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ASCT+B Validation Reports for Lymph_vasculature (2024-11-20)

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 right anterior mediastinal lymph node in the following 1 row 15.

  2. No term id was found for the name/label transverse cervical lymph node #2 in the following 1 row 19.

  3. No term id was found for the name/label collecting lymph trunk of lymphatics of soft parts covering posterior thoracic wall in the following 1 row 22.

  4. No term id was found for the name/label medial lymph trunk of principal axillary lymph vessel in the following 1 row 23.

  5. No term id was found for the name/label posterior extrathoracic lymph node in the following 7 rows 25, 26, 27, 28, 29, 30, 31.

  6. No term id was found for the name/label deep lymph node of neck in the following 3 rows 26, 27, 28.

  7. No term id was found for the name/label supraspinatus fossa lymph node in the following 2 rows 27, 28.

  8. No term id was found for the name/label supraescapular lymphatic channel in the following 1 row 28.

  9. No term id was found for the name/label circumflex lymphatic channel in the following 1 row 30.

  10. No term id was found for the name/label left lateral aortic lymph node in the following 1 row 35.

  11. No term id was found for the name/label right lateral aortic lymph node in the following 1 row 37.

  12. No term id was found for the name/label anterior lymph trunk of accompanying suprarenal vein in the following 1 row 41.

  13. No term id was found for the name/label left collecting lymph trunk of lymphatics of ovary in the following 1 row 46.

  14. No term id was found for the name/label medial lymph node of common illiac lymph nodes in the following 1 row 47.

  15. No term id was found for the name/label right collecting lymph trunk of lymphatics of testicle in the following 1 row 50.

  16. No term id was found for the name/label lymphatics of great omentum in the following 1 row 58.

  17. No term id was found for the name/label efferent lymphatics from fifth or sixth lowermost intercostal spaces in the following 1 row 63.

  18. No term id was found for the name/label efferent lymphatics from third, fourth, and fifth intercostal spaces in the following 1 row 64.

  19. No term id was found for the name/label left anterior mediastinal lymph node in the following 3 rows 67, 68, 69.

  20. No term id was found for the name/label left suprabronchial lymph node of superior lymph collecting vessel of superior inferior lobe of left lung in the following 1 row 68.

  21. No term id was found for the name/label lymphatics of pleura, pericardium, heart, thymus, and left lung in the following 1 row 69.

  22. No term id was found for the name/label cubital fossa lymph node in the following 10 rows 80, 81, 82, 83, 84, 85, 86, 87, 88, 89.

  23. No term id was found for the name/label deep radial lymphatic channel in the following 9 rows 81, 82, 83, 84, 85, 86, 87, 88, 89.

  24. No term id was found for the name/label index finger lateral lymphatic channel #2 in the following 1 row 82.

  25. No term id was found for the name/label index finger medial lymphatic channel #2 in the following 1 row 83.

  26. No term id was found for the name/label middle finger lateral lymphatic channel #2 in the following 1 row 84.

  27. No term id was found for the name/label middle finger medial lymphatic channel #2 in the following 1 row 85.

  28. No term id was found for the name/label palmar arch lymphatic channel #4 in the following 1 row 86.

  29. No term id was found for the name/label ring finger lateral lymphatic channel #2 in the following 1 row 87.

  30. No term id was found for the name/label thumb lateral lymphatic channel #2 in the following 1 row 88.

  31. No term id was found for the name/label thumb medial lymphatic channel #2 in the following 1 row 89.

  32. No term id was found for the name/label epitrochlear lymph node #2 in the following 1 row 90.

  33. No term id was found for the name/label superior ulnar lymph node in the following 20 rows 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110.

  34. No term id was found for the name/label anterior interosseous lymphatic channel in the following 12 rows 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103.

  35. No term id was found for the name/label palmar arch lymphatic channel in the following 11 rows 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103.

  36. No term id was found for the name/label index finger lateral lymphatic channel #3 in the following 1 row 94.

  37. No term id was found for the name/label index finger medial lymphatic channel #3 in the following 1 row 95.

  38. No term id was found for the name/label little finger lateral lymphatic channel #3 in the following 1 row 96.

  39. No term id was found for the name/label little finger medial lymphatic channel #3 in the following 1 row 97.

  40. No term id was found for the name/label middle finger lateral lymphatic channel #3 in the following 1 row 98.

  41. No term id was found for the name/label middle finger medial lymphatic channel #3 in the following 1 row 99.

  42. No term id was found for the name/label ring finger lateral lymphatic channel #3 in the following 1 row 100.

  43. No term id was found for the name/label ring finger medial lymphatic channel #3 in the following 1 row 101.

  44. No term id was found for the name/label thumb lateral lymphatic channel #3 in the following 1 row 102.

  45. No term id was found for the name/label thumb medial lymphatic channel #3 in the following 1 row 103.

  46. No term id was found for the name/label deep ulnar lymphatic channel in the following 5 rows 104, 105, 106, 107, 108.

  47. No term id was found for the name/label little finger lateral lymphatic channel #2 in the following 1 row 105.

  48. No term id was found for the name/label little finger medial lymphatic channel #2 in the following 1 row 106.

  49. No term id was found for the name/label palmar arch lymphatic channel #3 in the following 1 row 107.

  50. No term id was found for the name/label ring finger medial lymphatic channel #2 in the following 1 row 108.

  51. No term id was found for the name/label posterior interosseous lymphatic channel in the following 2 rows 109, 110.

  52. No term id was found for the name/label palmar arch lymphatic channel #2 in the following 1 row 110.

  53. No term id was found for the name/label medial lymphatic pathway of upper arm in the following 8 rows 111, 112, 113, 114, 115, 116, 117, 118.

  54. No term id was found for the name/label epitrochlear lymph node in the following 7 rows 112, 113, 114, 115, 116, 117, 118.

  55. No term id was found for the name/label superficial ulnar lymphatic channel in the following 6 rows 113, 114, 115, 116, 117, 118.

  56. No term id was found for the name/label little finger lateral lymphatic channel in the following 1 row 114.

  57. No term id was found for the name/label little finger medial lymphatic channel in the following 1 row 115.

  58. No term id was found for the name/label middle finger medial lymphatic channel in the following 1 row 116.

  59. No term id was found for the name/label ring finger lateral lymphatic channel in the following 1 row 117.

  60. No term id was found for the name/label ring finger medial lymphatic channel in the following 1 row 118.

  61. No term id was found for the name/label retropectoral lymph vessel in the following 1 row 119.

  62. No term id was found for the name/label subclavicular lymph node in the following 2 rows 120, 121.

  63. No term id was found for the name/label lateral lymphatic pathway of upper arm #2 in the following 1 row 121.

  64. No term id was found for the name/label lateral lymphatic pathway of upper arm in the following 7 rows 124, 125, 126, 127, 128, 129, 130.

  65. No term id was found for the name/label radial lymphatic channel in the following 6 rows 125, 126, 127, 128, 129, 130.

  66. No term id was found for the name/label index finger lateral lymphatic channel in the following 1 row 126.

  67. No term id was found for the name/label index finger medial lymphatic channel in the following 1 row 127.

  68. No term id was found for the name/label middle finger lateral lymphatic channel in the following 1 row 128.

  69. No term id was found for the name/label thumb lateral lymphatic channel in the following 1 row 129.

  70. No term id was found for the name/label thumb medial lymphatic channel in the following 1 row 130.

  71. No term id was found for the name/label transpectoral lymph vessel in the following 1 row 131.

  72. No term id was found for the name/label transverse cervical lymph node in the following 1 row 132.

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.

  1. The term FMA:5832 in the following 8 rows 12, 13, 14, 15, 16, 17, 18, 19 is from another ontology that is not validated in this process.

  2. The term FMA:276805 in the following 12 rows 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 is from another ontology that is not validated in this process.

  3. The term FMA:322627 in the following 2 rows 14, 65 is from another ontology that is not validated in this process.

  4. The term FMA:5831 in the following 1 row 16 is from another ontology that is not validated in this process.

  5. The term FMA:12251 in the following 1 row 17 is from another ontology that is not validated in this process.

  6. The term FMA:5830 in the following 1 row 18 is from another ontology that is not validated in this process.

  7. The term FMA:44313 in the following 1 row 24 is from another ontology that is not validated in this process.

  8. The term FMA:14187 in the following 3 rows 29, 30, 31 is from another ontology that is not validated in this process.

  9. The term FMA:234863 in the following 1 row 31 is from another ontology that is not validated in this process.

  10. The term FMA:9585 in the following 1 row 32 is from another ontology that is not validated in this process.

  11. The term FMA:5841 in the following 4 rows 34, 35, 36, 37 is from another ontology that is not validated in this process.

  12. The term FMA:323951 in the following 12 rows 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 is from another ontology that is not validated in this process.

  13. The term FMA:12765 in the following 20 rows 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57 is from another ontology that is not validated in this process.

  14. The term FMA:5842 in the following 12 rows 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50 is from another ontology that is not validated in this process.

  15. The term FMA:71813 in the following 2 rows 44, 45 is from another ontology that is not validated in this process.

  16. The term FMA:71841 in the following 1 row 45 is from another ontology that is not validated in this process.

  17. The term FMA:233577 in the following 1 row 57 is from another ontology that is not validated in this process.

  18. The term FMA:5840 in the following 4 rows 59, 60, 61, 62 is from another ontology that is not validated in this process.

  19. The term FMA:66175 in the following 1 row 60 is from another ontology that is not validated in this process.

  20. The term FMA:66172 in the following 1 row 61 is from another ontology that is not validated in this process.

  21. The term FMA:66174 in the following 1 row 62 is from another ontology that is not validated in this process.

  22. The term FMA:12250 in the following 1 row 66 is from another ontology that is not validated in this process.

  23. The term FMA:5834 in the following 1 row 70 is from another ontology that is not validated in this process.

  24. The term FMA:5032 in the following 1 row 71 is from another ontology that is not validated in this process.

  25. The term FMA:5955 in the following 1 row 72 is from another ontology that is not validated in this process.

  26. The term FMA:5033 in the following 1 row 73 is from another ontology that is not validated in this process.

  27. The term FMA:12252 in the following 58 rows 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 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 is from another ontology that is not validated in this process.

  28. The term FMA:323948 in the following 2 rows 75, 76 is from another ontology that is not validated in this process.

  29. The term FMA:71743 in the following 34 rows 76, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110 is from another ontology that is not validated in this process.

  30. The term FMA:71749 in the following 42 rows 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118 is from another ontology that is not validated in this process.

  31. The term FMA:234924 in the following 32 rows 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110 is from another ontology that is not validated in this process.

  32. The term FMA:234912 in the following 9 rows 122, 123, 124, 125, 126, 127, 128, 129, 130 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.

row_number s slabel user_slabel o olabel user_olabel deltaIC
26 56 UBERON:0015878 common iliac lymph node common iliac lymph node UBERON:0016386 paraaortic lymph node paraaortic lymph node 11.8079
27 55 UBERON:0015878 common iliac lymph node common iliac lymph node UBERON:0016386 paraaortic lymph node paraaortic lymph node 11.8079
28 54 UBERON:0015878 common iliac lymph node common iliac lymph node UBERON:0016386 paraaortic lymph node paraaortic lymph node 11.8079
29 53 UBERON:0015878 common iliac lymph node common iliac lymph node UBERON:0016386 paraaortic lymph node paraaortic lymph node 11.8079
30 52 UBERON:0015878 common iliac lymph node common iliac lymph node UBERON:0016386 paraaortic lymph node paraaortic lymph node 11.8079
35 55 UBERON:0001543 popliteal lymph node popliteal lymph node UBERON:0009006 deep inguinal lymph node deep inguinal lymph node 6.03847
37 53 UBERON:0015880 external iliac lymph node external iliac lymph node UBERON:0015878 common iliac lymph node common iliac lymph node nan
38 54 UBERON:0015880 external iliac lymph node external iliac lymph node UBERON:0015878 common iliac lymph node common iliac lymph node nan
39 54 UBERON:0009006 deep inguinal lymph node deep inguinal lymph node UBERON:0015880 external iliac lymph node external iliac lymph node nan
40 55 UBERON:0015880 external iliac lymph node external iliac lymph node UBERON:0015878 common iliac lymph node common iliac lymph node nan
41 55 UBERON:0009006 deep inguinal lymph node deep inguinal lymph node UBERON:0015880 external iliac lymph node external iliac lymph node nan
42 56 UBERON:0015881 internal iliac lymph node internal iliac lymph node UBERON:0015878 common iliac lymph node common iliac lymph node 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.

row_number s slabel user_slabel o olabel user_olabel deltaIC
0 58 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0005435 upper part of cisterna chyli cisterna chyli 23.2392
1 33 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0005435 upper part of cisterna chyli cisterna chyli 23.2392
2 34 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0005435 upper part of cisterna chyli cisterna chyli 23.2392
3 38 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0005435 upper part of cisterna chyli cisterna chyli 23.2392
4 56 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0015881 internal iliac lymph node internal iliac lymph node 23.2392
5 49 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0016402 mesocolic lymph node mesocolic lymph node 23.2392
6 51 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0016386 paraaortic lymph node paraaortic lymph node 23.2392
7 59 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0005435 upper part of cisterna chyli cisterna chyli 23.2392
8 43 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0016378 ileocolic lymph node ileocolic lymph node 15.9992
9 54 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0009006 deep inguinal lymph node deep inguinal lymph node 14.1033
10 124 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0035279 supraclavicular lymph node supraclavicular lymph node 14.1033
11 123 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0035279 supraclavicular lymph node supraclavicular lymph node 14.1033
12 63 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0001631 thoracic duct thoracic duct 12.6328
13 64 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0001631 thoracic duct thoracic duct 12.6328
14 65 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0001631 thoracic duct thoracic duct 12.6328
15 66 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0001631 thoracic duct thoracic duct 12.6328
16 20 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0001631 thoracic duct thoracic duct 12.6328
17 67 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0001631 thoracic duct thoracic duct 12.6328
18 70 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0001631 thoracic duct thoracic duct 12.6328
19 71 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0001631 thoracic duct thoracic duct 12.6328
20 72 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0001631 thoracic duct thoracic duct 12.6328
21 74 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0001631 thoracic duct thoracic duct 12.6328
22 73 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0001631 thoracic duct thoracic duct 12.6328
23 132 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0001631 thoracic duct thoracic duct 12.6328
24 21 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0001631 thoracic duct thoracic duct 12.6328
25 32 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0001631 thoracic duct thoracic duct 12.6328
31 53 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0015880 external iliac lymph node external iliac lymph node 11.4312
32 52 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0015878 common iliac lymph node common iliac lymph node 11.4312
33 55 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0001543 popliteal lymph node popliteal lymph node 8.06483
34 42 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0002508 celiac lymph node celiac lymph node 8.06483
36 48 CL:0002138 endothelial cell of lymphatic vessel lymphatic endothelial cell UBERON:0002509 mesenteric lymph node mesenteric lymph node 4.56793

New CL terms

Report

New UBERON terms

Report

Informative reports (valid relationships)

Indirect relationship

Report

Relationship AS has part CT

Report