Skip to content

ASCT+B Validation Reports for Trachea (2024-12-25)

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:8600012 has a different name/label in the source ontology in the following 3 rows 18, 22, 23. The name/label in the ASCT+B table is submucosal gland acini and the one in the ontology is submucosal gland acinus. For reference, the given name/label by SMEs is submucosal gland acini. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  2. The term CL:4033055 has a different name/label in the source ontology in the following 1 row 20. The name/label in the ASCT+B table is airway submucosal gland duct ciliated cell _ and the one in the ontology is _airway submucosal gland duct ciliated cell. For reference, the given name/label by SMEs is airway submucosal gland duct ciliated cell . Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  3. The term UBERON:8600011 has a different name/label in the source ontology in the following 1 row 20. The name/label in the ASCT+B table is terminal ciliated ducts for tracheal submucosal gland and the one in the ontology is tracheal submucosal gland ciliated duct. For reference, the given name/label by SMEs is terminal ciliated ducts for tracheal submucosal gland. 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.

  • No issues found.

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
5 UBERON:0005203 trachea gland tracheal submucosal gland UBERON:0002202 submucosa of trachea submucosa of trachea 18 1.65563
6 UBERON:0005203 trachea gland tracheal submucosal gland UBERON:0002202 submucosa of trachea submucosa of trachea 19 1.65563
7 UBERON:0005203 trachea gland tracheal submucosal gland UBERON:0002202 submucosa of trachea submucosa of trachea 20 1.65563
8 UBERON:0005203 trachea gland tracheal submucosal gland UBERON:0002202 submucosa of trachea submucosa of trachea 21 1.65563
9 UBERON:0005203 trachea gland tracheal submucosal gland UBERON:0002202 submucosa of trachea submucosa of trachea 22 1.65563
10 UBERON:0005203 trachea gland tracheal submucosal gland UBERON:0002202 submucosa of trachea submucosa of trachea 23 1.65563
14 UBERON:8600012 submucosal gland acinus submucosal gland acini UBERON:0005203 trachea gland tracheal submucosal gland 18 nan
16 UBERON:8600013 submucosal gland collecting duct submucosal gland collecting duct UBERON:0005203 trachea gland tracheal submucosal gland 19 nan
19 UBERON:8600013 submucosal gland collecting duct submucosal gland collecting duct UBERON:0005203 trachea gland tracheal submucosal gland 21 nan
21 UBERON:8600012 submucosal gland acinus submucosal gland acini UBERON:0005203 trachea gland tracheal submucosal gland 22 nan
23 UBERON:8600012 submucosal gland acinus submucosal gland acini UBERON:0005203 trachea gland tracheal submucosal gland 23 nan
26 UBERON:0004849 respiratory system venous endothelium respiratory system venous endothelium UBERON:0001592 bronchial vein bronchial vein 29 nan
28 UBERON:0012418 respiratory system venous smooth muscle venous system smooth muscle UBERON:0001592 bronchial vein bronchial vein 30 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
0 CL:0019019 tracheobronchial smooth muscle cell tracheobronchial smooth muscle cell UBERON:0006680 trachealis trachealis 17 22.1834
1 CL:0019018 blood vessel smooth muscle cell blood vessel smooth muscle cell UBERON:0012418 respiratory system venous smooth muscle venous system smooth muscle 30 20.6563
2 CL:0019002 tracheobronchial chondrocyte tracheobronchial chondrocyte UBERON:0006679 carina of trachea carina of trachea 24 19.3977
3 CL:0019018 blood vessel smooth muscle cell blood vessel smooth muscle cell UBERON:0012416 respiratory system arterial smooth muscle arterial system smooth muscle 32 16.0899
4 CL:1000413 endothelial cell of artery endothelial cell of artery UBERON:0004848 respiratory system arterial endothelium respiratory system arterial endothelium 31 11.8039
11 CL:0019002 tracheobronchial chondrocyte tracheobronchial chondrocyte UBERON:0003604 trachea cartilage trachea cartilage 25 1.13213
12 CL:0002145 ciliated columnar cell of tracheobronchial tree ciliated columnar cell of tracheobronchial tree UBERON:0001901 epithelium of trachea tracheal epithelium 12 nan
13 CL:1000223 lung neuroendocrine cell lung neuroendocrine cell UBERON:0001901 epithelium of trachea tracheal epithelium 13 nan
15 CL:1000330 serous cell of epithelium of trachea serous cell of epithelium of trachea UBERON:8600012 submucosal gland acinus submucosal gland acini 18 nan
17 CL:4033023 airway submucosal gland collecting duct epithelial cell airway submucosal gland collecting duct epithelial cell UBERON:8600013 submucosal gland collecting duct submucosal gland collecting duct 19 nan
18 CL:4033055 airway submucosal gland duct ciliated cell airway submucosal gland duct ciliated cell UBERON:8600011 tracheal submucosal gland ciliated duct terminal ciliated ducts for tracheal submucosal gland 20 nan
20 CL:4033024 airway submucosal gland duct basal cell airway submucosal gland duct basal cell UBERON:8600013 submucosal gland collecting duct submucosal gland collecting duct 21 nan
22 CL:4033020 mucus secreting cell of trachea gland mucus secreting cell of trachea gland UBERON:8600012 submucosal gland acinus submucosal gland acini 22 nan
24 CL:4033021 myoepithelial cell of trachea gland myoepithelial cell of trachea gland UBERON:8600012 submucosal gland acinus submucosal gland acini 23 nan
25 CL:4033025 perichondrial fibroblast perichondrial fibroblast UBERON:0003571 trachea connective tissue trachea connective tissue 28 nan
27 CL:4033008 vein endothelial cell of respiratory system vein endothelial cell of respiratory system UBERON:0004849 respiratory system venous endothelium respiratory system venous endothelium 29 nan

New CL terms

Report

New UBERON terms

Report

Informative reports (valid relationships)

Indirect relationship

Report

Relationship AS has part CT

Report