ASCT+B Validation Reports for Palatine_Tonsil (2024-12-25)
Table of contents
- Invalid terms
- Relationship reports
- New CL terms
- New UBERON terms
- Informative reports (valid relationships)
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.
- 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.
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No term id was found for the name/label plasma cell CD21 in the following 1 row 25.
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No term id was found for the name/label peritonsillar plexus of veins in the following 1 row 31.
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No term id was found for the name/label tonsil T cell zone in the following 4 rows 32, 33, 34, 35.
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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.
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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.
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No term id was found for the name/label Cycling B in the following 3 rows 36, 42, 55.
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No term id was found for the name/label germinal center B cell CD21 in the following 2 rows 50, 63.
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No term id was found for the name/label tonsil germinal center mantle zone in the following 3 rows 51, 52, 53.
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No term id was found for the name/label Centroblast in the following 1 row 54.
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No term id was found for the name/label tonsil germinal center light zone in the following 1 row 64.
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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.
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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.
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The term FMA:49555 in the following 1 row 27 is from another ontology that is not validated in this process.
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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 | 41.3705 |
5 | UBERON:0001981 | blood vessel | blood vessel | UBERON:0002373 | palatine tonsil | palatine tonsil | 28 | 41.3705 |
6 | UBERON:0001981 | blood vessel | blood vessel | UBERON:0002373 | palatine tonsil | palatine tonsil | 31 | 41.3705 |
7 | UBERON:0001981 | blood vessel | blood vessel | UBERON:0002373 | palatine tonsil | palatine tonsil | 29 | 41.3705 |
8 | UBERON:0001981 | blood vessel | blood vessel | UBERON:0002373 | palatine tonsil | palatine tonsil | 26 | 41.3705 |
9 | UBERON:0001981 | blood vessel | blood vessel | UBERON:0002373 | palatine tonsil | palatine tonsil | 27 | 41.3705 |
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 | |
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0 | CL:0000084 | T Cell | T Cell | UBERON:0013688 | tonsil germinal center | tonsil germinal center | 60 | 44.3668 |
1 | CL:0000236 | B cell | B cell | UBERON:0013688 | tonsil germinal center | tonsil germinal center | 58 | 44.3276 |
2 | CL:0000236 | B cell | B cell | UBERON:0013688 | tonsil germinal center | tonsil germinal center | 55 | 44.3276 |
3 | CL:0000236 | B cell | B cell | UBERON:0013688 | tonsil germinal center | tonsil germinal center | 54 | 44.3276 |
10 | CL:0000235 | Macrophage | macrophage | UBERON:0013688 | tonsil germinal center | tonsil germinal center | 61 | 35.2887 |
11 | CL:0000624 | CD4-positive, alpha-beta T cell | CD4 T cell | UBERON:0013688 | tonsil germinal center | tonsil germinal center | 56 | 34.1371 |
12 | CL:0000084 | T cell | T cell | UBERON:0002373 | palatine tonsil | palatine tonsil | 16 | 32.5629 |
13 | CL:0000236 | B cell | B cell | UBERON:0002373 | palatine tonsil | palatine tonsil | 21 | 32.5236 |
14 | CL:0000057 | Fibroblast | fibroblast | UBERON:0002373 | palatine tonsil | palatine tonsil | 19 | 30.3931 |
15 | CL:0000786 | Plasma Cell | plasma cell | UBERON:0013688 | tonsil germinal center | tonsil germinal center | 59 | 26.279 |
16 | CL:0000815 | regulatory T cell | regulatory T cell | UBERON:0013688 | tonsil germinal center | tonsil germinal center | 57 | 26.1559 |
17 | CL:0000451 | Dendritic Cell | dendritic cell | UBERON:0002373 | palatine tonsil | palatine tonsil | 22 | 23.5466 |
18 | CL:0000235 | Macrophage | macrophage | UBERON:0002373 | palatine tonsil | palatine tonsil | 23 | 23.4847 |
19 | CL:0000624 | CD4-positive, alpha-beta T cell | CD4 T cell | UBERON:0002373 | palatine tonsil | palatine tonsil | 17 | 22.3331 |
20 | CL:0000844 | germinal center B cell | germinal center B cell | UBERON:0013688 | tonsil germinal center | tonsil germinal center | 62 | 21.464 |
21 | CL:0000844 | germinal center B cell | germinal center B cell | UBERON:0013688 | tonsil germinal center | tonsil germinal center | 63 | 21.464 |
22 | CL:0000625 | CD8-positive, alpha-beta T cell | CD8 T cell | UBERON:0002373 | palatine tonsil | palatine tonsil | 18 | 18.9183 |
23 | CL:0000786 | Plasma Cell | plasma cell | UBERON:0002373 | palatine tonsil | palatine tonsil | 25 | 14.4751 |
24 | CL:0000786 | Plasma Cell | plasma cell | UBERON:0002373 | palatine tonsil | palatine tonsil | 24 | 14.4751 |
25 | CL:0000235 | Macrophage | macrophage | UBERON:0010754 | germinal center | germinal center | 48 | 12.254 |
26 | CL:0000432 | Reticular cell | reticular cells | UBERON:0002373 | palatine tonsil | palatine tonsil | 20 | 3.36527 |
27 | CL:0000786 | Plasma Cell | plasma cell | UBERON:0010754 | germinal center | germinal center | 46 | 3.24439 |
28 | CL:0000815 | regulatory T cell | regulatory T cell | UBERON:0010754 | germinal center | germinal center | 44 | 3.12125 |