Suggestions to make valid relationships in the lung table v1.3 (30/05/2023)
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 - Secondary Pulmonary Lobule → terminal bronchiole
secondary pulmonary lobule should be 'part of' some 'terminal bronchiole' PMID:3259815 Status: #2953
2 - subsegmental bronchus → cartilage of bronchus
It needs a 'has part' relationship. Status: Completed PR 204
3 - pulmonary alveolar duct → alveolus of lung
This relationship is difficult to validate, because single alveolus can be found as scattered outpockets of the respiratory bronchiole. I would recommend to have the alveolus of lung in the next column of pulmonary acinus. See issue 286
New hierarchy proposed (03/06/2023): Secondary pulmonary lobule → terminal bronchiole → with cells and ECM that compose that structure
Secondary pulmonary lobule →terminal bronchiole → pulmonary acinus → respiratory bronchiole → with the cells and ECM that compose the respiratory bronchiole
Secondary pulmonary lobule →terminal bronchiole → pulmonary acinus → respiratory bronchiole → alveolus of respiratory bronchiole (new term - or leave as alveolus of lung but this will come up again as part for the pulmonary acinus) → with the cells and ECM that compose that simple alveolar structure
Secondary pulmonary lobule →terminal bronchiole → pulmonary acinus → alveolar duct (that are vital to but not part for respiratory bronchioles) → with the cells and ECM that compose the alveolar ducts
Secondary pulmonary lobule →terminal bronchiole → pulmonary acinus → alveolus of lung →pulmonary alveolar parenchyma → with the cells and ECM that compose the parenchyma
4 - subsegmental bronchus → lobar bronchus mesenchyme
It needs a new term (either general bronchus mesenchyme and add 'has part' axiom, or subsegmental bronchus mesenchyme). Status: temporally it has been added 'has part' some 'lung mesenchyme' PR 204. However, GP requested NTR “mesenchyme of subsegmental bronchus”.
5 - subsegmental bronchus → bronchus smooth muscle
It needs a 'has part' relationship. Status: Completed PR 204
6 - lung → immune system
No actions for now.
7 - epithelium of segmental bronchus → bronchus submucosal gland
The bronchus submucosal gland are not part of an epithelium. I can add a 'has part' some 'bronchus sumucosal gland' to segmental bronchus, and this term replaces epithelium of segmental bronchus. Status: Has part completed, class needs to be changed PR 204
8 - pulmonary alveolar duct → pulmonary alveolar parenchyma
pulmonary alveolar parenchyma is parenchyma and (part of some alveolus of lung). Therefore, mapping to alveolus of lung instead of pulmonary alveolar duct will validate. Status: completed
9 - Tracheobronchial tree → pulmonary nerve plexus
It should have an overlaps relation.
10 - lobar bronchus → bronchus submucosal gland
It needs a 'has part' relationship. Status: Completed PR 204
11 - lobar bronchus → bronchus connective tissue
There is a lobar bronchus connective tissue UBERON:0003591. Status: completed
12 - lobar bronchus → bronchus smooth muscle
It needs a 'has part' relationship. Status: Completed PR 204
13 - lobar bronchus → cartilage of bronchus
It needs a 'has part' relationship. Status: Completed PR 204
14 - Segmental Bronchus → bronchus smooth muscle
It needs a 'has part' relationship. Status: Completed PR 204
15 - Segmental Bronchus → cartilage of bronchus
I can add for both structures a 'has part' some 'cartilage of bronchus' axiom (UBERON:0001956) (also for subsegmental bronchus). Status: Completed PR 204
16 - Segmental Bronchus → lobar bronchus mesenchyme
This can't validate, as the lobar bronchus masenchyme should map to lobar bronchus only. This problem will also occur for subsegmental bronchus once Ubergraph gets the new release. I can add for both structures a 'has part' some 'lung mesenchyme' axiom (UBERON:0004883) and that terms substitutes lobar bronchus mesenchyme. Second part Status: Completed PR 204
17 - subsegmental bronchus → epithelium of segmental bronchus
The correct term would be epithelium of bronchus (UBERON:0002031). It needs a has part axiom. However, in this case a new term might be beneficial.
18 - subsegmental bronchus → primary bronchiole
Primary bronchiole needs to be edited. This is tricky, because according of some literature, there is a ssub-subsegmental bronchus, and therefore any axiom would be not true.
19 - respiratory bronchiole → pulmonary alveolar duct
There should be a connected to relationship.
20 - pulmonary alveolar parenchyma → pulmonary capillary
Not sure of the expected relationship expected.
21 - pulmonary lymphatic vessel → respiratory system lymphatic vessel endothelium
It needs a 'has part' relationship. Status: Completed PR 204
22 - immune system → Pulmonary Acinus
We are still working for a solution for the immune system, but pulmonary acinus (and all child terms) are not part of the immune system. I would recommend to delete it or 'immune system' as last AS column.
CT→CT
No issues
AS→CT
1 - terminal bronchiole epithelium → club cell
It needs a 'has part' relationship.
2 - epithelium of segmental bronchus → club cell
It needs a 'has part' relationship.
3 - epithelium of respiratory bronchiole → club cell
It needs a 'has part' relationship.
4 - epithelium of bronchiole → club cell
It needs a 'has part' relationship.
5 - pulmonary alveolar parenchyma → type I pneumocyte
It needs a 'has part' relationship.
6 - pulmonary alveolar parenchyma → type II pneumocyte
It needs a 'has part' relationship.
7 - epithelium of segmental bronchus → brush cell of bronchus
It needs a 'has part' relationship.
8 - epithelium of segmental bronchus → basal epithelial cell of tracheobronchial tree
It needs a 'has part' relationship.
9 - epithelium of lobar bronchus → basal epithelial cell of tracheobronchial tree
It needs a 'has part' relationship.
10 - epithelium of lobar bronchus → ciliated cell of the bronchus
It needs a 'has part' relationship.
11 - epithelium of segmental bronchus → ciliated cell of the bronchus
It needs a 'has part' relationship.
12 - bronchus smooth muscle → bronchial smooth muscle cell
It needs a 'has part' relationship.
13 - respiratory system venous endothelium → adult endothelial progenitor cell
The textual definition of an adult endothelial progenitor cell is the following:
An adult angioblastic cell released from the bone marrow, or from the kidney in some teleost species, capable of blood circulation and participation in angiogenesis by differentiating into blood vessel endothelial cells.
Is this cell type meant to be resident or circulating? In case it is a resident type, it would need a new term. In case it is circulating, we will need a similar soultion as immune cells.
14 - respiratory system lymphatic vessel endothelium → endothelial cell of respiratory system lymphatic vessel
It is missing a part of relationship.
15- pulmonary alveolar parenchyma → lung pericyte
It needs a 'has part' relationship.
16 - pulmonary nerve plexus → sympathetic neuron
It needs a 'has part' relationship.
17 - epithelium of segmental bronchus → pulmonary ionocyte
It needs a 'has part' relationship.
18 - epithelium of lobar bronchus → pulmonary ionocyte
It needs a 'has part' relationship.
19 - cartilage of bronchus → tracheobronchial chondrocyte
It needs a 'has part' relationship.
20 - lobar bronchus mesenchyme → tracheobronchial smooth muscle cell
It needs a 'has part' relationship.
21 - epithelium of segmental bronchus → lung goblet cell
It needs a 'has part' relationship.
22 - epithelium of segmental bronchus → lung neuroendocrine cell
It needs a 'has part' relationship. This is a very general term, are there lung neuroendocrine cell subtypes needed?
23 - epithelium of bronchiole → lung ciliated cell
It needs a 'has part' relationship.
24 - terminal bronchiole epithelium → lung ciliated cell
It needs a 'has part' relationship.
25 - pulmonary capillary → alveolar capillary type 1 endothelial cell
According to this reference it is probably missing a part of relationship.
26 - pulmonary capillary → alveolar capillary type 2 endothelial cell
According to this reference it is probably missing a part of relationship.
27 - pulmonary alveolar parenchyma → alveolar type 1 fibroblast cell
It is missing a part of relationship.
28 - pulmonary alveolar parenchyma → alveolar type 2 fibroblast cell
It is missing a part of relationship. Include synonym 'resident interstitial lung fibroblasts'.
29 - respiratory system venous endothelium → vein endothelial cell of respiratory system
It is missing a part of relationship.
30 - smooth muscle tissue of terminal bronchiole → bronchiolar smooth muscle cell
It needs a 'has part' relationship.
31 - smooth muscle tissue of bronchiole → bronchiolar smooth muscle cell
It is missing a part of relationship.
32 - smooth muscle tissue of respiratory bronchiole → bronchiolar smooth muscle cell
It needs a 'has part' relationship.
33 - immune system → lung megakaryocyte
Megakaryocytes are not considered to be part of the immune system. It can directly map to lung.