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ASCT+B Validation Reports for Blood (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.

  • 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.

  • 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.

  • 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.

row_number s slabel user_slabel o olabel user_olabel deltaIC
0 20 CL:0000840 immature conventional dendritic cell transitional Dendritic Cell (tDC) CL:0001056 dendritic cell, human dendritic cell (DC) 11.2307
5 16 CL:0002394 CD141-positive myeloid dendritic cell dendritic cell type 1 (DC1) CL:0001056 dendritic cell, human dendritic cell (DC) nan
7 17 CL:0002399 CD1c-positive myeloid dendritic cell dendritic cell type 2 (DC2) CL:0001056 dendritic cell, human dendritic cell (DC) nan
9 18 CL:0002399 CD1c-positive myeloid dendritic cell dendritic cell type 3 (DC3) CL:0001056 dendritic cell, human dendritic cell (DC) nan
15 23 CL:0000775 neutrophil neutrophil CL:0000775 neutrophil neutrophilic granulocyte nan
28 35 CL:0000938 CD16-negative, CD56-bright natural killer cell, human CD56 bright Natural killer CL:0000814 mature NK T cell NK lymphocytes nan
30 36 CL:0000824 mature natural killer cell mature Natural killer CL:0000814 mature NK T cell NK lymphocytes nan

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.

row_number s slabel user_slabel o olabel user_olabel deltaIC
1 12 CL:0000816 immature B cell immature B cell UBERON:0000178 Blood Blood nan
2 13 CL:0000787 memory B cell memory B cell UBERON:0000178 Blood Blood nan
3 14 CL:0000788 naive B cell naive B cell UBERON:0000178 Blood Blood nan
4 15 CL:0000818 transitional stage B cell transitional B cell UBERON:0000178 Blood Blood nan
6 16 CL:0002394 CD141-positive myeloid dendritic cell dendritic cell type 1 (DC1) UBERON:0000178 Blood Blood nan
8 17 CL:0002399 CD1c-positive myeloid dendritic cell dendritic cell type 2 (DC2) UBERON:0000178 Blood Blood nan
10 18 CL:0002399 CD1c-positive myeloid dendritic cell dendritic cell type 3 (DC3) UBERON:0000178 Blood Blood nan
11 19 CL:0001058 plasmacytoid dendritic cell, human Plasmacytoid Dendritic Cell (pDC) UBERON:0000178 Blood Blood nan
12 20 CL:0000840 immature conventional dendritic cell transitional Dendritic Cell (tDC) UBERON:0000178 Blood Blood nan
13 21 CL:0001054 CD14-positive monocyte CD14 monocyte UBERON:0000178 Blood Blood nan
14 22 CL:0002396 CD14-low, CD16-positive monocyte CD16 monocyte UBERON:0000178 Blood Blood nan
16 23 CL:0000775 neutrophil neutrophil UBERON:0000178 Blood Blood nan
17 24 CL:0000771 eosinophil eosinophil UBERON:0000178 Blood Blood nan
18 25 CL:0000767 basophil basophil UBERON:0000178 Blood Blood nan
19 26 CL:0000895 naive thymus-derived CD4-positive, alpha-beta T cell CD4 naive UBERON:0000178 Blood Blood nan
20 27 CL:0000897 CD4-positive, alpha-beta memory T cell CD4 T cell memory UBERON:0000178 Blood Blood nan
21 28 CL:0000897 CD4-positive, alpha-beta memory T cell CD4 T cell memory UBERON:0000178 Blood Blood nan
22 29 CL:0001087 effector memory CD4-positive, alpha-beta T cell, terminally differentiated CD4 T cell effector memory CD45RA UBERON:0000178 Blood Blood nan
23 30 CL:0000900 naive thymus-derived CD8-positive, alpha-beta T cell CD8 naive UBERON:0000178 Blood Blood nan
24 31 CL:0000897 CD4-positive, alpha-beta memory T cell CD4 T cell memory UBERON:0000178 Blood Blood nan
25 32 CL:0001050 effector CD8-positive, alpha-beta T cell CD8 T cell effector memory UBERON:0000178 Blood Blood nan
26 33 CL:0001062 effector memory CD8-positive, alpha-beta T cell, terminally differentiated CD8 T cell effector memory CD45RA UBERON:0000178 Blood Blood nan
27 34 CL:0002437 mature CD8 single-positive thymocyte mature CD8 T cell UBERON:0000178 Blood Blood nan
29 35 CL:0000938 CD16-negative, CD56-bright natural killer cell, human CD56 bright Natural killer UBERON:0000178 Blood Blood nan
31 36 CL:0000824 mature natural killer cell mature Natural killer UBERON:0000178 Blood Blood nan
32 37 CL:0000815 regulatory T cell T regulatory UBERON:0000178 Blood Blood nan

New CL terms

Report

New UBERON terms

Report

Informative reports (valid relationships)

Indirect relationship

Report

Relationship AS has part CT

Report