ASCT+B Validation Reports for Kidney (2024-07-04)
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.
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The term UBERON:8600037 has a different name/label in the source ontology in the following 1 row 33. The name/label in the ASCT+B table is long descending limb of the loop of Henle in the inner medulla and the one in the ontology is kidney loop of Henle long descending thin limb inner medulla. For reference, the given name/label by SMEs is descending thin limb of loop of Henle 3. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
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The term UBERON:8600036 has a different name/label in the source ontology in the following 1 row 17. The name/label in the ASCT+B table is long descending limb of the loop of Henle in the outer medulla _ and the one in the ontology is _kidney loop of Henle long descending thin limb outer medulla. For reference, the given name/label by SMEs is descending thin limb of loop of Henle 2. 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 capsule mesenchymal stromal cell in the following 1 row 12.
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No term id was found for the name/label Transitional principal-intercalated cell in the following 1 row 52.
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No term id was found for the name/label Kidney Lymphatic Vessel in the following 1 row 65.
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No term id was found for the name/label Monocyte Derived Cell in the following 1 row 81.
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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 | vasa recta ascending limb | Ascending Vasa Recta | 64 | 38.1204 |
| 1 | UBERON:0001986 | endothelium | Endothelium (non glomerular) | UBERON:0009202 | vasa recta descending limb | Descending Vasa Recta | 63 | 38.1204 |
| 3 | UBERON:0004188 | glomerular epithelium | Glomerular Epithelium | UBERON:0002189 | outer cortex of kidney | outer cortex of kidney | 13 | 24.2429 |
| 4 | UBERON:0004188 | glomerular epithelium | Glomerular Epithelium | UBERON:0005271 | juxtamedullary cortex | juxtamedullary cortex | 14 | 24.2429 |
| 5 | UBERON:0004188 | glomerular epithelium | Glomerular Epithelium | UBERON:0001284 | renal column | renal column (column of Bertin) | 20 | 24.2429 |
| 6 | UBERON:0004640 | renal efferent arteriole | Efferent Arteriole | UBERON:0034884 | juxtaglomerular arteriole | Juxtaglomerular Arteriole | 61 | 16.3864 |
| 7 | UBERON:0004639 | renal afferent arteriole | Afferent Arteriole | UBERON:0034884 | juxtaglomerular arteriole | Juxtaglomerular Arteriole | 60 | 15.8126 |
| 10 | UBERON:0001986 | endothelium | Endothelium (non glomerular) | UBERON:0003517 | kidney blood vessel | Kidney Blood Vessel | 59 | 14.4437 |
| 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 | 7.55144 |
| 12 | UBERON:0004203 | cortical collecting duct | Collecting Duct (Cortex) | UBERON:0009883 | medullary ray | medullary ray | 15 | 4.57088 |
| 16 | UBERON:0002335 | macula densa | Macula Densa | UBERON:0001291 | thick ascending limb of loop of Henle | Loop of Henle (Thick Limb/ Cortex) | 38 | 1.01653 |
| 17 | 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 | 0.573786 |
| 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 | vasa recta descending limb | 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 | vasa recta descending limb | 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 |
| 28 | 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 |
| 29 | 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 |
| 31 | 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 |
| 33 | UBERON:0001232 | collecting duct of renal tubule | Collecting Duct | UBERON:0001232 | collecting duct of renal tubule | Tubules | 47 | nan |
| 34 | UBERON:0001232 | collecting duct of renal tubule | Collecting Duct | UBERON:0001232 | collecting duct of renal tubule | Tubules | 48 | nan |
| 35 | UBERON:0001232 | collecting duct of renal tubule | Collecting Duct | UBERON:0001232 | collecting duct of renal tubule | Tubules | 52 | nan |
| 36 | UBERON:0001232 | collecting duct of renal tubule | Collecting Duct | UBERON:0001232 | collecting duct of renal tubule | Tubules | 53 | nan |
| 37 | UBERON:0001232 | collecting duct of renal tubule | Collecting Duct | UBERON:0001232 | collecting duct of renal tubule | Tubules | 54 | nan |
| 38 | UBERON:0001232 | collecting duct of renal tubule | Collecting Duct | UBERON:0001232 | collecting duct of renal tubule | Tubules | 57 | nan |
| 39 | UBERON:0004726 | vasa recta | Vasa Recta | UBERON:0006544 | kidney vasculature | Vessels | 63 | nan |
| 40 | UBERON:0004726 | vasa recta | Vasa Recta | UBERON:0006544 | kidney vasculature | Vessels | 64 | nan |
| 42 | 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 | 25.3693 |
| 8 | CL:0000084 | T cell | T Cell | UBERON:0005215 | kidney interstitium | Interstitium | 82 | 15.4744 |
| 9 | CL:0000236 | B cell | B cell | UBERON:0005215 | kidney interstitium | Interstitium | 85 | 15.4586 |
| 13 | CL:0000576 | monocyte | Monocyte | UBERON:0005215 | kidney interstitium | Interstitium | 80 | 3.73726 |
| 14 | CL:0000623 | natural killer cell | Natural Killer Cell | UBERON:0005215 | kidney interstitium | Interstitium | 75 | 1.91766 |
| 15 | CL:0000775 | neutrophil | Neutrophil | UBERON:0005215 | kidney interstitium | Interstitium | 87 | 1.66642 |
| 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 |
| 25 | CL:4030009 | epithelial cell of proximal tubule segment 1 | Proximal Tubule Epithelial Cell Segment 1 | UBERON:0004196 | proximal convoluted tubule segment 1 | proximal convoluted tubule segment 1 | 27 | nan |
| 26 | CL:4030010 | epithelial cell of proximal tubule segment 2 | Proximal Tubule Epithelial Cell Segment 2 | UBERON:0004197 | proximal convoluted tubule segment 2 | proximal convoluted tubule segment 2 | 28 | nan |
| 27 | CL:4030011 | epithelial cell of proximal tubule segment 3 | Proximal Tubule Cell Epithelial Segment 3 | UBERON:0001290 | proximal straight tubule | proximal straight tubule segment 3 | 29 | nan |
| 30 | 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 |
| 32 | 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 |
| 41 | CL:1001318 | renal interstitial pericyte | Vascular Smooth Muscle Cell/Pericyte (general) | UBERON:0003517 | kidney blood vessel | Kidney Blood Vessel | 66 | nan |
| 43 | CL:0000875 | non-classical monocyte | non Classical Monocyte | UBERON:0005215 | kidney interstitium | Interstitium | 74 | nan |
| 44 | CL:0000814 | mature NK T cell | Natural Killer T Cell | UBERON:0005215 | kidney interstitium | Interstitium | 76 | nan |
| 45 | CL:0001056 | dendritic cell, human | Dendritic Cell (general) | UBERON:0005215 | kidney interstitium | Interstitium | 77 | nan |
| 46 | CL:0001058 | plasmacytoid dendritic cell, human | Dendritic Cell (plasmatoid) | UBERON:0005215 | kidney interstitium | Interstitium | 79 | nan |
| 47 | CL:0000910 | cytotoxic T cell | Cytotoxic T Cell | UBERON:0005215 | kidney interstitium | Interstitium | 83 | nan |
| 48 | CL:0000815 | regulatory T cell | regulatory T cell | UBERON:0005215 | kidney interstitium | Interstitium | 84 | nan |
| 49 | CL:0000786 | plasma cell | Plasma cell | UBERON:0005215 | kidney interstitium | Interstitium | 86 | nan |
| 50 | CL:0000097 | mast cell | Mast cell | UBERON:0005215 | kidney interstitium | Interstitium | 88 | nan |