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ASCT+B Validation Reports for Kidney (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.

  1. No term id was found for the name/label capsule mesenchymal stromal cell in the following 1 row 12.

  2. No term id was found for the name/label Transitional principal-intercalated cell in the following 1 row 52.

  3. No term id was found for the name/label Kidney Lymphatic Vessel in the following 1 row 65.

  4. No term id was found for the name/label Monocyte Derived Cell in the following 1 row 81.

  5. No term id was found for the name/label Papillary Tip Epithelium in the following 1 row 89.

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:0001986 endothelium Endothelium (non glomerular) UBERON:0009091 ascending vasa recta Ascending Vasa Recta 64 38.3957
1 UBERON:0001986 endothelium Endothelium (non glomerular) UBERON:0009202 descending vasa recta Descending Vasa Recta 63 38.3957
3 UBERON:0004188 glomerular epithelium Glomerular Epithelium UBERON:0002189 outer cortex of kidney outer cortex of kidney 13 24.2191
4 UBERON:0004188 glomerular epithelium Glomerular Epithelium UBERON:0005271 juxtamedullary cortex juxtamedullary cortex 14 24.2191
5 UBERON:0004188 glomerular epithelium Glomerular Epithelium UBERON:0001284 renal column renal column (column of Bertin) 20 24.2191
6 UBERON:0004640 renal efferent arteriole Efferent Arteriole UBERON:0034884 juxtaglomerular arteriole Juxtaglomerular Arteriole 61 16.3703
7 UBERON:0004639 renal afferent arteriole Afferent Arteriole UBERON:0034884 juxtaglomerular arteriole Juxtaglomerular Arteriole 60 15.7971
10 UBERON:0001986 endothelium Endothelium (non glomerular) UBERON:0003517 kidney blood vessel Kidney Blood Vessel 59 15.0682
11 UBERON:0001289 descending limb of loop of Henle Loop of Henle (Thin Limb) UBERON:0004201 kidney outer medulla inner stripe kidney outer medulla inner stripe 17 7.83686
12 UBERON:0004203 cortical collecting duct Collecting Duct (Cortex) UBERON:0009883 medullary ray medullary ray 15 4.56639
16 UBERON:0001291 thick ascending limb of loop of Henle Loop of Henle (Thick Limb/Medulla) UBERON:0004202 kidney outer medulla outer stripe kidney outer medulla outer stripe 16 1.20112
17 UBERON:0002335 macula densa Macula Densa UBERON:0001291 thick ascending limb of loop of Henle Loop of Henle (Thick Limb/ Cortex) 38 1.01553
18 UBERON:8600036 kidney loop of Henle long descending thin limb outer medulla descending thin limb of loop of Henle 2 UBERON:0001289 descending limb of loop of Henle Loop of Henle (Thin Limb) 17 nan
20 UBERON:0009202 descending vasa recta Descending Vasa Recta UBERON:0001294 inner medulla of kidney inner medulla of kidney 18 nan
22 UBERON:0001284 renal column renal column (column of Bertin) UBERON:0001225 cortex of kidney renal cortex 20 nan
23 UBERON:0009202 descending vasa recta Descending Vasa Recta UBERON:0004200 kidney pyramid renal pyramid 21 nan
24 UBERON:0005215 kidney interstitium Interstitium UBERON:0001229 Renal Corpuscle Renal Corpuscle 25 nan
25 UBERON:0005099 short descending thin limb descending thin limb of loop of Henle 1 UBERON:0001289 descending limb of loop of Henle Loop of Henle (Thin Limb) 31 nan
26 UBERON:8600036 kidney loop of Henle long descending thin limb outer medulla descending thin limb of loop of Henle 2 UBERON:0001289 descending limb of loop of Henle Loop of Henle (Thin Limb) 32 nan
28 UBERON:8600037 kidney loop of Henle long descending thin limb inner medulla descending thin limb of loop of Henle 3 UBERON:0001289 descending limb of loop of Henle Loop of Henle (Thin Limb) 33 nan
30 UBERON:0001232 collecting duct of renal tubule Collecting Duct UBERON:0001232 collecting duct of renal tubule Tubules 47 nan
31 UBERON:0001232 collecting duct of renal tubule Collecting Duct UBERON:0001232 collecting duct of renal tubule Tubules 48 nan
32 UBERON:0001232 collecting duct of renal tubule Collecting Duct UBERON:0001232 collecting duct of renal tubule Tubules 52 nan
33 UBERON:0001232 collecting duct of renal tubule Collecting Duct UBERON:0001232 collecting duct of renal tubule Tubules 53 nan
34 UBERON:0001232 collecting duct of renal tubule Collecting Duct UBERON:0001232 collecting duct of renal tubule Tubules 54 nan
35 UBERON:0001232 collecting duct of renal tubule Collecting Duct UBERON:0001232 collecting duct of renal tubule Tubules 57 nan
37 UBERON:0002303 juxtaglomerular apparatus Juxtaglomerular Apparatus UBERON:0003517 kidney blood vessel Kidney Blood Vessel 68 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
2 CL:0000499 stromal cell stromal cell UBERON:0002015 kidney capsule kidney capsule 12 25.3644
8 CL:0000084 T cell T Cell UBERON:0005215 kidney interstitium Interstitium 82 15.4985
9 CL:0000236 B cell B cell UBERON:0005215 kidney interstitium Interstitium 85 15.4592
13 CL:0000576 monocyte Monocyte UBERON:0005215 kidney interstitium Interstitium 80 3.87228
14 CL:0000623 natural killer cell Natural Killer Cell UBERON:0005215 kidney interstitium Interstitium 75 1.97706
15 CL:0000775 neutrophil Neutrophil UBERON:0005215 kidney interstitium Interstitium 87 1.66478
19 CL:4030013 kidney loop of Henle long descending thin limb outer medulla epithelial cell Descending Thin Limb Cell Type 2 UBERON:8600036 kidney loop of Henle long descending thin limb outer medulla descending thin limb of loop of Henle 2 17 nan
21 CL:1000718 kidney inner medulla collecting duct principal cell Inner Medullary Collecting Duct Cell UBERON:0009095 tip of renal papilla papillary tip 19 nan
27 CL:4030013 kidney loop of Henle long descending thin limb outer medulla epithelial cell Descending Thin Limb Cell Type 2 UBERON:8600036 kidney loop of Henle long descending thin limb outer medulla descending thin limb of loop of Henle 2 32 nan
29 CL:4030014 kidney loop of Henle long descending thin limb inner medulla epithelial cell Descending Thin Limb Cell Type 3 UBERON:8600037 kidney loop of Henle long descending thin limb inner medulla descending thin limb of loop of Henle 3 33 nan
36 CL:1001318 renal interstitial pericyte Vascular Smooth Muscle Cell/Pericyte (general) UBERON:0003517 kidney blood vessel Kidney Blood Vessel 66 nan
38 CL:0000875 non-classical monocyte non Classical Monocyte UBERON:0005215 kidney interstitium Interstitium 74 nan
39 CL:0000814 mature NK T cell Natural Killer T Cell UBERON:0005215 kidney interstitium Interstitium 76 nan
40 CL:0001056 dendritic cell, human Dendritic Cell (general) UBERON:0005215 kidney interstitium Interstitium 77 nan
41 CL:0001058 plasmacytoid dendritic cell, human Dendritic Cell (plasmatoid) UBERON:0005215 kidney interstitium Interstitium 79 nan
42 CL:0000910 cytotoxic T cell Cytotoxic T Cell UBERON:0005215 kidney interstitium Interstitium 83 nan
43 CL:0000815 regulatory T cell regulatory T cell UBERON:0005215 kidney interstitium Interstitium 84 nan
44 CL:0000786 plasma cell Plasma cell UBERON:0005215 kidney interstitium Interstitium 86 nan
45 CL:0000097 mast cell Mast cell UBERON:0005215 kidney interstitium Interstitium 88 nan

New CL terms

Report

New UBERON terms

Report

Informative reports (valid relationships)

Indirect relationship

Report

Relationship AS has part CT

Report