Decide on strategy for shadowing material immaterial entities as material anatomical entities

[cmungall]

See:

• Proposed grouping above material and immaterial entity OBOFoundry/COB#87
• anatomical entity as root-level logically defined class OBOFoundry/COB#99

Let's keep the discussion about the relative benefits of having a distinction and a grouping class over there.

The question here for Uberon is to what extent we "shadow" immaterial entities as material entities, or wholesale move categories over. This would primarily apply to spaces/cavities/sinuses/lumens, but to a certain extent boundaries and similar entities as well.

There are a lot of current entities whose placement is arguable, e.g

• Query UBERON_0006174 pronephric sinus  #2274

Note the GO editors just removed the logical definition that referred to this because we took too long to deal with it!

[dosumis]

Can you elaborate more on what you mean by shadow? I think the confusion is often between the enclosing structure and lumen and whether we have terms for both. It can be important to be able to record the location of some cell types in a lumen rather than the enclosing epithelium or endotherlium - e.g. alvoeolar macrophages and Kupffer cells.

"Pronephric sinus" looks like a case of misleading terminology to me. As Bradley pointed out, the term in XAO seems to refer to a plexus of capillaries.

[gouttegd]

I think the confusion is often between the enclosing structure and lumen

Of note, an immaterial entity may not always have a clearly defined enclosing structure and may not contain something like a lumen.

I’ve recently came across the case of 'intercostal space' (while working on #2453). Such a space has a clear “bottom” boundary (the rib below it), a clear “top” boundary (the rib above it), and I guess the pleura may act as the boundary on the innermost side, but what is the boundary on the outermost side?

And I don’t think the “contents” of the intercostal space (which includes muscles, lymph nodes, and various vessels) can be qualified as a “lumen”, either.

So in such a case, should we have a material entity term shadowing the concept of intercostal space, and what should that term represent exactly?