Bronchiole hierarchy needs to be revised

[aleixpuigb]

Suggested revision and reasons
Researching to fix issue #2952, I realised that there are some problems in the bronchiole hierarchy:

• bronchiole is 'part of' some 'pulmonary lobule'. This is not true, as not all bronchioles are part of a 'pulmonary lobule'. Edit pulmonary hierarchy #2957
• 'pulmonary acinus' should be 'part of' some 'secondary pulmonary lobule'. Edit pulmonary hierarchy #2957
• Merge between 'pulmonary lobule' and 'secondary pulmonary lobule' #2956
  The text definition of 'pulmonary lobule' defines a 'secondary pulmonary lobule'. The text definition should define also pulmonary acinus, otherwise it is an exact synonym of 'secondary pulmonary lobule', and not a parent term of 'pulmonary acinus'. If a definition can not be found, this term maybe should be merged. According to this reference, "For all intents and purposes, the terms "secondary pulmonary lobule", "primary pulmonary lobule", and "pulmonary lobule" are used synonymously".
• 'pulmonary lobule' 'has part' some 'terminal bronchiole'. This is not true, as 'pulmonary acinus' does not contain 'terminal bronchioles. This can be solved removing this axiom and with ticket Relationship between 'terminal bronchiole' and 'secondary pulmonary lobule' #2952. Edit pulmonary hierarchy #2957
• Add new axioms: 'terminal bronchiole' is ' distally connected to' some 'pulmonary acinus', and 'pulmonary acinus' is 'connected to' some 'terminal bronchiole'. Edit pulmonary hierarchy #2957
• Edit 'pulmonary acinus' #2970

[JoshuaFortriede]

As I noted on #2952, here is my cheat sheet for structures and spaces:

I do not believe I would state that the terminal bronchiole is connected to the pulmonary acinus. The lung is like a big city, where the airways (bronchus, bronchioles, alveolar ducts, alveolus of lung) are smaller and smaller streets into smaller and smaller sections of the city. These sections (lung, bronchopulmonary segment, pulmonary lobule, secondary pulmonary lobule, pulmonary acinus, alveolar sac) represent the different sections of the city (East side vs West side, townships, neighborhoods, sections of neighborhoods, and finally the houses within a cul-de-sac).

As such, I would make sure the relationships match appropriately.

[aleixpuigb]

Thank you for your comment, @JoshuaFortriede. This schematic is very helpful. One of the points above (and I have created a separate ticket to deal with it) is about the 'pulmonary lobule' term. The definition is very similar to 'secondary pulmonary lobule' and what is striking is that in the ontology 'secondary pulmonary lobule' and 'pulmonary acinus' are a subclass of 'pulmonary lobule'. Definition

The smallest anatomical unit of the lung, measuring 0.50 to 2.00 cm in diameter. Each lobule is composed of 4-8 terminal bronchioles and their distal alveolar ducts and sacs. The lobules are separated by fibrous interlobular septa.

According to your schematic, a 'secondary pulmonary lobule' is part of a 'pulmonary lobule'. I have done some research and they are sometimes used as synonyms, but I have not found a reference for a separate entity (from you sheet, it would involve all bronchiolar and alveolar structures + parenchyma). Can you confirm that this is the case and that 'secondary pulmonary lobule' is part_of 'pulmonary lobule' and not is_a 'pulmonary lobule'?

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