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Addresses #2952 terminal bronchiole part of secondary pulmonary lobule #2953

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Jul 18, 2023
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Addresses #2952 terminal bronchiole part of secondary pulmonary lobule #2953

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Addresses #2952 terminal bronchiole part of secondary pulmonary lobule
aleixpuigb Jul 6, 2023
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Merge branch 'master' into 2952_terminal_bronchiole-secondary_pulmona…
aleixpuigb Jul 10, 2023
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Minor edit in definition
aleixpuigb Jul 18, 2023
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3 changes: 2 additions & 1 deletion src/ontology/uberon-edit.obo
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Expand Up @@ -43847,7 +43847,7 @@ property_value: structure_notes "lacks submucosa and cartilage plates; they have
[Term]
id: UBERON:0002187
name: terminal bronchiole
def: "The last conducting structure of non-respiratory bronchioles; after this point, the airways have alveoli in their walls." [ISBN:0-397-51047-0, MGI:cwg, MP:0002268]
def: "A bronchiole that is part of a secondary pulmonary lobule and the last conducting structure of a non-respiratory bronchiole; after this point, the airways have alveoli in their walls." [ISBN:0-397-51047-0, MGI:cwg, MP:0002268, PMID:16543587]
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Given the ambiguity you detail in the linked issue, keeping the original definition (which doesn't seem contested) and using the relationship "overlaps" may be a less controversial solution. Will defer to @JoshuaFortriede or another SME for confirmation.

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Webb 2006 (paywall article) states:

Each secondary lobule is supplied by a small bronchiole

and Ohno 2021 states:

The secondary pulmonary lobule is supplied by a lobular bronchiole

These definitions match my understanding; that the primary bronchiole is the street into the neighborhood (secondary pulmonary lobule), and the terminal bronchioles are the main streets contained within that neighborhood. As such, I believe the new definition works.

I would also suggest adding that the terminal bronchiole is between the primary bronchiole and respiratory bronchiole. Specifically the terminal is distal to the primary, and proximal to the respiratory.

Here is my cheat sheet that I made to keep these airways/structures and space/segments together. The "Type" or RO might not be completely accurate.
image

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@aleixpuigb aleixpuigb Jul 14, 2023 •
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Thank you for your input and clarification, @JoshuaFortriede. The cheat sheet is very useful!

I would also suggest adding that the terminal bronchiole is between the primary bronchiole and respiratory bronchiole. Specifically the terminal is distal to the primary, and proximal to the respiratory.

In a different ticket #2957 I have already added 'terminal bronchiole' SubclassOf ' distally connected to' some 'respiratory bronchiole'. However, mice have none or few respiratory bronchioles, and therefore 'terminal bronchioles' are connected to alveolar ducts. Therefore I will have to revert that axiom in a different ticket. On the other side, the lobular bronchiole can be found between the primary bronchiole and the respiratory bronchiole. I would like to investigate a bit more before adding that axiom.

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Consider using singular form in the def:

A bronchiole that is part of a secondary pulmonary lobule and the last conducting structure of a non-respiratory bronchiole; after this point, the airways have alveoli in their walls.

subset: pheno_slim
subset: uberon_slim
synonym: "bronchioli terminalis" RELATED LATIN [Wikipedia:Terminal_bronchiole]
Expand All @@ -43862,6 +43862,7 @@ xref: SCTID:278981008
xref: UMLS:C0225666 {source="ncithesaurus:Terminal_Bronchiole"}
xref: Wikipedia:Terminal_bronchiole
is_a: UBERON:0002186 ! bronchiole
relationship: part_of UBERON:0010369 ! secondary pulmonary lobule
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See above. Consider overlaps.

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Given Joshua's comment, I think part_of is ok

relationship: distally_connected_to UBERON:0002188 ! respiratory bronchiole
relationship: distally_connected_to UBERON:0008874 ! pulmonary acinus
property_value: depicted_by "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI
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