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

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:0000624 has a different name/label in the source ontology in the following 2 rows 43, 56. The name/label in the ASCT+B table is CD4-positive alpha-beta T cells and the one in the ontology is CD4-positive, alpha-beta T cell. For reference, the given name/label by SMEs is CD4 T cell. 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 plasma cell CD21 in the following 1 row 25.

  2. No term id was found for the name/label peritonsillar plexus of veins in the following 1 row 31.

  3. No term id was found for the name/label tonsil T cell zone in the following 4 rows 32, 33, 34, 35.

  4. No term id was found for the name/label tonsil follicle in the following 30 rows 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65.

  5. No term id was found for the name/label tonsil secondary follicle in the following 30 rows 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65.

  6. No term id was found for the name/label Cycling B in the following 3 rows 36, 42, 55.

  7. No term id was found for the name/label germinal center B cell CD21 in the following 2 rows 50, 63.

  8. No term id was found for the name/label tonsil germinal center mantle zone in the following 3 rows 51, 52, 53.

  9. No term id was found for the name/label Centroblast in the following 1 row 54.

  10. No term id was found for the name/label tonsil germinal center light zone in the following 1 row 64.

  11. No term id was found for the name/label tonsil germinal center dark zone in the following 1 row 65.

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.

  1. The term FMA:55221 in the following 14 rows 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 34, 35 is from another ontology that is not validated in this process.

  2. The term FMA:49555 in the following 1 row 27 is from another ontology that is not validated in this process.

  3. The term FMA:49497 in the following 1 row 29 is from another ontology that is not validated in this process.

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
4 UBERON:0001981 blood vessel blood vessel UBERON:0002373 palatine tonsil palatine tonsil 30 41.3968
5 UBERON:0001981 blood vessel blood vessel UBERON:0002373 palatine tonsil palatine tonsil 28 41.3968
6 UBERON:0001981 blood vessel blood vessel UBERON:0002373 palatine tonsil palatine tonsil 31 41.3968
7 UBERON:0001981 blood vessel blood vessel UBERON:0002373 palatine tonsil palatine tonsil 29 41.3968
8 UBERON:0001981 blood vessel blood vessel UBERON:0002373 palatine tonsil palatine tonsil 26 41.3968
9 UBERON:0001981 blood vessel blood vessel UBERON:0002373 palatine tonsil palatine tonsil 27 41.3968
29 UBERON:0010423 primary lymphoid nodule of tonsil primary nodular lymphoid tissue UBERON:0002373 palatine tonsil palatine tonsil 12 nan
30 UBERON:0012181 tonsil crypt tonsil crypt UBERON:0002373 palatine tonsil palatine tonsil 13 nan
31 UBERON:0005207 tonsil capsule tonsil capsule UBERON:0002373 palatine tonsil palatine tonsil 14 nan
32 UBERON:0013696 tonsil epithelium tonsil epithelium UBERON:0002373 palatine tonsil palatine tonsil 15 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:0000084 T Cell T Cell UBERON:0013688 tonsil germinal center tonsil germinal center 60 44.3818
1 CL:0000236 B cell B cell UBERON:0013688 tonsil germinal center tonsil germinal center 58 44.3425
2 CL:0000236 B cell B cell UBERON:0013688 tonsil germinal center tonsil germinal center 55 44.3425
3 CL:0000236 B cell B cell UBERON:0013688 tonsil germinal center tonsil germinal center 54 44.3425
10 CL:0000235 Macrophage macrophage UBERON:0013688 tonsil germinal center tonsil germinal center 61 35.3006
11 CL:0000624 CD4-positive, alpha-beta T cell CD4 T cell UBERON:0013688 tonsil germinal center tonsil germinal center 56 34.1486
12 CL:0000084 T cell T cell UBERON:0002373 palatine tonsil palatine tonsil 16 32.5739
13 CL:0000236 B cell B cell UBERON:0002373 palatine tonsil palatine tonsil 21 32.5346
14 CL:0000057 Fibroblast fibroblast UBERON:0002373 palatine tonsil palatine tonsil 19 30.4033
15 CL:0000786 Plasma Cell plasma cell UBERON:0013688 tonsil germinal center tonsil germinal center 59 26.2879
16 CL:0000815 regulatory T cell regulatory T cell UBERON:0013688 tonsil germinal center tonsil germinal center 57 26.1647
17 CL:0000451 Dendritic Cell dendritic cell UBERON:0002373 palatine tonsil palatine tonsil 22 23.5545
18 CL:0000235 Macrophage macrophage UBERON:0002373 palatine tonsil palatine tonsil 23 23.4927
19 CL:0000624 CD4-positive, alpha-beta T cell CD4 T cell UBERON:0002373 palatine tonsil palatine tonsil 17 22.3407
20 CL:0000844 germinal center B cell germinal center B cell UBERON:0013688 tonsil germinal center tonsil germinal center 62 21.4713
21 CL:0000844 germinal center B cell germinal center B cell UBERON:0013688 tonsil germinal center tonsil germinal center 63 21.4713
22 CL:0000625 CD8-positive, alpha-beta T cell CD8 T cell UBERON:0002373 palatine tonsil palatine tonsil 18 18.9247
23 CL:0000786 Plasma Cell plasma cell UBERON:0002373 palatine tonsil palatine tonsil 25 14.48
24 CL:0000786 Plasma Cell plasma cell UBERON:0002373 palatine tonsil palatine tonsil 24 14.48
25 CL:0000235 Macrophage macrophage UBERON:0010754 germinal center germinal center 48 12.2581
26 CL:0000432 Reticular cell reticular cells UBERON:0002373 palatine tonsil palatine tonsil 20 3.3664
27 CL:0000786 Plasma Cell plasma cell UBERON:0010754 germinal center germinal center 46 3.24548
28 CL:0000815 regulatory T cell regulatory T cell UBERON:0010754 germinal center germinal center 44 3.1223

New CL terms

Report

New UBERON terms

Report

Informative reports (valid relationships)

Indirect relationship

Report

Relationship AS has part CT

Report