ASCT+B Validation Reports for Ureter (2024-12-25)
Table of contents
- Invalid terms
- Relationship reports
- New CL terms
- New UBERON terms
- Informative reports (valid relationships)
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.
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The term CL:1001428 has a different name/label in the source ontology in the following 3 rows 12, 13, 14. 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.
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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.
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.
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No term id was found for the name/label basal cell of ureter urothelium in the following 1 row 12.
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No term id was found for the name/label intermediate cell of ureter urothelium in the following 1 row 13.
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No term id was found for the name/label superficial cell of ureter urothelium in the following 1 row 14.
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No term id was found for the name/label detrusor smooth muscle cell of ureter in the following 1 row 15.
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No term id was found for the name/label myofibroblast cell of ureter in the following 1 row 16.
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No term id was found for the name/label PI16+ fibroblast cell of ureter in the following 1 row 17.
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No term id was found for the name/label DPT+ fibroblast cell of ureter in the following 1 row 18.
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No term id was found for the name/label lipofibroblast cell of ureter in the following 1 row 19.
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No term id was found for the name/label endothelial cell of ureter in the following 1 row 20.
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No term id was found for the name/label vascular smooth muscle cell of ureter in the following 1 row 21.
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No term id was found for the name/label pericyte cell of ureter in the following 1 row 22.
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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 |
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lens | lens | UBERON:0000965 | ciliary zonules | suspensory ligament of lens | UBERON:0006762 |
In the Relationship Report
s | slabel | user_slabel | o | olabel | user_olabel |
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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 | |
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0 | UBERON:0001254 | urothelium of ureter | urothelium of ureter | UBERON:0005005 | mucosa of left ureter | mucosa of left ureter | 12 | 15.1692 |
1 | UBERON:0001254 | urothelium of ureter | urothelium of ureter | UBERON:0005005 | mucosa of left ureter | mucosa of left ureter | 13 | 15.1692 |
2 | UBERON:0001254 | urothelium of ureter | urothelium of ureter | UBERON:0005005 | mucosa of left ureter | mucosa of left ureter | 14 | 15.1692 |
3 | UBERON:0009919 | ureter smooth muscle | ureter detrusor smooth muscle | UBERON:0036376 | wall of left ureter | wall of left ureter | 15 | 10.6028 |
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 | |
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4 | CL:1000708 | ureter adventitial cell | myofibroblast | UBERON:0001253 | lamina propria of ureter | lamina propria of ureter | 16 | 4.56639 |
5 | CL:1000708 | ureter adventitial cell | fibroblast | UBERON:0001253 | lamina propria of ureter | lamina propria of ureter | 19 | 4.56639 |
6 | CL:1000708 | ureter adventitial cell | endothelium | UBERON:0001253 | lamina propria of ureter | lamina propria of ureter | 20 | 4.56639 |
7 | CL:1000708 | ureter adventitial cell | smooth muscle | UBERON:0001253 | lamina propria of ureter | lamina propria of ureter | 21 | 4.56639 |
8 | CL:1000708 | ureter adventitial cell | smooth muscle | UBERON:0001253 | lamina propria of ureter | lamina propria of ureter | 22 | 4.56639 |
9 | CL:1001428 | bladder urothelial cell | urothelium | UBERON:0001254 | urothelium of ureter | urothelium of ureter | 12 | 3.49573 |
10 | CL:1001428 | bladder urothelial cell | urothelium | UBERON:0001254 | urothelium of ureter | urothelium of ureter | 13 | 3.49573 |
11 | CL:1001428 | bladder urothelial cell | urothelium | UBERON:0001254 | urothelium of ureter | urothelium of ureter | 14 | 3.49573 |
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 |