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ASCT+B Validation Reports for Urinary_bladder (2024-11-20)

Table of contents

Invalid terms

These are the reports related to issues in the terms found in the ASCT+B table. We validate only CL, UBERON and PCL terms.

Terms not found

This report provides a list of terms not found neither in UBERON nor in CL. Please remove these terms from the ASCT+B table - disconsider this message if a term was recently added to the ontology.

  • No issues found.

Typos or punctuation mistakes

This report provides a general quality check of the terms used in the ASCT+B table. Typos, font case (upper case), punctuation mistakes in IDs: two colons, spaces, underscore instead of a colon.

  • No issues found.

Different labels

This report provides a list of terms having different names/labels found in the ontology and related to the one found in the ASCT+B table. Make sure to add the term's name/label in the column AS/N/LABEL or CT/N/LABEL. If the SME wants to give another name/label, please use the column AS/N or CT/N. N is the number in the column.

If the term's name/label and the name/label given by SME are too different, please make sure the term ID and its name/label are matching in OLS.

If the name/label in the ontology contains obsolete, please look into OLS, clicking on the term ID, for its replacement.

  1. The term CL:0000186 has a different name/label in the source ontology in the following 3 rows 16, 16, 36. The name/label in the ASCT+B table is myofibroblast and the one in the ontology is myofibroblast cell. For reference, the given name/label by SMEs is myofibroblast. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

Blank ontology ID

This report provides a list of blank spreadsheet cells that often mean no ontology mapping found by the author. However, in some cases, a term with a synonym already exists. Please search in OLS.

You can find more information on the New CL terms or New UBERON terms reports.

  1. No term id was found for the name/label basal cell of bladder urothelium in the following 1 row 12.

  2. No term id was found for the name/label intermediate cell of bladder urothelium in the following 1 row 13.

  3. No term id was found for the name/label superficial cell of bladder urothelium in the following 1 row 14.

  4. No term id was found for the name/label detrusor smooth muscle cell of bladder in the following 1 row 15.

  5. No term id was found for the name/label myofibroblast cell of bladder in the following 1 row 16.

  6. No term id was found for the name/label fibroblast of urinary bladder in the following 2 rows 17, 18.

  7. No term id was found for the name/label PI16+ fibroblast cell of bladder in the following 1 row 17.

  8. No term id was found for the name/label DPT+ fibroblast cell of bladder in the following 1 row 18.

  9. No term id was found for the name/label lipofibroblast cell of bladder in the following 2 rows 19, 39.

  10. No term id was found for the name/label endothelial cell of bladder in the following 1 row 20.

  11. No term id was found for the name/label vascular smooth muscle cell of urinary bladder in the following 2 rows 21, 40.

  12. No term id was found for the name/label pericyte cell of urinary bladder in the following 2 rows 22, 41.

  13. No term id was found for the name/label superficial epithelial cell of urinary bladder in the following 1 row 29.

  14. No term id was found for the name/label basal epithelia in the following 1 row 30.

  15. No term id was found for the name/label intermediate epithelia in the following 1 row 31.

  16. No term id was found for the name/label urinary bladder stroma in the following 14 rows 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45.

  17. No term id was found for the name/label fibroblast cell of urinary bladder in the following 2 rows 33, 35.

  18. No term id was found for the name/label CXCL14 fibroblast in the following 1 row 33.

  19. No term id was found for the name/label urinary bladder interstitial fibroblast in the following 2 rows 34, 37.

  20. No term id was found for the name/label minor interstitial fibroblast in the following 1 row 34.

  21. No term id was found for the name/label periurothelial fibroblast in the following 1 row 35.

  22. No term id was found for the name/label myofibroblast cell of urinary bladder in the following 1 row 36.

  23. No term id was found for the name/label major interstitial fibroblast in the following 1 row 37.

  24. No term id was found for the name/label neruofibroblast of urinary bladder in the following 1 row 38.

  25. No term id was found for the name/label vascular arterial endothelial cell of urinary bladder in the following 1 row 42.

  26. No term id was found for the name/label vascular capillary endothelial cell of urinary bladder in the following 1 row 43.

  27. No term id was found for the name/label vascular venous endothelial cell of urinary bladder in the following 1 row 44.

  28. No term id was found for the name/label lymphatic endothelial cell of urinary bladder in the following 1 row 45.

Blank ontology ID missing parent

This report provides a list of CT terms with blank ontology ID without an upper term from Cell Ontology. 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. The term PI16+ fibroblast cell of bladder without ontology ID has no parent that is from the CL ontology in the following 1 row 17.

  2. The term DPT+ fibroblast cell of bladder without ontology ID has no parent that is from the CL ontology in the following 1 row 18.

  3. The term CXCL14 fibroblast without ontology ID has no parent that is from the CL ontology in the following 1 row 33.

  4. The term minor interstitial fibroblast without ontology ID has no parent that is from the CL ontology in the following 1 row 34.

  5. The term periurothelial fibroblast without ontology ID has no parent that is from the CL ontology in the following 1 row 35.

  6. The term major interstitial fibroblast without ontology ID has no parent that is from the CL ontology in the following 1 row 37.

Terms from another ontology

This report provides a list of terms from another ontologies that we do not validate. Foundational Model of Anatomy (FMA) ontology IDs are provided when an adequate term is not found in UBERON. Same case for Anatomic Ontology for Human Lung Maturation (LMHA) and Interlex IDs (ILX) from Stimulating Peripheral Activity to Relieve Conditions (SPARC). You can request cross-database request the same way a new term request. Please be sure if a term with a related synonym is already in the source ontologies CL or UBERON or PCL.

  • No issues found.

Relationship reports

These reports are other representations of the ASCT+B table. We split each row into pairs with adjacent terms, resulting in a table with two primary columns, object (o), left side and subject (s), right side. The experts' labels for the subject and object are in the columns user_slabel and user_olabel. The other columns are the subject label (s_label) and object label (o_label), the label from the source ontologies.

The report means it could not find a partonomy relationship in the source ontologies, but it doesn't mean this relationship is entirely invalid. In some cases, the pair is in the inverse order. In other cases, the relationship is missing in the source ontologies. Finally, how it was modelled in the ASCT+B table is not aligned with the ontologies sources and needs a more general discussion.

How to read a table entry

In the ASCT+B table

AS/2 AS/2/LABEL AS/2/ID AS/3 AS/3/LABEL AS/3/ID
lens lens UBERON:0000965 ciliary zonules suspensory ligament of lens UBERON:0006762

In the Relationship Report

s slabel user_slabel o olabel user_olabel
UBERON:0006762 suspensory ligament of lens ciliary zonules UBERON:0000965 lens lens

Relationship AS-AS report

This table contains terms for anatomical structures that are related to each other according to the ASCT+B table but are not related to each other in source ontologies via one of the relation types we consider valid for ASCT+B tables. Valid relationships are: part_of, e.g. corneal endothelium part_of cornea; subClassOf, e.g. left kidney subClassOf (is_a) kidney; and overlaps (has some part in), e.g. ureter overlaps kidney; connected_to, e.g. TBA. part_of and subClassOf relationships should be specific to general, e.g. left kidney (specific) to kidney (general); corneal endothelium (specific) to cornea (general). The deltaIC score is included because a high score (>50) can indicate that this order is reversed, e.g. TBA.

s slabel user_slabel o olabel user_olabel row_number deltaIC
3 UBERON:0004237 blood vessel smooth muscle vascular smooth muscle UBERON:0012239 urinary bladder vasculature urinary bladder vasculature 40 21.6381
20 UBERON:0001261 lamina propria of urinary bladder lamina propria of urinary bladder UBERON:0004943 submucosa of urinary bladder submucosa of urinary bladder 16 nan
22 UBERON:0001261 lamina propria of urinary bladder lamina propria of urinary bladder UBERON:0004943 submucosa of urinary bladder submucosa of urinary bladder 17 nan
23 UBERON:0001261 lamina propria of urinary bladder lamina propria of urinary bladder UBERON:0004943 submucosa of urinary bladder submucosa of urinary bladder 18 nan
24 UBERON:0001261 lamina propria of urinary bladder lamina propria of urinary bladder UBERON:0004943 submucosa of urinary bladder submucosa of urinary bladder 19 nan
25 UBERON:0012239 urinary bladder vasculature urinary bladder vasculature UBERON:0001256 wall of urinary bladder wall of urinary bladder 20 nan
27 UBERON:0012239 urinary bladder vasculature urinary bladder vasculature UBERON:0001256 wall of urinary bladder wall of urinary bladder 21 nan
29 UBERON:0012239 urinary bladder vasculature urinary bladder vasculature UBERON:0001256 wall of urinary bladder wall of urinary bladder 22 nan
30 UBERON:0011945 luminal layer of epithelium luminal layer of epithelium UBERON:0004645 urinary bladder urothelium urinary bladder urothelium 29 nan

Relationship CT-CT report

In the case of the CT-CT relationship, for each couple of terms, we verify for sub class of, part of and overlaps in the source ontologies. The deltaIC score is included because a high score (>50) can indicate that this order is reversed, e.g. TBA.

s slabel user_slabel o olabel user_olabel row_number deltaIC
0 CL:0000669 pericyte pericyte CL:0002597 smooth muscle cell of bladder smooth muscle cell of bladder 22 29.5807
13 CL:1000486 basal cell of urothelium basal cell of urothelium CL:1001428 bladder urothelial cell bladder urothelial cell 12 nan
15 CL:4030055 intermediate cell of urothelium intermediate cell of urothelium CL:1001428 bladder urothelial cell bladder urothelial cell 13 nan
17 CL:4030056 umbrella cell of urothelium umbrella cell of urothelium CL:1001428 bladder urothelial cell bladder urothelial cell 14 nan
21 CL:0000186 myofibroblast cell myofibroblast CL:1001319 bladder cell bladder cell 16 nan

Relationship CT-AS report

In the case of the AS-CT relationship, for each couple of terms, we verify for connected to and has part in the source ontologies.

s slabel user_slabel o olabel user_olabel row_number deltaIC
1 CL:0000669 pericyte pericyte UBERON:0012239 urinary bladder vasculature urinary bladder vasculature 22 22.3407
2 CL:0000669 pericyte pericyte UBERON:0012239 urinary bladder vasculature urinary bladder vasculature 41 22.3407
4 CL:0002138 endothelial cell of lymphatic vessel endothelial cell of lymphatic vessel UBERON:0012239 urinary bladder vasculature urinary bladder vasculature 45 15.9992
5 CL:1001319 bladder cell bladder cell UBERON:0001261 lamina propria of urinary bladder lamina propria of urinary bladder 19 12.5023
6 CL:0002543 vein endothelial cell vein endothelial cell UBERON:0012239 urinary bladder vasculature urinary bladder vasculature 44 12.5023
7 CL:0002144 capillary endothelial cell capillary endothelial cell UBERON:0012239 urinary bladder vasculature urinary bladder vasculature 43 9.66334
8 CL:0000186 myofibroblast cell myofibroblast UBERON:0001261 lamina propria of urinary bladder lamina propria of urinary bladder 16 9.13585
9 CL:1000413 endothelial cell of artery endothelial cell of artery UBERON:0012239 urinary bladder vasculature urinary bladder vasculature 42 9.13585
10 CL:0000646 basal cell basal cell UBERON:0004645 urinary bladder urothelium urinary bladder urothelium 30 5.92771
11 CL:0000057 fibroblast fibroblast UBERON:0001255 urinary bladder urinary bladder 38 4.98381
12 CL:0000057 fibroblast fibroblast UBERON:0001255 urinary bladder urinary bladder 39 4.98381
14 CL:1000486 basal cell of urothelium basal cell of urothelium UBERON:0004645 urinary bladder urothelium urinary bladder urothelium 12 nan
16 CL:4030055 intermediate cell of urothelium intermediate cell of urothelium UBERON:0004645 urinary bladder urothelium urinary bladder urothelium 13 nan
18 CL:4030056 umbrella cell of urothelium umbrella cell of urothelium UBERON:0004645 urinary bladder urothelium urinary bladder urothelium 14 nan
19 CL:0002597 smooth muscle cell of bladder smooth muscle UBERON:0000381 urinary bladder detrusor smooth muscle urinary bladder detrusor smooth muscle 15 nan
26 CL:2000040 bladder microvascular endothelial cell bladder microvascular endothelial cell UBERON:0012239 urinary bladder vasculature urinary bladder vasculature 20 nan
28 CL:0002597 smooth muscle cell of bladder smooth muscle cell of bladder UBERON:0012239 urinary bladder vasculature urinary bladder vasculature 21 nan
31 CL:4030055 intermediate cell of urothelium intermediate cell of urothelium UBERON:0004645 urinary bladder urothelium urinary bladder urothelium 31 nan
32 CL:0002597 smooth muscle cell of bladder smooth muscle cell of bladder UBERON:0012378 muscle layer of urinary bladder muscle layer of urinary bladder 32 nan
33 CL:0000186 myofibroblast cell myofibroblast UBERON:0001255 urinary bladder urinary bladder 36 nan

New CL terms

Report

New UBERON terms

Report

Informative reports (valid relationships)

Indirect relationship

Report

Relationship AS has part CT

Report