Open dosumis opened 9 years ago
Notes on reasoning about shape via PATO
Subclasses of 'structure, cavities'
Right now, pato has:
cystic monocystic polycystic fluid-filled hollow tubular imperforate inflated lumenized perforate cribiform saccular uninflated unlumenized vacuolated
Maybe:
lumenized tubular sacular
Note - lumenized is different from hollow in that a lumen apparently has substances in it. But from http://en.wikipedia.org/wiki/Lumen_%28anatomy%29, examples include vagina and bronchi. Also commonly used for trachea. So perhaps make lumen - typically contains some substance.
bearer_of some lumenized subClassOf 'has part' some lumen bearer_of some unlumenized subClassOf not ('has part' some lumen)
How to document the patterns using this - in CARO or as separate patterns?
'should lumen be in CARO? Should we have (other) abstract geometrical classes defined using CARO: 'anatomical tube' , 'anatomical tube wall' etc as a way of recording design patterns?
"anatomical tube" comment: Not to be used as an asserted genus term EquivalentTo: anatomical structure that 'bearer of' some tubular SubClassOf has_part some lumen
'region of anatomical tube wall'. A part of the wall of an anatomical tube that spans the full thickness of the wall for its entire lateral extent. subClassOf not has_part some 'anatomical space'
segment of anatomical tube: "A subdivision of an anatomical tube along its long axis"
X wall: The region of the Y wall coincident with X
SubClassOf region of gut wall SubClassOf part_of some stomach
We currently have
'anatomical chamber': "Anatomical structure that surrounds an immaterial anatomical entity." subClassOf: 'connected anatomical structure'
The aim of this term is to provide a way to refer to the the wall of a tube or sac because the general terms for tubes and sacs include the lumen as parts.
e.g. stomach < po lumen of stomach < po stomach chamber: "All the bits of the stomach, minus the lumen." (not has_part some 'anatomical space')
There are a couple of problems with this:
Proposed solution from specific example:
'region of gut wall'. A part of the gut wall - including all layers.
subClassOf not has_part some 'anatomical space'
stomach wall: The region of gut wall coincindent with the stomach. SubClassOf region of gut wall SubClassOf part_of some stomach
TODO: Before we obsolete the term, we need to come up a with a more generic way to document this design pattern & release it as part of CARO 2.0