ASCT+B Validation Reports for Mammary_Gland (2024-11-20)

Table of contents

• Invalid terms
  • Terms not found
  • Typos or punctuation mistakes
  • Different labels
  • Blank ontology ID
  • Blank ontology ID missing parent
  • Terms from another ontology
• Relationship reports
  • How to read a table entry
  • Relationship AS-AS report
  • Relationship CT-CT report
  • Relationship CT-AS report
• New CL terms
• New UBERON terms
• Informative reports (valid relationships)
  • Indirect relationship
  • Relationship AS has part CT

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.

• No issues found.

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 in the following 1 row 12.

2. No term id was found for the name/label estrogen receptor negative luminal progenitor cell in the following 1 row 13.

3. No term id was found for the name/label mature luminal cell in the following 1 row 14.

4. No term id was found for the name/label Endothelial cell 1 in the following 1 row 15.

5. No term id was found for the name/label Endothelial cell 2 in the following 1 row 16.

6. No term id was found for the name/label Adipocyte 1 in the following 1 row 17.

7. No term id was found for the name/label Adipocyte 2 in the following 1 row 18.

8. No term id was found for the name/label Fibroblast in the following 1 row 19.

9. No term id was found for the name/label T-cell in the following 1 row 20.

10. No term id was found for the name/label Macrophage in the following 1 row 21.

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.

1. The term Basal cell without ontology ID has no parent that is from the CL ontology in the following 1 row 12.

2. The term estrogen receptor negative luminal progenitor cell without ontology ID has no parent that is from the CL ontology in the following 1 row 13.

3. The term mature luminal cell without ontology ID has no parent that is from the CL ontology in the following 1 row 14.

4. The term Endothelial cell 1 without ontology ID has no parent that is from the CL ontology in the following 1 row 15.

5. The term Endothelial cell 2 without ontology ID has no parent that is from the CL ontology in the following 1 row 16.

6. The term Adipocyte 1 without ontology ID has no parent that is from the CL ontology in the following 1 row 17.

7. The term Adipocyte 2 without ontology ID has no parent that is from the CL ontology in the following 1 row 18.

8. The term Fibroblast without ontology ID has no parent that is from the CL ontology in the following 1 row 19.

9. The term T-cell without ontology ID has no parent that is from the CL ontology in the following 1 row 20.

10. The term Macrophage without ontology ID has no parent that is from the CL ontology in the following 1 row 21.

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.

• No issues found.

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.

• No issues found.

New CL terms

Report

New UBERON terms

Report

Informative reports (valid relationships)

Indirect relationship

Report

Relationship AS has part CT

Report