Suggestions to make valid relationships in the skin table v1.4 (20/03/2024)
Please, add a comment below if you want to address any of the actions to be taken. Please, indicate the number before the comment. IMPORTANT The order of the two classes in these pages is the same as it is found in the tables (e.g. AS4 → AS5)
AS→AS
1 - hypodermis → vasculature of integument
vasculature of integument is too general. A new term is needed.
2 - skin epidermis → stratum corneum of epidermis
This has been solved with the last release in PR #3231
3 - dermis → sebaceous gland
This looks correct, but both in Uberon and FMA is part of the epidermis. It will need to be edited.
4 - dermis → eccrine sweat gland
This looks correct, but both in Uberon and FMA is part of the epidermis. It will need to be edited.
5 - dermis → apocrine gland
This looks correct, but both in Uberon and FMA is part of the epidermis. It will need to be edited.
6 - dermis → vasculature of integument
vasculature of integument is too general. A new term is needed.
7 - skin of body → hypodermis
I have found conflicting information. There are sources that support this relationship. However, there are others that consider the hypodermis ("under the skin" in greek) as part of the integument, but not part of the skin. Uberon follows the second view. However, I might be able to add a relationship that can validate.
8 - hypodermis → skin nerve field
The author's lable 'nerve' and the Uberon term 'skin nerve field' are not equivalent. The 'skin nerve field' is innerveted by nerves.
CT→CT
No issues
AS→CT
1 - skin nerve field → Neuron
Neuron is too broad. Is the relationship expected innervates? There has been some discussion recently about using relationships that are not 'part of' and they are discouraged.
2 - vasculature of integument → endothelial cell
'endothelial cell' is too broad. A compound term would be the best solution, otherwise a new term is required.
3 - hypodermis → B cell
For immune system no action is planned yet. Compound terms can be a solution.
4 - stratum granulosum of epidermis → keratinocyte
The specific keratinocyte for the stratum granulosum in CL is granular cell of epidermis (CL:0002189), it can be used instead of keratinocyte.
5 - hypodermis → macrophage
For immune system no action is planned yet. Compound terms can be a solution.
6 - hypodermis → neutrophil
For immune system no action is planned yet. Compound terms can be a solution.
7 - hypodermis → mast cell
For immune system no action is planned yet. Compound terms can be a solution.
8 - stratum granulosum of epidermis → epidermal Langerhans cell
A 'has part' axiom can be added. Need to confirm that they are present across species in the stratum granulosum.
9 - stratum spinosum of epidermis → epidermal Langerhans cell
A 'has part' axiom can be added.
10 - stratum spinosum of epidermis → Merkel cell
Merkel cells are only found in the stratum basale.
11 - stratum basale of epidermis → epidermal Langerhans cell
A 'has part' axiom can be added. Need to confirm that they are present across species in the stratum basale.
12 - stratum basale of epidermis → melanocyte of skin
That is correct, it should be edited (overlaps Cichorek et al., 2013) or add 'has part'.
13 - hair follicle → keratinocyte stem cell
This relationship is reflected in the 'keratinocyte stem cell' textual definition, but it is missing the axiom.
14 - eccrine sweat gland → myoepithelial cell of sweat gland
A more specific new term can be created.
15 - apocrine gland → myoepithelial cell of sweat gland
A more specific new term can be created.
16 - dermis → myoepithelial cell of sweat gland
A more specific new term can be created.
17 - dermis → mast cell
For immune system no action is planned yet. Compound terms can be a solution.
18 - dermis → macrophage
For immune system no action is planned yet. Compound terms can be a solution.
19 - dermis → T-helper 1 cell
For immune system no action is planned yet. Compound terms can be a solution.
20 - dermis → cytotoxic T cell
For immune system no action is planned yet. Compound terms can be a solution.
21 - dermis → regulatory T cell
For immune system no action is planned yet. Compound terms can be a solution.
22 - dermis → natural killer cell
For immune system no action is planned yet. Compound terms can be a solution.
23 - dermis → group 1 innate lymphoid cell
A compound term would be a good solution, otherwise a new cell term will be the best solution.
24 - dermis → group 2 innate lymphoid cell
A compound term would be a good solution, otherwise a new cell term will be the best solution.
25 - dermis → group 3 innate lymphoid cell
A compound term would be a good solution, otherwise a new cell term will be the best solution.
26 - dermis → B cell
For immune system no action is planned yet. Compound terms can be a solution.
27 - dermis → plasma cell
For immune system no action is planned yet. Compound terms can be a solution.
28 - dermis → neutrophil
For immune system no action is planned yet. Compound terms can be a solution.
29 - dermis → eosinophil
For immune system no action is planned yet. Compound terms can be a solution.
30 - dermis → Schwann cell
This is a very broad term, not specific for skin. A compound term would be a good solution, or add a 'has part' axiom.
31 - dermis → perineurial cell
This might be resolved either with compound terms or with 'has part' axioms.
32 - dermis → vascular associated smooth muscle cell
A compound term would be a good solution, otherwise a new cell term will be the best solution.
33 - dermis → type I cell of carotid body
Is glomus body (aka glomus coccygeum) the structure that the SME was thinking of? All the markers and literature are for glomus cell, but it isn't located in the skin.
34 - dermis → pericyte
This might be resolved either with compound terms or with 'has part' axioms.
35 - dermis → pericyte cell
This row is duplicated and should be erased.
36 - hypodermis → endothelial cell of lymphatic vessel
This might be resolved either with compound terms or with 'has part' axioms.
37 - hypodermis → skin fibroblast
This might be resolved either with compound terms or with 'has part' axioms.
38 - hypodermis → T-helper 1 cell
For immune system no action is planned yet. Compound terms can be a solution.
39 - hypodermis → cytotoxic T cell
For immune system no action is planned yet. Compound terms can be a solution.
40 - hypodermis → regulatory T cell
For immune system no action is planned yet. Compound terms can be a solution.
41 - hypodermis → eosinophil
For immune system no action is planned yet. Compound terms can be a solution.
42 - hypodermis → Schwann cell
This is a very broad term, not specific for hypodermis. A compound term would be a good solution, or add a 'has part' axiom.
43 - hypodermis → perineurial cell
This is a very broad term, not specific for hypodermis. A compound term would be a good solution, or add a 'has part' axiom.
44 - hypodermis → smooth muscle cell
A compound terms would be the best solution, if not I could create a new term.
45 - hypodermis → type I cell of carotid body
Is glomus body (aka glomus coccygeum) the structure that the SME was thinking of? All the markers and literature are for glomus cell, but it isn't located in the skin.
46 - dermis → skin fibroblast
There is a more specific term: fibroblast of dermis (CL:0002551). Currently it validates with 'has part'.