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ASCT+B Validation Reports for Prostate (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:0009112 has a different name/label in the source ontology in the following 1 row 24. The name/label in the ASCT+B table is pericyte and the one in the ontology is centroblast. For reference, the given name/label by SMEs is perictye. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  2. The term CL:0002573 has a different name/label in the source ontology in the following 1 row 25. The name/label in the ASCT+B table is satellite glial cell and the one in the ontology is Schwann cell. For reference, the given name/label by SMEs is Schwann cell. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  3. The term CL:0002573 has a different name/label in the source ontology in the following 1 row 26. The name/label in the ASCT+B table is endoneurial fibroblast and the one in the ontology is Schwann cell. For reference, the given name/label by SMEs is endoneurial 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.

  1. No term id was found for the name/label ionocyte epithelia in the following 1 row 15.

  2. No term id was found for the name/label glial cell in the following 1 row 25.

  3. No term id was found for the name/label endoneurial fibroblast in the following 1 row 26.

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
0 UBERON:0007798 vascular system vascular system UBERON:0002367 prostate gland prostate gland 23 20.2423
1 UBERON:0007798 vascular system vascular system UBERON:0002367 prostate gland prostate gland 24 20.2423
2 UBERON:0000010 peripheral nervous system peripheral nervous system UBERON:0002367 prostate gland prostate gland 25 20.2349
3 UBERON:0000010 peripheral nervous system peripheral nervous system UBERON:0002367 prostate gland prostate gland 26 20.2349
4 UBERON:0004537 blood vasculature vascular system UBERON:0002367 prostate gland prostate gland 19 17.7999
5 UBERON:0004537 blood vasculature vascular system UBERON:0002367 prostate gland prostate gland 20 17.7999
6 UBERON:0004537 blood vasculature vascular system UBERON:0002367 prostate gland prostate gland 21 17.7999
9 UBERON:0004243 prostate gland smooth muscle Prostate Glandular Acinus UBERON:0004184 prostate gland stroma prostate stroma 16 nan
10 UBERON:0015131 subepithelial connective tissue of prostatic gland Prostate Glandular Acinus UBERON:0004184 prostate gland stroma prostate stroma 17 nan
12 UBERON:0015131 subepithelial connective tissue of prostatic gland Prostate Glandular Acinus UBERON:0004184 prostate gland stroma prostate stroma 18 nan
14 UBERON:0004536 lymph vasculature lymph vasculature UBERON:0002367 prostate gland prostate gland 22 nan
16 UBERON:0000010 peripheral nervous system peripheral nervous system UBERON:0000010 peripheral nervous system peripheral nervous system 25 nan
17 UBERON:0000010 peripheral nervous system peripheral nervous system UBERON:0000010 peripheral nervous system peripheral nervous system 26 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
7 CL:0005006 ionocyte ionocyte epithelia UBERON:0004179 Prostate Glandular Acinus Prostate Glandular Acinus 15 1.01553
8 CL:0017002 prostate neuroendocrine cell neuroendocrine epithelia UBERON:0004179 Prostate Glandular Acinus Prostate Glandular Acinus 14 nan
11 CL:1000301 fibroblast of subepithelial connective tissue of prostatic gland periprostatic fibroblast UBERON:0015131 subepithelial connective tissue of prostatic gland Prostate Glandular Acinus 17 nan
13 CL:1000299 fibroblast of connective tissue of prostate interstitial fibroblast UBERON:0015131 subepithelial connective tissue of prostatic gland Prostate Glandular Acinus 18 nan
15 CL:0009112 centroblast perictye UBERON:0001981 blood vessel blood vessel 24 nan

New CL terms

Report

New UBERON terms

Report

Informative reports (valid relationships)

Indirect relationship

Report

Relationship AS has part CT

Report