ASCT+B Validation Reports for Skin (2024-11-20)
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:0002073 has a different name/label in the source ontology in the following 1 row 34. The name/label in the ASCT+B table is hair follicle bulge and the one in the ontology is hair follicle. For reference, the given name/label by SMEs is hair bulge. Please correct it in the columns AS/N/LABEL or CT/N/LABEL in the ASCT+B table.
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The term CL:0000669 has a different name/label in the source ontology in the following 1 row 66. The name/label in the ASCT+B table is pericyte cell and the one in the ontology is pericyte. For reference, the given name/label by SMEs is Pericyte. 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:0002033 has a different name/label in the source ontology in the following 1 row 31. The name/label in the ASCT+B table is arrector pili muscle of vibrissa and the one in the ontology is arrector muscle of hair. For reference, the given name/label by SMEs is Arrector pili muscle. 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 term id was found for the name/label connective tissue sheath in the following 1 row 32.
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 | |
|---|---|---|---|---|---|---|---|---|
| 8 | UBERON:0035549 | vasculature of integument | Blood vessels | UBERON:0002072 | hypodermis | Subcutaneous | 82 | 1.21635 |
| 9 | UBERON:0008974 | apocrine gland | Apocrine glands | UBERON:0001820 | sweat gland | sweat gland | 37 | 1.04392 |
| 17 | UBERON:0000412 | dermal papilla | Hair papilla | UBERON:0002073 | hair follicle | Hair follicles | 25 | nan |
| 18 | UBERON:0005184 | hair medulla | medulla | UBERON:0002074 | hair shaft | Hair shaft | 30 | nan |
| 19 | UBERON:0002073 | hair follicle | hair bulge | UBERON:0002073 | hair follicle | Hair follicles | 34 | nan |
| 20 | UBERON:0001821 | sebaceous gland | Sebaceous glands | UBERON:0002073 | hair follicle | Hair follicles | 35 | nan |
| 40 | UBERON:0035549 | vasculature of integument | Blood vessels | UBERON:0002067 | dermis | Dermis | 62 | nan |
| 45 | UBERON:0002072 | hypodermis | Subcutaneous | UBERON:0002097 | skin of body | skin | 68 | nan |
| 47 | UBERON:0002072 | hypodermis | Subcutaneous | UBERON:0002097 | skin of body | skin | 69 | nan |
| 48 | UBERON:0002072 | hypodermis | Subcutaneous | UBERON:0002097 | skin of body | skin | 70 | nan |
| 50 | UBERON:0002072 | hypodermis | Subcutaneous | UBERON:0002097 | skin of body | skin | 71 | nan |
| 51 | UBERON:0002072 | hypodermis | Subcutaneous | UBERON:0002097 | skin of body | skin | 72 | nan |
| 52 | UBERON:0002072 | hypodermis | Subcutaneous | UBERON:0002097 | skin of body | skin | 73 | nan |
| 54 | UBERON:0002072 | hypodermis | Subcutaneous | UBERON:0002097 | skin of body | skin | 74 | nan |
| 56 | UBERON:0002072 | hypodermis | Subcutaneous | UBERON:0002097 | skin of body | skin | 75 | nan |
| 58 | UBERON:0002072 | hypodermis | Subcutaneous | UBERON:0002097 | skin of body | skin | 76 | nan |
| 59 | UBERON:0002072 | hypodermis | Subcutaneous | UBERON:0002097 | skin of body | skin | 77 | nan |
| 60 | UBERON:0002072 | hypodermis | Subcutaneous | UBERON:0002097 | skin of body | skin | 78 | nan |
| 62 | UBERON:0002072 | hypodermis | Subcutaneous | UBERON:0002097 | skin of body | skin | 79 | nan |
| 63 | UBERON:0007121 | skin nerve field | nerve | UBERON:0002072 | hypodermis | Subcutaneous | 79 | nan |
| 64 | UBERON:0002072 | hypodermis | Subcutaneous | UBERON:0002097 | skin of body | skin | 80 | nan |
| 66 | UBERON:0002072 | hypodermis | Subcutaneous | UBERON:0002097 | skin of body | skin | 81 | nan |
| 68 | UBERON:0002072 | hypodermis | Subcutaneous | UBERON:0002097 | skin of body | skin | 82 | nan |
| 69 | UBERON:0002072 | hypodermis | Subcutaneous | UBERON:0002097 | skin of body | skin | 83 | nan |
| 71 | UBERON:0002072 | hypodermis | Subcutaneous | UBERON:0002097 | skin of body | skin | 84 | 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 | Neuron | UBERON:0007121 | skin nerve field | nerve | 59 | 66.7927 |
| 1 | CL:0000540 | Neuron | Neuron | UBERON:0007121 | skin nerve field | nerve | 79 | 66.7927 |
| 2 | CL:0000115 | endothelial cell | Endothelial cell | UBERON:0035549 | vasculature of integument | Blood vessels | 62 | 17.8563 |
| 3 | CL:0000115 | endothelial cell | Endothelial cell | UBERON:0035549 | vasculature of integument | Blood vessels | 82 | 17.8563 |
| 4 | CL:0000236 | B cell | B cell | UBERON:0002072 | hypodermis | Subcutaneous | 76 | 15.9782 |
| 5 | CL:0000312 | keratinocyte | Keratinocyte (Granular) | UBERON:0002069 | stratum granulosum of epidermis | Stratum granulosum (SG) | 13 | 12.269 |
| 6 | CL:0000235 | macrophage | Macrophage | UBERON:0002072 | hypodermis | Subcutaneous | 71 | 6.93625 |
| 7 | CL:0000775 | neutrophil | Neutrophil | UBERON:0002072 | hypodermis | Subcutaneous | 77 | 2.17912 |
| 10 | CL:0000097 | mast cell | Mast cell | UBERON:0002072 | hypodermis | Subcutaneous | 72 | 0.175747 |
| 11 | CL:0002457 | epidermal Langerhans cell | Langerhans cell | UBERON:0002069 | stratum granulosum of epidermis | Stratum granulosum (SG) | 14 | nan |
| 12 | CL:0002457 | epidermal Langerhans cell | Langerhans cell | UBERON:0002026 | stratum spinosum of epidermis | Stratum spinosum (SS) | 16 | nan |
| 13 | CL:0000242 | Merkel cell | Merkel cell | UBERON:0002026 | stratum spinosum of epidermis | Stratum spinosum (SS) | 17 | nan |
| 14 | CL:0002457 | epidermal Langerhans cell | Langerhans cell | UBERON:0002025 | stratum basale of epidermis | Stratum basale (SB) | 19 | nan |
| 15 | CL:1000458 | melanocyte of skin | Melanocyte | UBERON:0002025 | stratum basale of epidermis | Stratum basale (SB) | 21 | nan |
| 16 | CL:0002483 | hair follicle melanocyte | Melanocyte | UBERON:0005932 | bulb of hair follicle | Hair bulb | 24 | nan |
| 21 | CL:1000417 | myoepithelial cell of sweat gland | myoepithelial cell | UBERON:0000423 | eccrine sweat gland | Eccrine (sweat) glands | 36 | nan |
| 22 | CL:1000417 | myoepithelial cell of sweat gland | myoepithelial cell | UBERON:0008974 | apocrine gland | Apocrine glands | 37 | nan |
| 23 | CL:0002337 | keratinocyte stem cell | keratinocyte stem cell | UBERON:0002073 | hair follicle | Hair follicles | 38 | nan |
| 24 | CL:1000417 | myoepithelial cell of sweat gland | myoepithelial cell | UBERON:0002067 | dermis | Dermis | 40 | nan |
| 25 | CL:0000097 | mast cell | Mast cell | UBERON:0002067 | dermis | Dermis | 42 | nan |
| 26 | CL:0000235 | macrophage | Macrophage | UBERON:0002067 | dermis | Dermis | 47 | nan |
| 27 | CL:0000545 | T-helper 1 cell | T helper | UBERON:0002067 | dermis | Dermis | 48 | nan |
| 28 | CL:0000910 | cytotoxic T cell | T killer | UBERON:0002067 | dermis | Dermis | 49 | nan |
| 29 | CL:0000815 | regulatory T cell | T reg | UBERON:0002067 | dermis | Dermis | 50 | nan |
| 30 | CL:0000623 | natural killer cell | Natural killer cell | UBERON:0002067 | dermis | Dermis | 51 | nan |
| 31 | CL:0001067 | group 1 innate lymphoid cell | Natural killer cell / Innate lymphoid cell 1 | UBERON:0002067 | dermis | Dermis | 52 | nan |
| 32 | CL:0001069 | group 2 innate lymphoid cell | Innate lymphoid cell 2 | UBERON:0002067 | dermis | Dermis | 53 | nan |
| 33 | CL:0001071 | group 3 innate lymphoid cell | Innate lymphoid cell 3 | UBERON:0002067 | dermis | Dermis | 54 | nan |
| 34 | CL:0000236 | B cell | B cell | UBERON:0002067 | dermis | Dermis | 55 | nan |
| 35 | CL:0000786 | plasma cell | Plasma cell | UBERON:0002067 | dermis | Dermis | 56 | nan |
| 36 | CL:0000775 | neutrophil | Neutrophil | UBERON:0002067 | dermis | Dermis | 57 | nan |
| 37 | CL:0000771 | eosinophil | Eosinophil | UBERON:0002067 | dermis | Dermis | 58 | nan |
| 38 | CL:0002573 | Schwann cell | Schwann cell | UBERON:0002067 | dermis | Dermis | 60 | nan |
| 39 | CL:0002576 | perineurial cell | perineurial cells | UBERON:0002067 | dermis | Dermis | 61 | nan |
| 41 | CL:0000359 | vascular associated smooth muscle cell | Perivascular smooth muscle cell | UBERON:0002067 | dermis | Dermis | 63 | nan |
| 42 | CL:0002292 | type I cell of carotid body | Glomus cell | UBERON:0002067 | dermis | Dermis | 64 | nan |
| 43 | CL:0000669 | pericyte | pericyte | UBERON:0002067 | dermis | Dermis | 65 | nan |
| 44 | CL:0000669 | pericyte | Pericyte | UBERON:0002067 | dermis | Dermis | 66 | nan |
| 46 | CL:0002138 | endothelial cell of lymphatic vessel | Lymphatic | UBERON:0002072 | hypodermis | Subcutaneous | 68 | nan |
| 49 | CL:0002620 | skin fibroblast | Fibroblast | UBERON:0002072 | hypodermis | Subcutaneous | 70 | nan |
| 53 | CL:0000545 | T-helper 1 cell | T helper | UBERON:0002072 | hypodermis | Subcutaneous | 73 | nan |
| 55 | CL:0000910 | cytotoxic T cell | T killer | UBERON:0002072 | hypodermis | Subcutaneous | 74 | nan |
| 57 | CL:0000815 | regulatory T cell | T reg | UBERON:0002072 | hypodermis | Subcutaneous | 75 | nan |
| 61 | CL:0000771 | eosinophil | Eosinophil | UBERON:0002072 | hypodermis | Subcutaneous | 78 | nan |
| 65 | CL:0002573 | Schwann cell | Schwann cell | UBERON:0002072 | hypodermis | Subcutaneous | 80 | nan |
| 67 | CL:0002576 | perineurial cell | Perineural cell | UBERON:0002072 | hypodermis | Subcutaneous | 81 | nan |
| 70 | CL:0000359 | vascular associated smooth muscle cell | Perivascular smooth muscle cell | UBERON:0002072 | hypodermis | Subcutaneous | 83 | nan |
| 72 | CL:0002292 | type I cell of carotid body | Glomus cell | UBERON:0002072 | hypodermis | Subcutaneous | 84 | nan |