Obsolete `aggregate regional part of brain`

anitacaron commented 1 year ago

on reflection, this is a poor grouping class:

id: UBERON:0010009
name: aggregate regional part of brain
def: "A regional part of brain consisting of multiple brain regions that are not related through a simple volummetric part of hierarchy, e.g., basal ganglia[NIF]." [NLXANAT:20090509]
subset: non_informative
synonym: "set of nuclei of neuraxis" RELATED [FMA:256381]
xref: FMA:256381
xref: NLXANAT:20090509
intersection_of: UBERON:0034923 ! disconnected anatomical group
intersection_of: has_member UBERON:0002616 ! regional part of brain
intersection_of: part_of UBERON:0000955 ! brain
property_value: editor_note "May be obsoleted." xsd:string

The over-eager logical definition does not match the textual definition, I am not even sure I understand the textual definition

As a grouping class it doesn't do much work, grouping only 3 regions:

[] BFO:0000001 ! entity
- [i] BFO:0000002 ! continuant
  - [i] BFO:0000004 ! independent continuant
    - [i] CARO:0030000 ! biological entity
      - [i] CARO:0000000 ! anatomical entity
        
        [i] UBERON:0010009 ! aggregate regional part of brain
        
        [i] UBERON:0014370 ! extrastriate cortex
        
        [i] UBERON:0010011 ! collection of basal ganglia
        
        [i] UBERON:0023920 ! basal ganglia of rodent
        
        [i] UBERON:0000431 ! ventral medial complex of thalamus

If there really is something distinct about these then this should be asserted using something like pato characteristics (and it should be done consistently with reasonable completeness)

Conservative solution: replace the logical definition with is_a regional part of brain
My preferred solution: obsolete the grouping and rewire the above terms to RPoB

Originally posted by @cmungall in https://github.com/obophenotype/uberon/issues/2495#issuecomment-1208532662

cmungall commented 1 year ago

@tgbugs this came from NIFSTD (which may have taken it from FMA). Do you all have any specific attachment to this term?

tgbugs commented 1 year ago

I think that it is a useful term, but the label is perhaps a bit confusing, because it is explicitly trying to deal only with spatially disconnected structures, or rather structures that have at least one spatial disconnection.

That said, the use of has member demonstrates that this class is mostly an implementation detail because it must explicitly be composed of other regional parts. A more robust solution would be to add spatial disjointness axioms between entities and then classify any term that has at least one pair of spatially disjoint entities as parts as this aggregate class.

In terms of modelling, it seems strange to me to use PATO, because there are no qualities or dispositions that these structures have beyond being composted of parts at least one of which is spatially disconnected. The axioms are being used to capture the reality of a naming convention and clarify that the parts are not spatially contiguous.

You could model aggregateness as a quality ... but that would be like trying to talk about the aggregate nature of bulk sand by saying that it has some aggregate quality rather than just saying that it is composed of of many spatially disjoint sand grains. For sand that might be relevant because being composed of many different grains has certain implications and consequences, however for brain regions there aren't actually any consequences for this because it is just a naming convention, or in some cases it might be that they are derived from some shared developmental origin, but that would be completely by accident.

That said, if there are somehow already aggregate qualities that could be leveraged to deal with spatial disconnectedness then by all means.

dosumis commented 1 year ago

My instinct is that we should drop the class and simplify as Chris suggests.

@tgbugs - do we have a use case for this grouping that any biologist cares about - either directly because they find the classification useful, or indirectly because it will improve our modelling/QC of other things they care about? (See Phil Lord's Pici principle)

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obophenotype / uberon

Obsolete `aggregate regional part of brain` #2627