obsolete anatomical chamber and define pattern as replacement

[dosumis]

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:

1. Chamber has connotations of space, rather than wall: see http://en.wiktionary.org/wiki/chamber
   • suggested solution: use wall instead
2. This term is extremely abstract as a genus - it specifies no granularity at all. It could refer to a chamber in a protein complex in a membrane as easily as some big multi-tissue structure like a segment of gut.

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

[dosumis]

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