:NNNNNNN or CL:NNNNNNN or PCL:NNNNNNN. The ontology name in upper case. N is a number, and it should have exactly 7 numbers after the colon. Please change it in the ASCT+B table.

Different labels

1. CORRECTED: The term CL:0000413 has a different name/label in the source ontology in the following 1 row 19. The name/label in the ASCT+B table is endothelial cell of artery and the one in the ontology is haploid cell. For reference, the given name/label by SMEs is endothelial cell of artery. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

The intended cell type was CL:1000413 endothelial cell of artery; note one number off in CL ID between them CL:0000413 haploid cell.

2. CORRECTED 2 instances: The term UBERON:0001085 has a different name/label in the source ontology in the following 1 row 23. The name/label in the ASCT+B table is vascular system and the one in the ontology is skin of trunk. For reference, the given name/label by SMEs is vascular system. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

The intended term was vascular system UBERON:0007798

3. CORRECTED removed cell type from AS column; correct CT was already in CT column. The term UBERON:0004167 has a different name/label in the source ontology in the following 1 row 22. The name/label in the ASCT+B table is lymphatic endothelial cell and the one in the ontology is orbitofrontal cortex. For reference, the given name/label by SMEs is lymphatic endothelial cell. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

[emquardokus]

Prostate_v1.1
https://docs.google.com/spreadsheets/d/1hlSptGNXzyM7vxsH930YMf6gZkHVgHUE-Qc_4uFAmoU/edit#gid=1239199370
The term The term used in table was: hematopoietic system was replaced with lymph vasculature lymph vasculature UBERON:0004536 as parent of lymphatic vessel UBERON:0001473