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Positioning 'life cycle' and 'life cycle stage' under 'process' #3464

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ddooley opened this issue Jan 17, 2025 · 1 comment
Open

Positioning 'life cycle' and 'life cycle stage' under 'process' #3464

ddooley opened this issue Jan 17, 2025 · 1 comment

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@ddooley
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ddooley commented Jan 17, 2025

Uberon term
life cycle
life cycle stage

Suggested revision and reasons
COB had a discussion about various occurrent subclasses such as UBERON's 'life cycle', and the suggestion for COB compatibility was to move 'life cycle' and 'life cycle stage' from its current "processual entity" parent to be under "process" instead, thus helping eliminate "occurent" class in COB integrated ontologies.

I see however COB still needs to find a home for life cycle temporal boundary . I think COB needs to recognize use of some OWLTime classes directly, where this would find a home, or indirectly by importing BFO "temporal region" as well.

@cmungall
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Do you want to make a COB ticket or place alongside this?

I don't think Uberon cares about upper level representation of this, we have 3 terms that appear to be useless vestiges of the heady days of over-formalization:

  • [] UBERON:0000000 ! processual entity "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity."
    • [i] UBERON:0035943 ! life cycle temporal boundary "A temporal boundary connecting two life cycle stages that follow in immediate succession. A temporal boundary is an abstract, instantaneous entity."
      • [i] UBERON:0035946 ! start of neonate stage "A life cycle temporal boundary that marks the start of the neonate stage of the organism."
      • [i] UBERON:0035945 ! start of life cycle "A life cycle temporal boundary that marks the start of the life cycle of the organism."
      • [i] UBERON:0035944 ! life-death temporal boundary "A life cycle temporal boundary that marks the end of the life cycle of the organism."

these strange sounding terms might be better colloquially called conception, birth, death. IMO 0D is overmodeling, we are better just treating these concepts analogous to how we treat 3D boundaries in uberon, as actually having some extent, albeit minimal

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