ASCT+B Validation Reports for Mouth (2025-06-25)
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.
- The term UBERON:0004923 has a different name/label in the source ontology in the following 1 row 15. The name/label in the ASCT+B table is mucosa of the lip and the one in the ontology is organ component layer. For reference, the given name/label by SMEs is mucosa of the lip. 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 tongue in the following 1 row 12.
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No term id was found for the name/label basal ductal cell in the following 3 rows 18, 36, 53.
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No term id was found for the name/label excretory duct epithelial cell in the following 2 rows 21, 57.
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No term id was found for the name/label helper T in the following 3 rows 22, 40, 58.
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No term id was found for the name/label ionocyte in the following 3 rows 25, 43, 61.
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No term id was found for the name/label myoepithelial cell in the following 3 rows 28, 47, 65.
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No term id was found for the name/label periacinar fibroblast in the following 3 rows 29, 48, 66.
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No term id was found for the name/label periductal fibroblast in the following 3 rows 31, 50, 68.
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No term id was found for the name/label serous acinar cell in the following 1 row 32.
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No term id was found for the name/label tuft cell in the following 2 rows 35, 72.
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No term id was found for the name/label demilune acinar cell in the following 2 rows 37, 54.
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No term id was found for the name/label mucous acinar cell in the following 2 rows 46, 64.
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No term id was found for the name/label seromucosal acinar cell in the following 2 rows 51, 69.
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.
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The term basal ductal cell without ontology ID has no parent that is from the CL ontology in the following 3 rows 18, 36, 53.
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The term excretory duct epithelial cell without ontology ID has no parent that is from the CL ontology in the following 2 rows 21, 57.
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The term helper T without ontology ID has no parent that is from the CL ontology in the following 3 rows 22, 40, 58.
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The term ionocyte without ontology ID has no parent that is from the CL ontology in the following 3 rows 25, 43, 61.
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The term myoepithelial cell without ontology ID has no parent that is from the CL ontology in the following 3 rows 28, 47, 65.
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The term periacinar fibroblast without ontology ID has no parent that is from the CL ontology in the following 3 rows 29, 48, 66.
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The term periductal fibroblast without ontology ID has no parent that is from the CL ontology in the following 3 rows 31, 50, 68.
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The term serous acinar cell without ontology ID has no parent that is from the CL ontology in the following 1 row 32.
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The term tuft cell without ontology ID has no parent that is from the CL ontology in the following 2 rows 35, 72.
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The term demilune acinar cell without ontology ID has no parent that is from the CL ontology in the following 2 rows 37, 54.
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The term mucous acinar cell without ontology ID has no parent that is from the CL ontology in the following 2 rows 46, 64.
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The term seromucosal acinar cell without ontology ID has no parent that is from the CL ontology in the following 2 rows 51, 69.
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 | |
---|---|---|---|---|---|---|---|---|
2 | UBERON:0004923 | organ component layer | mucosa of the lip | UBERON:0003729 | mouth mucosa | mouth mucosa | 15 | 23.1326 |
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 | |
---|---|---|---|---|---|---|---|---|
0 | CL:0000115 | endothelial cell | endothelial cell | UBERON:0001832 | sublingual gland | sublingual gland | 39 | 24.0656 |
1 | CL:0000115 | endothelial cell | endothelial cell | UBERON:0001736 | submandibular gland | submandibular gland | 56 | 24.0656 |
3 | CL:0000115 | endothelial cell | endothelial cell | UBERON:0001831 | parotid gland | parotid gland | 20 | 20.8561 |
4 | CL:0000192 | smooth muscle cell | smooth muscle cell | UBERON:0001832 | sublingual gland | sublingual gland | 52 | 15.0772 |
5 | CL:0000192 | smooth muscle cell | smooth muscle cell | UBERON:0001736 | submandibular gland | submandibular gland | 70 | 15.0772 |
6 | CL:0000451 | dendritic cell | dendritic cell | UBERON:0001832 | sublingual gland | sublingual gland | 38 | 12.5872 |
7 | CL:0000451 | dendritic cell | dendritic cell | UBERON:0001736 | submandibular gland | submandibular gland | 55 | 12.5872 |
8 | CL:0000235 | macrophage | macrophage | UBERON:0001736 | submandibular gland | submandibular gland | 62 | 12.2159 |
9 | CL:0000235 | macrophage | macrophage | UBERON:0001832 | sublingual gland | sublingual gland | 44 | 12.2159 |
10 | CL:0000192 | smooth muscle cell | smooth muscle cell | UBERON:0001831 | parotid gland | parotid gland | 33 | 11.8677 |
11 | CL:0000451 | dendritic cell | dendritic cell | UBERON:0001831 | parotid gland | parotid gland | 19 | 9.37768 |
12 | CL:0000235 | macrophage | macrophage | UBERON:0001831 | parotid gland | parotid gland | 26 | 9.00643 |
13 | CL:0000669 | pericyte | pericyte | UBERON:0001832 | sublingual gland | sublingual gland | 49 | 6.50147 |
14 | CL:0000669 | pericyte | pericyte | UBERON:0001736 | submandibular gland | submandibular gland | 67 | 6.50147 |
15 | CL:0000097 | mast cell | mast cell | UBERON:0001832 | sublingual gland | sublingual gland | 45 | 5.10265 |
16 | CL:0000097 | mast cell | mast cell | UBERON:0001736 | submandibular gland | submandibular gland | 63 | 5.10265 |
17 | CL:0000136 | adipocyte | adipocyte | UBERON:0001831 | parotid gland | parotid gland | 17 | 5.00778 |
18 | CL:0000669 | pericyte | pericyte | UBERON:0001831 | parotid gland | parotid gland | 30 | 3.292 |
19 | CL:0000097 | mast cell | mast cell | UBERON:0001831 | parotid gland | parotid gland | 27 | 1.89317 |
20 | CL:0000987 | IgA plasma cell | IgA secreting plasma cell | UBERON:0001831 | parotid gland | parotid gland | 23 | nan |
21 | CL:4052048 | intercalated cell of salivary gland | intercalated duct epithelial cell | UBERON:0001831 | parotid gland | parotid gland | 24 | nan |
22 | CL:4052049 | striated cell of salivary gland | striated duct epithelial cell | UBERON:0001831 | parotid gland | parotid gland | 34 | nan |
23 | CL:0000987 | IgA plasma cell | IgA secreting plasma cell | UBERON:0001832 | sublingual gland | sublingual gland | 41 | nan |
24 | CL:4052048 | intercalated cell of salivary gland | intercalated duct epithelial cell | UBERON:0001832 | sublingual gland | sublingual gland | 42 | nan |
25 | CL:0000987 | IgA plasma cell | IgA secreting plasma cell | UBERON:0001736 | submandibular gland | submandibular gland | 59 | nan |
26 | CL:4052048 | intercalated cell of salivary gland | intercalated duct epithelial cell | UBERON:0001736 | submandibular gland | submandibular gland | 60 | nan |
27 | CL:4052049 | striated cell of salivary gland | striated duct epithelial cell | UBERON:0001736 | submandibular gland | submandibular gland | 71 | nan |