ccf-validation-tools/Kidney/comments/

[giscus[bot]]

ccf-validation-tools/Kidney/comments/

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

[emquardokus]

Kidney_v1.3_DRAFT https://docs.google.com/spreadsheets/d/1aXnWkwArSRmDnhyq0n_ptISWnmRwXvD4X0BPa9WQfmg/edit#gid=949267305
Different labels

1. Fixed In row 46, the term CL:4030021 has different name/label in the source ontology. The name/label in the ASCT+B table is connecting tubule intercalated cell type B and the one in the ontology is kidney connecting tubule beta-intercalated cell.

2. Fixed uberon ID to correct one juxtaglomerular arteriole UBERON:0034884 not UBERON:0001916
   In row 60, the term UBERON:0001916 has different name/label in the source ontology. The name/label in the ASCT+B table is juxtaglomerular arteriole and the one in the ontology is endothelium of arteriole
3. Fixed In row 45, the term CL:4030020 has different name/label in the source ontology. The name/label in the ASCT+B table is connecting tubule intercalated cell type A and the one in the ontology is kidney connecting tubule alpha-intercalated cell.
4. Fixed; In row 44, the term CL:4030019 has different name/label in the source ontology. The name/label in the ASCT+B table is connecting tubule intercalated cell and the one in the ontology is kidney connecting tubule intercalated cell.
5. Fixed: In row 70, the term CL:4030022 has different name/label in the source ontology. The name/label in the ASCT+B table is medullary fibroblast and the one in the ontology is renal medullary fibroblast.
6. fixed; In row 20, the term UBERON:0001284 has different name/label in the source ontology. The name/label in the ASCT+B table is renal column (column of Bertin) and the one in the ontology is renal column.
7. fixed typo: In row 59, the term CL:0000115 has different name/label in the source ontology. The name/label in the ASCT+B table is endothlial cell and the one in the ontology is endothelial cell. For reference, the given name/label by SMEs is Endothelial Cell.
8. fixed: In row 54, the term CL:4030015 has different name/label in the source ontology. The name/label in the ASCT+B table is collecting duct intercalated cell type A and the one in the ontology is kidney collecting duct alpha-intercalated cell.
9. fixed: In row 43, the term CL:4030018 has different name/label in the source ontology. The name/label in the ASCT+B table is connecting tubule principal cell and the one in the ontology is kidney connecting tubule principal cell.
   10 fixed rows:42-46 In row 42, the term UBERON:0005097 has different name/label in the source ontology. The name/label in the ASCT+B table is connecting tubule and the one in the ontology is renal connecting tubule.
   11.Replaced obsolete with merged term ID UBERON:0005751 in rows 13, 14, 20 and 23 In row 13, the term UBERON:0006852 has different name/label in the source ontology. The name/label in the ASCT+B table is glomerular visceral epithelium and the one in the ontology is obsolete glomerular visceral epithelium.
10. fixed 9 instances rows: 17, 30-34
    In row 17, the term UBERON:0001289 has different name/label in the source ontology. The name/label in the ASCT+B table is descending thin limb of loop of Henle and the one in the ontology is descending limb of loop of Henle.
    13, fixed In row 34, the term UBERON:0004193 has different name/label in the source ontology. The name/label in the ASCT+B table is ascending thin limb of loop of Henle and the one in the ontology is loop of Henle ascending limb thin segment.

[emquardokus]

Kidney_v1.3_DRAFT https://docs.google.com/spreadsheets/d/1aXnWkwArSRmDnhyq0n_ptISWnmRwXvD4X0BPa9WQfmg/edit#gid=949267305
Blank ontology ID
Several of these were added from New term request google sheet: https://docs.google.com/spreadsheets/d/1BihrOU9vWrsA_wYjcbdPUr42_Sb22CO3gkBDieiYQPs/edit#gid=1063693910

This report seems old as some of the blank ontology IDs were added to CL as new term requests quite a while ago and the table was updated in the last v1.2 release.
These problems were resolved in the previous release table:

1. In row 17, no term id was found for the name/label Descending Thin Limb Cell Type 2. is as follows:
   Descending Thin Limb Cell Type 2 kidney loop of Henle long descending thin limb outer medulla epithelial cell CL:4030013

**Fixed in draft v1.3: **

1. .Fixed; In row 63, no term id was found for the name/label Endothelium (non glomerular).
2. Fixed; In row 64, no term id was found for the name/label Endothelium (non glomerular).
3. Removed "immune" from AS/3 column and added it instead to AS/2/NOTES column; In rows 72 through 88, no term id was found for the name/label Immune.
4. Fixed incorrect labe used; meant regulatory T cell, added CL:0000815 In row 84, no term id was found for the name/label Cytotoxic T Cell.

Things that remain: Probable new term requests; asked author re: definitions and references

1. In row 12, no term id was found for the name/label capsule mesenchymal stromal cell.
2. In row 17, no term id was found for the name/label descending thin limb of loop of Henle 2.
3. In row 31, no term id was found for the name/label descending thin limb of loop of Henle 1.
4. In row 32, no term id was found for the name/label descending thin limb of loop of Henle 2.
5. In row 33, no term id was found for the name/label descending thin limb of loop of Henle 3.
6. In row 52, no term id was found for the name/label Transitional principal-intercalated cell.
7. In row 89, no term id was found for the name/label Papillary Tip Epithelium

[emquardokus]

AS-AS relationship corrections

Row 24 renal glomerulus renal glomerulus UBERON:0000074 replaced generic blood vessel and resolves

Removed 9 instances of UBERON:0001981 blood vessel Blood Vessel where it was was parent of UBERON:0006544 kidney vasculature ; added notes column for author to convey blood vasculature and lymph vasculature in table.

Removed instance of UBERON:0004190 renal glomerulus vasculature Glomerulus Vasculature UBERON:0001981 blood vessel and replaced with renal glomerulus--> renal glomerulus vasculature which has part of relationship in uberon.

renal glomerulus renal glomerulus UBERON:0000074--> Glomerulus Vasculature renal glomerulus vasculature UBERON:0004190--> glomerular capillary endothelium glomerular capillary endothelium UBERON:0004294

outstanding issues that need ontology support

1. No lymphatic vasculature specific to kidney (renal), there are instances to support other organs like colon, respiratory system.
2. Juxaglomerular apparatus --discussing with author about ontology relationships vs depiction in table.

Removed instnaces of UBERON:0002303 juxtaglomerular apparatus Juxtaglomerular Apparatus UBERON:0001981 blood vessel to resolve part of relationship

[emquardokus]

@aleixpuigb New term requests kidney tab: https://docs.google.com/spreadsheets/d/1BihrOU9vWrsA_wYjcbdPUr42_Sb22CO3gkBDieiYQPs/edit#gid=1063693910

[emquardokus]

Filed uberon ticket June 7, 2023: Revise subclass relationship: vasa recta #2914
obophenotype/uberon#2914

[aleixpuigb]

Thank you, @emquardokus

[emquardokus]

Kidney_v1.4-DRAFT
https://docs.google.com/spreadsheets/d/19B_iDwpVTzLl6JLUl7g943p8b14YxYRwOshm-PLbIwk/edit#gid=949267305

Edits made 9-13-2023 after validation run; changes will be reflected in 9-20-2023 reports Ellen

Blank ontology ID

Added stromal cell parent as CT/1 stromal cell stromal cell CL:0000499; however, new term requested
In row 12, no term id was found for the name/label capsule mesenchymal stromal cell.
@aleixpuigb what is status of new term requests for kidney: https://docs.google.com/spreadsheets/d/1BihrOU9vWrsA_wYjcbdPUr42_Sb22CO3gkBDieiYQPs/edit#gid=1063693910
New term requests:
In row 17, no term id was found for the name/label descending thin limb of loop of Henle 2.
In row 31, no term id was found for the name/label descending thin limb of loop of Henle 1.
In row 32, no term id was found for the name/label descending thin limb of loop of Henle 2.
In row 33, no term id was found for the name/label descending thin limb of loop of Henle 3.
In row 65, no term id was found for the name/label Kidney Lymphatic Vessel.
In row 89, no term id was found for the name/label Papillary Tip Epithelium.

Added kidney collecting duct epithelial cell CL:1000454 as CT/1; however, New term requested: In row 52, no term id was found for the name/label Transitional principal-intercalated cell.

Fixed added UBERON:0002113 In row 13, no term id was found for the name/label kidney.

the lineage of this cell type is difficult and being discussed. In row 81, no term id was found for the name/label Monocyte Derived Cell; however, a new term is requested;

[emquardokus]

Kidney_v1.4-DRAFT
https://docs.google.com/spreadsheets/d/19B_iDwpVTzLl6JLUl7g943p8b14YxYRwOshm-PLbIwk/edit#gid=949267305

Blank ontology ID missing parent
ADDED mononuclear phagocyte CL:0000113 as parent CT/1 to New term request In row 81, the term Monocyte Derived Cell without ontology ID has no parent that is from the CL ontology.

[emquardokus]

Kidney v1.4 finalizaiton metadata validation pipeline updates:
https://docs.google.com/spreadsheets/d/19B_iDwpVTzLl6JLUl7g943p8b14YxYRwOshm-PLbIwk/edit#gid=949267305

Validation feedback for Missing Uberon or CL IDs?
WARNING: Missing Uberon/CL ID at Column: AC, Row: 12 (Code 6) NTR capsule mesenchymal stromal cell
WARNING: Missing Uberon/CL ID at Column: AP, Row: 15 (Code 6) "fixed: FXYD4 FXYD domain containing ion transport regulator 4 HGNC:4028"
WARNING: Missing Uberon/CL ID at Column: Q, Row: 17 (Code 6) NTR: descending thin limb of loop of Henle 2
WARNING: Missing Uberon/CL ID at Column: AX, Row: 30 (Code 6) "fixed: SLC44A5 solute carrier family 44 member 5 HGNC:28524 "
WARNING: Missing Uberon/CL ID at Column: Q, Row: 31 (Code 6) NTR: descending thin limb of loop of Henle 1
WARNING: Missing RDFS Label for ID HGNC:2303 at Column: BE, Row: 31 (Code 6) "fixed: CPE carboxypeptidase E HGNC:2303"
WARNING: Missing Uberon/CL ID at Column: Q, Row: 32 (Code 6) NTR: descending thin limb of loop of Henle 2
WARNING: Missing Uberon/CL ID at Column: Q, Row: 33 (Code 6) NTR: descending thin limb of loop of Henle 3
WARNING: Missing RDFS Label for ID HGNC:2026 at Column: BA, Row: 34 (Code 6) fixed chloride voltage-gated channel Ka
WARNING: Missing Uberon/CL ID at Column: AP, Row: 46 (Code 6) "fixed: TLDC2 TBC/LysM-associated domain containing 2 HGNC:16112"
WARNING: Missing Uberon/CL ID at Column: AC, Row: 52 (Code 6) "NTR: Transitional principal-intercalated cell tPC-IC"
WARNING: Missing Uberon/CL ID at Column: J, Row: 65 (Code 6) NTR: Kidney Lymphatic Vessel
WARNING: Missing Uberon/CL ID at Column: AC, Row: 81 (Code 6) "NTR: Monocyte Derived Cell MDC"
WARNING: Missing Uberon/CL ID at Column: AH, Row: 81 (Code 6) "fixed: MSR1 macrophage scavenger receptor 1 HGNC:7376"
WARNING: Missing Uberon/CL ID at Column: AL, Row: 81 (Code 6) "fixed: ITGAX fms related receptor tyrosine kinase 3 HGNC:6152"
WARNING: Missing Uberon/CL ID at Column: AP, Row: 81 (Code 6) "fixed: HLA-DQA1 major histocompatibility complex, class II, DQ alpha 1 HGNC:4942"
WARNING: Missing Uberon/CL ID at Column: Q, Row: 89 (Code 6) NTR: Papillary Tip Epithelium
WARNING: Missing Uberon/CL ID at Column: AP, Row: 89 (Code 6) "fixed: GPX2 glutathione peroxidase 2 HGNC:4554"

[aleixpuigb]

New terms from other projects (BICAN, CAP)

CL:4030066 ureteric bud cell

[aleixpuigb]

New terms added in Uberon in the last release (v2024-01-18):

Kidney: 'kidney loop of Henle long descending thin limb outer medulla' (UBERON:8600036)
Kidney: 'kidney loop of Henle long descending thin limb inner medulla' (UBERON:8600037)

[emquardokus]

Kidney v1.5 https://docs.google.com/spreadsheets/d/1SqNmcPDB8PrZF1BhzgdKBxkfLcCR8VYMAkSIbnK_AXA/edit#gid=949267305

Blank ontology ID

1. No term id was found for the name/label descending thin limb of loop of Henle 2 in the following 2 rows 17, 32.
   ADD descending thin limb of loop of Henle 2 long descending limb of the loop of Henle in the outer medulla UBERON:8600036
2. No term id was found for the name/label descending thin limb of loop of Henle 1 in the following 1 row 31.
   From MIRACL for Kidney, https://docs.google.com/spreadsheets/d/1BihrOU9vWrsA_wYjcbdPUr42_Sb22CO3gkBDieiYQPs/edit#gid=1063693910
   Use descending thin limb of loop of Henle 1 short descending thin limb UBERON:0005099
3. No term id was found for the name/label descending thin limb of loop of Henle 3 in the following 1 row 33.
   ADD descending thin limb of loop of Henle 3 long descending limb of the loop of Henle in the inner medulla UBERON:8600037