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ASCT+B Validation Reports for Small_intestine (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.

  1. The term CL:0000186 has a different name/label in the source ontology in the following 1 row 232. The name/label in the ASCT+B table is myofibroblast and the one in the ontology is myofibroblast cell. For reference, the given name/label by SMEs is myofibroblasts. 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 serosa in the following 18 rows 52, 53, 54, 136, 137, 138, 178, 179, 180, 220, 221, 222, 303, 304, 305, 344, 345, 346.

  2. No term id was found for the name/label BCHE (butyrylcholinesterase) cell in the following 1 row 62.

  3. No term id was found for the name/label lymphatic in the following 4 rows 64, 84, 251, 334.

  4. No term id was found for the name/label nerve in the following 2 rows 67, 85.

  5. No term id was found for the name/label CD4+ T in the following 3 rows 71, 238, 321.

  6. No term id was found for the name/label regulatory CD4+ T in the following 3 rows 72, 239, 322.

  7. No term id was found for the name/label CD8+ T in the following 3 rows 73, 240, 323.

  8. No term id was found for the name/label nerves in the following 11 rows 82, 234, 249, 252, 258, 259, 317, 332, 335, 341, 342.

  9. No term id was found for the name/label endoethlial in the following 1 row 83.

  10. No term id was found for the name/label muscle in the following 9 rows 86, 248, 253, 254, 260, 331, 336, 337, 343.

  11. No term id was found for the name/label mucosa in the following 107 rows 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331.

  12. No term id was found for the name/label submucosa in the following 23 rows 124, 125, 126, 127, 128, 166, 167, 168, 169, 170, 208, 209, 210, 211, 212, 291, 292, 293, 332, 333, 334, 335, 336.

  13. No term id was found for the name/label muscularis propria in the following 14 rows 129, 130, 131, 132, 133, 134, 135, 171, 172, 173, 174, 175, 176, 177.

  14. No term id was found for the name/label Lamina propria/Gut associated lymphoid tissue (GALT) in the following 55 rows 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330.

  15. No term id was found for the name/label lymphatics in the following 2 rows 231, 314.

  16. No term id was found for the name/label myenteric plexus of Auerbach in the following 6 rows 259, 260, 301, 302, 342, 343.

  17. No term id was found for the name/label connective tissue in the following 4 rows 262, 263, 303, 304.

  18. No term id was found for the name/label muscularis mucosa in the following 2 rows 290, 331.

  19. No term id was found for the name/label submucosal plexus of Meissner in the following 4 rows 294, 295, 335, 336.

  20. No term id was found for the name/label muscularis externa in the following 14 rows 296, 297, 298, 299, 300, 301, 302, 337, 338, 339, 340, 341, 342, 343.

  21. No term id was found for the name/label circular/longitudinal muscle in the following 10 rows 296, 297, 298, 299, 300, 337, 338, 339, 340, 341.

  22. No term id was found for the name/label Epithelium in the following 7 rows 306, 307, 308, 309, 310, 311, 312.

  23. No term id was found for the name/label epithelial stem cells in the following 1 row 306.

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.

  1. The term BCHE (butyrylcholinesterase) cell without ontology ID has no parent that is from the CL ontology in the following 1 row 62.

  2. The term lymphatic without ontology ID has no parent that is from the CL ontology in the following 3 rows 64, 251, 334.

  3. The term nerve without ontology ID has no parent that is from the CL ontology in the following 2 rows 67, 85.

  4. The term CD4+ T without ontology ID has no parent that is from the CL ontology in the following 3 rows 71, 238, 321.

  5. The term regulatory CD4+ T without ontology ID has no parent that is from the CL ontology in the following 3 rows 72, 239, 322.

  6. The term CD8+ T without ontology ID has no parent that is from the CL ontology in the following 3 rows 73, 240, 323.

  7. The term muscle without ontology ID has no parent that is from the CL ontology in the following 9 rows 86, 248, 253, 254, 260, 331, 336, 337, 343.

  8. The term lymphatics without ontology ID has no parent that is from the CL ontology in the following 2 rows 231, 314.

  9. The term nerves without ontology ID has no parent that is from the CL ontology in the following 10 rows 234, 249, 252, 258, 259, 317, 332, 335, 341, 342.

  10. The term epithelial stem cells without ontology ID has no parent that is from the CL ontology in the following 1 row 306.

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:17101 in the following 27 rows 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39 is from another ontology that is not validated in this process.

  2. The term FMA:17107 in the following 5 rows 40, 41, 42, 43, 44 is from another ontology that is not validated in this process.

  3. The term FMA:17113 in the following 7 rows 45, 46, 47, 48, 49, 50, 51 is from another ontology that is not validated in this process.

  4. The term FMA:14926 in the following 42 rows 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96 is from another ontology that is not validated in this process.

  5. The term FMA:14928 in the following 42 rows 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138 is from another ontology that is not validated in this process.

  6. The term FMA:14929 in the following 42 rows 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180 is from another ontology that is not validated in this process.

  7. The term FMA:14930 in the following 42 rows 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222 is from another ontology that is not validated in this process.

  8. The term FMA:17116 in the following 7 rows 213, 214, 215, 216, 217, 218, 219 is from another ontology that is not validated in this process.

  9. The term FMA:14966 in the following 41 rows 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346 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
39 UBERON:8410064 submucous nerve plexus of small intestine submucosal plexus of Meissner submucosal plexus (Meissners plexus, plexus of the submucosa, plexus submucosus) UBERON:0003332 submucosa of duodenum submucosa 85 nan
40 UBERON:8410064 submucous nerve plexus of small intestine submucosal plexus of Meissner UBERON:0003332 submucosa of duodenum submucosa 86 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:0000115 endothelial cell endothelial UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) 63 47.4061
1 CL:0000115 endothelial cell endoethlial UBERON:0003333 submucosa of jejunum submucosa 250 47.4061
2 CL:0000236 B cell B cell UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) 69 44.3276
3 CL:0000115 endothelial cell endothelial cells UBERON:0003337 serosa of jejunum serosa 263 42.8397
4 CL:0000115 endothelial cell endothelial UBERON:0012377 muscle layer of jejunum muscularis externa 257 42.8397
5 CL:0000057 fibroblast fibroblast UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) 66 42.197
6 CL:0000034 stem cell stem cell UBERON:0008346 duodenal epithelium Epithelium 61 40.3254
7 CL:0000057 fibroblast fibroblasts UBERON:0012377 muscle layer of jejunum muscularis externa 256 37.6306
8 CL:0000057 fibroblast fibroblasts UBERON:0003337 serosa of jejunum serosa 262 37.6306
9 CL:0000115 endothelial cell endothelial cells UBERON:0003336 serosa of duodenum serosa 96 36.8033
10 CL:0000451 dendritic cell dendritic cell (DC) UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) 79 35.3505
11 CL:0000235 macrophage macrophage UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) 74 35.2887
12 CL:0001065 innate lymphoid cell innate lyphoid cell (ILC) UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) 80 31.861
13 CL:0000057 fibroblast fibroblasts UBERON:0003336 serosa of duodenum serosa 95 31.5942
14 CL:0000623 natural killer cell natural killer (NK) cell UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) 78 30.8454
15 CL:0000775 neutrophil neutrophil UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) 77 30.5331
16 CL:0000115 endothelial cell endothelial UBERON:0000399 jejunal mucosa mucosa 230 30.5085
17 CL:0000097 mast cell mast cell UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) 76 28.5304
18 CL:0000236 B cell B cell UBERON:0000399 jejunal mucosa mucosa 236 27.4299
19 CL:0000786 plasma cell plasma UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) 70 26.279
20 CL:0000771 eosinophil eosinophil UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) 75 25.9025
21 CL:0000057 fibroblast fibroblasts UBERON:0000399 jejunal mucosa mucosa 233 25.2994
22 CL:0000036 epithelial fate stem cell epithelial stem cells UBERON:0000400 jejunal epithelium Epithelium 223 22.7803
23 CL:0000451 dendritic cell DCs UBERON:0000399 jejunal mucosa mucosa 246 18.4529
24 CL:0000235 macrophage macrophages UBERON:0000399 jejunal mucosa mucosa 241 18.391
25 CL:0000186 myofibroblast cell myofibroblast UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) 65 16.3703
26 CL:0000682 M cell of gut M cell UBERON:0015834 duodenum lamina propria Lamina propria/Gut associated lymphoid tissue (GALT) 68 15.1692
27 CL:0001065 innate lymphoid cell ILCs UBERON:0000399 jejunal mucosa mucosa 247 14.9633
28 CL:0000584 enterocyte enterocytes UBERON:0000400 jejunal epithelium Epithelium 228 14.6556
29 CL:0000623 natural killer cell NK cells UBERON:0000399 jejunal mucosa mucosa 245 13.9478
30 CL:0000775 neutrophil neutrophils UBERON:0000399 jejunal mucosa mucosa 244 13.6355
31 CL:0000097 mast cell mast cells UBERON:0000399 jejunal mucosa mucosa 243 11.6328
32 CL:0000584 enterocyte enterocyte UBERON:0008346 duodenal epithelium Epithelium 59 10.0892
33 CL:0000786 plasma cell plasma UBERON:0000399 jejunal mucosa mucosa 237 9.3814
34 CL:0000771 eosinophil eosinophils UBERON:0000399 jejunal mucosa mucosa 242 9.00485
35 CL:0002088 interstitial cell of Cajal Interstitial cells of Cajal UBERON:0012377 muscle layer of jejunum muscularis externa 255 7.23755
36 CL:1000344 paneth cell of epithelium proper of small intestine Paneth cell UBERON:0008346 duodenal epithelium Epithelium 55 nan
37 CL:0009080 tuft cell of small intestine tuft cell UBERON:0008346 duodenal epithelium Epithelium 57 nan
38 CL:0000212 absorptive cell absorptive UBERON:0008346 duodenal epithelium Epithelium 58 nan
41 CL:1000344 paneth cell of epithelium proper of small intestine Paneth UBERON:0000400 jejunal epithelium Epithelium 224 nan
42 CL:0000212 absorptive cell absorptive UBERON:0000400 jejunal epithelium Epithelium 226 nan
43 CL:0009080 tuft cell of small intestine Tuft cells UBERON:0000400 jejunal epithelium Epithelium 229 nan
44 CL:0000186 myofibroblast cell myofibroblasts UBERON:0000399 jejunal mucosa mucosa 232 nan
45 CL:0000682 M cell of gut M cell UBERON:0000399 jejunal mucosa mucosa 235 nan

New CL terms

Report

New UBERON terms

Report

Informative reports (valid relationships)

Indirect relationship

Report

Relationship AS has part CT

Report