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ASCT+B Validation Reports for Ureter (2024-07-04)

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 UBERON:0009919 has a different name/label in the source ontology in the following 1 row 15. The name/label in the ASCT+B table is ureter detrusor smooth muscle and the one in the ontology is ureter smooth muscle. For reference, the given name/label by SMEs is ureter detrusor smooth muscle. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  2. The term CL:1001428 has a different name/label in the source ontology in the following 1 row 12. The name/label in the ASCT+B table is ureter urothelial cell and the one in the ontology is bladder urothelial cell. For reference, the given name/label by SMEs is urothelium. 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 ureter urothelium in the following 1 row 12.

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

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

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

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

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

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

  8. No term id was found for the name/label lipofibroblast cell of ureter in the following 1 row 19.

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

  10. No term id was found for the name/label vascular smooth muscle cell of ureter in the following 1 row 21.

  11. No term id was found for the name/label pericyte cell of ureter in the following 1 row 22.

  12. No term id was found for the name/label ureter vasculature in the following 1 row 23.

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.

  • No issues found.

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
0 UBERON:0001254 urothelium of ureter urothelium of ureter UBERON:0005005 mucosa of left ureter mucosa of left ureter 12 15.1841
1 UBERON:0001254 urothelium of ureter urothelium of ureter UBERON:0005005 mucosa of left ureter mucosa of left ureter 13 15.1841
2 UBERON:0001254 urothelium of ureter urothelium of ureter UBERON:0005005 mucosa of left ureter mucosa of left ureter 14 15.1841
3 UBERON:0009919 ureter smooth muscle ureter detrusor smooth muscle UBERON:0036376 wall of left ureter wall of left ureter 15 10.6133
13 UBERON:0001253 lamina propria of ureter lamina propria of ureter UBERON:0036376 wall of left ureter wall of left ureter 16 nan
14 UBERON:0001253 lamina propria of ureter lamina propria of ureter UBERON:0036376 wall of left ureter wall of left ureter 17 nan
16 UBERON:0001253 lamina propria of ureter lamina propria of ureter UBERON:0036376 wall of left ureter wall of left ureter 18 nan
18 UBERON:0001253 lamina propria of ureter lamina propria of ureter UBERON:0036376 wall of left ureter wall of left ureter 19 nan
19 UBERON:0001253 lamina propria of ureter lamina propria of ureter UBERON:0036376 wall of left ureter wall of left ureter 20 nan
20 UBERON:0001253 lamina propria of ureter lamina propria of ureter UBERON:0036376 wall of left ureter wall of left ureter 21 nan
21 UBERON:0001253 lamina propria of ureter lamina propria of ureter UBERON:0036376 wall of left ureter wall of left ureter 22 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.

  • No issues found.

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
4 CL:1000708 ureter adventitial cell myofibroblast UBERON:0001253 lamina propria of ureter lamina propria of ureter 16 4.57088
5 CL:1000708 ureter adventitial cell fibroblast UBERON:0001253 lamina propria of ureter lamina propria of ureter 19 4.57088
6 CL:1000708 ureter adventitial cell endothelium UBERON:0001253 lamina propria of ureter lamina propria of ureter 20 4.57088
7 CL:1000708 ureter adventitial cell smooth muscle UBERON:0001253 lamina propria of ureter lamina propria of ureter 21 4.57088
8 CL:1000708 ureter adventitial cell smooth muscle UBERON:0001253 lamina propria of ureter lamina propria of ureter 22 4.57088
9 CL:1001428 bladder urothelial cell urothelium UBERON:0001254 urothelium of ureter urothelium of ureter 12 3.49917
10 CL:1001428 bladder urothelial cell urothelium UBERON:0001254 urothelium of ureter urothelium of ureter 13 3.49917
11 CL:1001428 bladder urothelial cell urothelium UBERON:0001254 urothelium of ureter urothelium of ureter 14 3.49917
12 CL:1000979 ureter smooth muscle cell ureter smooth muscle cell UBERON:0009919 ureter smooth muscle ureter detrusor smooth muscle 15 nan
15 CL:1000308 fibrocyte of adventitia of ureter fibroblast UBERON:0001253 lamina propria of ureter lamina propria of ureter 17 nan
17 CL:1000308 fibrocyte of adventitia of ureter fibroblast UBERON:0001253 lamina propria of ureter lamina propria of ureter 18 nan

New CL terms

Report

New UBERON terms

Report

Informative reports (valid relationships)

Indirect relationship

Report

Relationship AS has part CT

Report