Request for comments: model anatomical spaces as material entities, consistent with GO

Preamble: this is a large change ontologically, as such it will require considerable discussion and buy in from stakeholders, and would not be undertaken lightly.

Proposal: Consider modeling UBERON:0000464 anatomical space as a material entity.

The details may vary, the essence would change the def from:

Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures.

To something like

Material anatomical entity of three dimensions, that is the contents of <previous definition of "anatomical space">

Advantages:

• consistent with GO (e.g lysosomal lumen is the contents)
• material entities can have physical properties such as acidity, temperature. If we make lysosomal lumen immaterial, we have to consider how allow for statements about properties such as acidity
• current version of COB does not have a grouping 'anatomical entity', which means AOs would be 'cleaved in two' by COB see https://github.com/OBOFoundry/COB/issues/87
• IEs in general cause many problems. Even OWL/BFO experts make frequent errors in axiomatization
• IEs confuse domain scientists and curators

Considerations for linked ontologies/annotations

• in axiomatization relationship to FMA we could have something like: Uberon/GO:lumen-of-X = occupies some (FMA:X-cavity and part-of some Homo sapiens)
• I believe the MOD AOs would be good with this
• would need to be synced with CARO, which itself would need to be synced with PO

This proposal pertains to spaces. It could also be extended to include lines, but it may be OK for these to live in a separate hierarchy.

Start by reading the proposal and its considerations for COB, FMA, CARO, PO, and linked annotations, including COB issue 87. This is complete only after stakeholder agreement on the anatomical-space model and the required ontology axiomatization and synchronization work are defined.