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ASCT+B Validation Reports for Main_Bronchus (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 CL:0019002 has a different name/label in the source ontology in the following 1 row 22. The name/label in the ASCT+B table is lung perichondrial fibroblast and the one in the ontology is tracheobronchial chondrocyte. For reference, the given name/label by SMEs is lung perichondrial fibroblast. 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:0001956 cartilage of bronchus cartilage of bronchus UBERON:0002182 main bronchus extrapulmonary bronchus 21 0.507012
6 UBERON:8410043 bronchus submucosal gland bronchial submucosal gland UBERON:0002182 main bronchus extrapulmonary bronchus 15 nan
8 UBERON:8410043 bronchus submucosal gland bronchial submucosal gland UBERON:0002182 main bronchus extrapulmonary bronchus 16 nan
9 UBERON:8600013 submucosal gland collecting duct submucosal gland collecting duct UBERON:8410043 bronchus submucosal gland bronchial submucosal gland 16 nan
11 UBERON:8410043 bronchus submucosal gland bronchial submucosal gland UBERON:0002182 main bronchus extrapulmonary bronchus 17 nan
12 UBERON:8600012 submucosal gland acinus submucosal gland acinus UBERON:8410043 bronchus submucosal gland bronchial submucosal gland 17 nan
14 UBERON:8410043 bronchus submucosal gland bronchial submucosal gland UBERON:0002182 main bronchus extrapulmonary bronchus 18 nan
15 UBERON:8600012 submucosal gland acinus submucosal gland acinus UBERON:8410043 bronchus submucosal gland bronchial submucosal gland 18 nan
17 UBERON:8410043 bronchus submucosal gland bronchial submucosal gland UBERON:0002182 main bronchus extrapulmonary bronchus 19 nan
18 UBERON:8600012 submucosal gland acinus submucosal gland acinus UBERON:8410043 bronchus submucosal gland bronchial submucosal gland 19 nan
20 UBERON:8410043 bronchus submucosal gland bronchial submucosal gland UBERON:0002182 main bronchus extrapulmonary bronchus 20 nan
21 UBERON:8600013 submucosal gland collecting duct submucosal gland collecting duct UBERON:8410043 bronchus submucosal gland bronchial submucosal gland 20 nan
30 UBERON:0004849 respiratory system venous endothelium respiratory system venous endothelium UBERON:0001592 bronchial vein bronchial vein 33 nan
32 UBERON:0012418 respiratory system venous smooth muscle venous system smooth muscle UBERON:0001592 bronchial vein bronchial vein 34 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:0019018 blood vessel smooth muscle cell blood vessel smooth muscle cell UBERON:0012418 respiratory system venous smooth muscle venous system smooth muscle 34 20.6563
1 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
2 CL:1000413 endothelial cell of artery endothelial cell of artery UBERON:0004848 respiratory system arterial endothelium respiratory system arterial endothelium 31 11.8039
3 CL:0017000 pulmonary ionocyte pulmonary ionocyte UBERON:0002340 epithelium of main bronchus epithelium of main bronchus 23 6.03643
4 CL:0002332 ciliated cell of the bronchus ciliated cell of the bronchus UBERON:0002340 epithelium of main bronchus epithelium of main bronchus 26 6.03643
7 CL:4033055 airway submucosal gland duct ciliated cell airway submucosal gland duct ciliated cell UBERON:8600010 bronchial submucosal gland ciliated duct bronchial submucosal gland ciliated duct 15 nan
10 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 16 nan
13 CL:1000331 serous cell of epithelium of bronchus serous cell of epithelium of bronchus UBERON:8600012 submucosal gland acinus submucosal gland acinus 17 nan
16 CL:4033022 mucus secreting cell of bronchus submucosal gland mucus secreting cell of bronchus submucosal gland UBERON:8600012 submucosal gland acinus submucosal gland acinus 18 nan
19 CL:4033003 myoepithelial cell of bronchus submucosal gland myoepithelial cell of bronchus submucosal gland UBERON:8600012 submucosal gland acinus submucosal gland acinus 19 nan
22 CL:4033024 airway submucosal gland duct basal cell airway submucosal gland duct basal cell UBERON:8600013 submucosal gland collecting duct submucosal gland collecting duct 20 nan
23 CL:0019002 tracheobronchial chondrocyte lung perichondrial fibroblast UBERON:0002182 main bronchus extrapulmonary bronchus 22 nan
24 CL:4033010 neuroendocrine cell of epithelium of lobar bronchus neuroendocrine cell of epithelium of lobar bronchus UBERON:0002340 epithelium of main bronchus epithelium of main bronchus 24 nan
25 CL:4033048 respiratory suprabasal cell respiratory suprabasal cell UBERON:0002340 epithelium of main bronchus epithelium of main bronchus 25 nan
26 CL:4033007 brush cell of epithelium of lobar bronchus tuft cell UBERON:0002340 epithelium of main bronchus epithelium of main bronchus 27 nan
27 CL:4033044 deuterosomal cell airway deuterosomal cell UBERON:0002340 epithelium of main bronchus epithelium of main bronchus 28 nan
28 CL:4033009 goblet cell of epithelium of lobar bronchus goblet cell of epithelium of lobar bronchus UBERON:0002340 epithelium of main bronchus epithelium of main bronchus 29 nan
29 CL:1000349 basal cell of epithelium of bronchus basal cell of bronchus UBERON:0002340 epithelium of main bronchus epithelium of main bronchus 30 nan
31 CL:4033008 vein endothelial cell of respiratory system vein endothelial cell of respiratory system UBERON:0004849 respiratory system venous endothelium respiratory system venous endothelium 33 nan

New CL terms

Report

New UBERON terms

Report

Informative reports (valid relationships)

Indirect relationship

Report

Relationship AS has part CT

Report