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ASCT+B Validation Reports for Spinal_Cord (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 UBERON:0006458 has a different name/label in the source ontology in the following 1 row 114. The name/label in the ASCT+B table is second thoracic spinal cord segment and the one in the ontology is T2 segment of thoracic spinal cord. For reference, the given name/label by SMEs is T2 segment of thoracic spinal cord. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  2. The term UBERON:0006461 has a different name/label in the source ontology in the following 1 row 132. The name/label in the ASCT+B table is second sacral spinal cord segment and the one in the ontology is S2 segment of sacral spinal cord. For reference, the given name/label by SMEs is S2 sacral spinal cord segment. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  3. The term UBERON:0006453 has a different name/label in the source ontology in the following 1 row 117. The name/label in the ASCT+B table is fifth thoracic spinal cord segment and the one in the ontology is T5 segment of thoracic spinal cord. For reference, the given name/label by SMEs is T5 segment of thoracic spinal cord. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  4. The term UBERON:0006464 has a different name/label in the source ontology in the following 1 row 135. The name/label in the ASCT+B table is fifth sacral spinal cord segment and the one in the ontology is S5 segment of sacral spinal cord. For reference, the given name/label by SMEs is S5 sacral spinal cord segment. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  5. The term UBERON:0006466 has a different name/label in the source ontology in the following 1 row 122. The name/label in the ASCT+B table is tenth thoracic spinal cord segment and the one in the ontology is T10 segment of thoracic spinal cord. For reference, the given name/label by SMEs is T10 thoracic spinal cord segment. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  6. The term UBERON:0006452 has a different name/label in the source ontology in the following 1 row 116. The name/label in the ASCT+B table is fourth thoracic spinal cord segment and the one in the ontology is T4 segment of thoracic spinal cord. For reference, the given name/label by SMEs is T4 segment of thoracic spinal cord. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  7. The term UBERON:0006465 has a different name/label in the source ontology in the following 1 row 121. The name/label in the ASCT+B table is ninth thoracic spinal cord segment and the one in the ontology is T9 segment of thoracic spinal cord. For reference, the given name/label by SMEs is T9 segment of thoracic spinal cord. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  8. The term UBERON:0006455 has a different name/label in the source ontology in the following 1 row 119. The name/label in the ASCT+B table is seventh thoracic spinal cord segment and the one in the ontology is T7 segment of thoracic spinal cord. For reference, the given name/label by SMEs is T7 segment of thoracic spinal cord. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  9. The term UBERON:0006468 has a different name/label in the source ontology in the following 1 row 124. The name/label in the ASCT+B table is twelfth thoracic spinal cord segment and the one in the ontology is T12 segment of thoracic spinal cord. For reference, the given name/label by SMEs is T12 thoracic spinal cord segment. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  10. The term UBERON:0006459 has a different name/label in the source ontology in the following 1 row 115. The name/label in the ASCT+B table is third thoracic spinal cord segment and the one in the ontology is T3 segment of thoracic spinal cord. For reference, the given name/label by SMEs is T3 segment of thoracic spinal cord. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  11. The term UBERON:0006460 has a different name/label in the source ontology in the following 1 row 131. The name/label in the ASCT+B table is first sacral spinal cord segment and the one in the ontology is S1 segment of sacral spinal cord. For reference, the given name/label by SMEs is S1 sacral spinal cord segment. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  12. The term UBERON:0006463 has a different name/label in the source ontology in the following 1 row 134. The name/label in the ASCT+B table is fourth sacral spinal cord segment and the one in the ontology is S4 segment of sacral spinal cord. For reference, the given name/label by SMEs is S4 sacral spinal cord segment. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  13. The term UBERON:0006462 has a different name/label in the source ontology in the following 1 row 133. The name/label in the ASCT+B table is third sacral spinal cord segment and the one in the ontology is S3 segment of sacral spinal cord. For reference, the given name/label by SMEs is S3 sacral spinal cord segment. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  14. The term UBERON:0006451 has a different name/label in the source ontology in the following 1 row 111. The name/label in the ASCT+B table is fourth lumbar spinal cord segment and the one in the ontology is L4 segment of lumbar spinal cord. For reference, the given name/label by SMEs is L4 lumbar spinal cord segment. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  15. The term UBERON:0006448 has a different name/label in the source ontology in the following 1 row 108. The name/label in the ASCT+B table is first lumbar spinal cord segment and the one in the ontology is L1 segment of lumbar spinal cord. For reference, the given name/label by SMEs is L1 lumbar spinal cord segment. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  16. The term UBERON:0006467 has a different name/label in the source ontology in the following 1 row 123. The name/label in the ASCT+B table is eleventh thoracic spinal cord segment and the one in the ontology is T11 segment of thoracic spinal cord. For reference, the given name/label by SMEs is T11 thoracic spinal cord segment. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  17. The term UBERON:0006454 has a different name/label in the source ontology in the following 1 row 118. The name/label in the ASCT+B table is sixth thoracic spinal cord segment and the one in the ontology is T6 segment of thoracic spinal cord. For reference, the given name/label by SMEs is T6 segment of thoracic spinal cord. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  18. The term UBERON:0006449 has a different name/label in the source ontology in the following 1 row 110. The name/label in the ASCT+B table is third lumbar spinal cord segment and the one in the ontology is L3 segment of lumbar spinal cord. For reference, the given name/label by SMEs is L3 lumbar spinal cord segment. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  19. The term UBERON:0006457 has a different name/label in the source ontology in the following 1 row 113. The name/label in the ASCT+B table is first thoracic spinal cord segment and the one in the ontology is T1 segment of thoracic spinal cord. For reference, the given name/label by SMEs is T1 segment of thoracic spinal cord. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  20. The term UBERON:0006456 has a different name/label in the source ontology in the following 1 row 120. The name/label in the ASCT+B table is eighth thoracic spinal cord segment and the one in the ontology is T8 segment of thoracic spinal cord. For reference, the given name/label by SMEs is T8 segment of thoracic spinal cord. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  21. The term UBERON:0006447 has a different name/label in the source ontology in the following 1 row 112. The name/label in the ASCT+B table is fifth lumbar spinal cord segment and the one in the ontology is L5 segment of lumbar spinal cord. For reference, the given name/label by SMEs is L5 lumbar spinal cord segment. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.

  22. The term UBERON:0006450 has a different name/label in the source ontology in the following 1 row 109. The name/label in the ASCT+B table is second lumbar spinal cord segment and the one in the ontology is L2 segment of lumbar spinal cord. For reference, the given name/label by SMEs is L2 lumbar spinal cord segment. 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.

  • 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.

s slabel user_slabel o olabel user_olabel row_number deltaIC
23 UBERON:0014620 cervical spinal cord dorsal horn cervical spinal cord dorsal horn UBERON:0014613 cervical spinal cord gray matter cervical spinal cord gray matter 141 2.67116
24 UBERON:0014620 cervical spinal cord dorsal horn cervical spinal cord dorsal horn UBERON:0014613 cervical spinal cord gray matter cervical spinal cord gray matter 142 2.67116
25 UBERON:0014609 thoracic spinal cord dorsal horn thoracic spinal cord dorsal horn UBERON:0014636 thoracic spinal cord gray matter thoracic spinal cord gray matter 145 2.67116
26 UBERON:0014609 thoracic spinal cord dorsal horn thoracic spinal cord dorsal horn UBERON:0014636 thoracic spinal cord gray matter thoracic spinal cord gray matter 146 2.67116
27 UBERON:0014543 lumbar division of spinal cord central canal lumbar division of spinal cord central canal UBERON:0002792 lumbar spinal cord lumbar spinal cord 20 nan
28 UBERON:0014541 thoracic division of spinal cord central canal thoracic division of spinal cord central canal UBERON:0003038 thoracic spinal cord thoracic spinal cord 35 nan
29 UBERON:0014547 sacral division of spinal cord central canal sacral division of spinal cord central canal UBERON:0005843 sacral spinal cord sacral spinal cord 36 nan
30 UBERON:0014619 cervical spinal cord lateral horn cervical spinal cord lateral horn UBERON:0014613 cervical spinal cord gray matter cervical spinal cord gray matter 48 nan
31 UBERON:0014621 cervical spinal cord ventral horn cervical spinal cord ventral horn UBERON:0014613 cervical spinal cord gray matter cervical spinal cord gray matter 49 nan
32 UBERON:0007836 cervical spinal cord ventral commissure cervical spinal cord ventral commissure UBERON:0014613 cervical spinal cord gray matter cervical spinal cord gray matter 50 nan
33 UBERON:0007834 lumbar spinal cord ventral commissure lumbar spinal cord ventral commissure UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 61 nan
34 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 62 nan
35 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 63 nan
36 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 64 nan
37 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 65 nan
38 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 66 nan
39 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 67 nan
40 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 68 nan
41 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 69 nan
42 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 70 nan
43 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 71 nan
44 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 72 nan
45 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 73 nan
46 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 74 nan
47 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 75 nan
48 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 76 nan
49 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 77 nan
50 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 78 nan
51 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 79 nan
52 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 80 nan
53 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 81 nan
54 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 82 nan
55 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 83 nan
56 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 84 nan
57 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 85 nan
58 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 86 nan
59 UBERON:0014607 thoracic spinal cord lateral horn thoracic spinal cord lateral horn UBERON:0014636 thoracic spinal cord gray matter thoracic spinal cord gray matter 127 nan
60 UBERON:0014610 thoracic spinal cord ventral horn thoracic spinal cord ventral horn UBERON:0014636 thoracic spinal cord gray matter thoracic spinal cord gray matter 128 nan
61 UBERON:0007837 thoracic spinal cord ventral commissure thoracic spinal cord ventral commissure UBERON:0014636 thoracic spinal cord gray matter thoracic spinal cord gray matter 129 nan
62 UBERON:0007835 sacral spinal cord ventral commissure sacral spinal cord ventral commissure UBERON:0029503 sacral spinal cord gray matter sacral spinal cord gray matter 136 nan
63 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 143 nan
64 UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn UBERON:0029636 lumbar spinal cord gray matter lumbar spinal cord gray matter 144 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:0000540 neuron Medial Inhibitory Neuron 1 UBERON:0031906 lumbar spinal cord lateral horn lumbar spinal cord lateral horn 103 66.7665
1 CL:0000540 neuron Medial Excitatory Neuron 4 UBERON:0031906 lumbar spinal cord lateral horn lumbar spinal cord lateral horn 102 66.7665
2 CL:0000540 neuron Medial Excitatory Neuron 3 UBERON:0031906 lumbar spinal cord lateral horn lumbar spinal cord lateral horn 101 66.7665
3 CL:0000540 neuron Medial Excitatory Neuron 2 UBERON:0031906 lumbar spinal cord lateral horn lumbar spinal cord lateral horn 100 66.7665
4 CL:0000540 neuron Medial Excitatory Neuron 1 UBERON:0031906 lumbar spinal cord lateral horn lumbar spinal cord lateral horn 99 66.7665
5 CL:0000115 Endothelial Cell Endothelial Cell UBERON:0030276 lumbar spinal cord ventral horn lumbar spinal cord ventral horn 98 47.4061
6 CL:0000115 Endothelial Cell Endothelial Cell UBERON:0031906 lumbar spinal cord lateral horn lumbar spinal cord lateral horn 107 47.4061
7 CL:0000115 Endothelial Cell Endothelial Cell UBERON:0026386 lumbar spinal cord white matter lumbar spinal cord white matter 25 47.4061
8 CL:0000115 Endothelial Cell Endothelial Cell UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn 86 40.1686
9 CL:0000127 Astrocyte Astrocyte UBERON:0031906 lumbar spinal cord lateral horn lumbar spinal cord lateral horn 105 32.6485
10 CL:0000127 Astrocyte Astrocyte UBERON:0030276 lumbar spinal cord ventral horn lumbar spinal cord ventral horn 96 32.6485
11 CL:0000127 Astrocyte Astrocyte UBERON:0026386 lumbar spinal cord white matter lumbar spinal cord white matter 23 32.6485
12 CL:0000128 Oligodendrocyte Oligodendrocyte UBERON:0030276 lumbar spinal cord ventral horn lumbar spinal cord ventral horn 95 27.8939
13 CL:0000128 Oligodendrocyte Oligodendrocyte UBERON:0026386 lumbar spinal cord white matter lumbar spinal cord white matter 21 27.8939
14 CL:0000128 Oligodendrocyte Oligodendrocyte UBERON:0031906 lumbar spinal cord lateral horn lumbar spinal cord lateral horn 104 27.8939
15 CL:0002453 Oligodendrocyte Precursor Cell Oligodendrocyte Precursor Cell UBERON:0026386 lumbar spinal cord white matter lumbar spinal cord white matter 22 25.9025
16 CL:0000127 Astrocyte Astrocyte UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn 84 25.411
17 CL:0000129 microglial cell Microglia UBERON:0030276 lumbar spinal cord ventral horn lumbar spinal cord ventral horn 97 23.7884
18 CL:0000129 microglial cell Microglia UBERON:0026386 lumbar spinal cord white matter lumbar spinal cord white matter 24 23.7884
19 CL:0000129 microglial cell Microglia UBERON:0031906 lumbar spinal cord lateral horn lumbar spinal cord lateral horn 106 23.7884
20 CL:0000128 Oligodendrocyte Oligodendrocyte UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn 83 20.6563
21 CL:0000129 microglial cell Microglia UBERON:0014638 lumbar spinal cord dorsal horn lumbar spinal cord dorsal horn 85 16.5508
22 CL:0000065 Ependymal Cell Ependymal Cell UBERON:0014543 lumbar division of spinal cord central canal lumbar division of spinal cord central canal 20 16.3703

New CL terms

Report

New UBERON terms

Report

Informative reports (valid relationships)

Indirect relationship

Report

Relationship AS has part CT

Report