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Fix some ZFA mapping errors #3361

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merged 6 commits into from
Oct 23, 2024
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Commits on Sep 12, 2024

  1. Remap ZFA's 'griseum centrale'.

    ZFA's 'griseum centrale' (ZFA:0000518) is mapped to Uberon's 'central
    gray substance of midbrain' (UBERON:0003040).
    
    This is likely incorrect as the ZFA term refers to a structure that is
    part of the hindbrain, whereas the Uberon term refers to a midbrain
    structure.
    
    The correct mapping is most likely 'central gray substance of medulla'
    (UBERON:0002867), which is part of the hindbrain.
    
    partially addresses #3353
    gouttegd committed Sep 12, 2024
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  2. Remap ZFA's 'coelom'.

    ZFA's 'coelom' (ZFA:0001438) is mapped to Uberon's 'coelemic cavity
    lumen' (UBERON:0002323).
    
    This is incorrect as the ZFA terms refers to a multi-tissue structure
    and therefore to a material entity, whereas the Uberon term refers to
    the anatomical cavity *within* the coelom (an immaterial entity).
    
    Uberon has another term to refer to the (material) anatomical structure
    that forms the coelemic cavity: 'coelom' (UBERON:0011997), the ZFA term
    should be mapped to that term instead.
    
    partially addresses #3353
    gouttegd committed Sep 12, 2024
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  3. Remap ZFA's 'inferior raphe nucleus'.

    ZFA's 'inferior raphe nucleus' (ZFA:0000366) is mapped to Uberon's
    'dorsal raphe nucleus' (UBERON:0002043).
    
    This is likely wrong for at least two reasons:
    
    * the ZFA term refers to a nucleus that is part of the hindbrain,
      whereas the Uberon term refers to a nucleus that is part of the
      midbrain;
    * according to Beecher, Beamer & Bartlett 2019 [1], the 'dorsal raphe
      nucleus' is one of the *superior* raphe nuclei, which makes it
      doubtful, even considering possible terminological differences across
      species, that it should be mapped to an *inferior* raphe nucleus.
    
    The same reference states that the 'inferior raphe nucleus' is a complex
    comprising the following nuclei:
    
    * the 'nucleus raphe obscurus' (UBERON:0002684),
    * the 'nucleus raphe pallidus' (UBERON:0002157),
    * and the 'nucleus raphe magnus' (UBERON:0002156).
    
    In Uberon, those three nuclei are the parts that make up the 'medullary
    raphe nuclear complex' (UBERON:0002692), leading me to believe that this
    complex is in fact what ZFA (along with Beecher, Beamer, & Bartlett)
    calls the 'inferior raphe nucleus'.
    
    So here, we remap ZFA's 'inferior raphe nucleus' to 'medullary raphe
    nuclear complex', and also add a 'inferior raphe nuclei' synonym to the
    Uberon term.
    
    closes #3356
    
    [1] doi:10.1016/B978-0-12-800050-2.00006-1
    gouttegd committed Sep 12, 2024
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Commits on Oct 21, 2024

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  2. Remove mapping with ZFA:0000366.

    We had re-mapped ZFA:0000366 ('inferior raphe nucleus') from
    UBERON:0002043 ('dorsal raphe nucleus') to UBERON:0002692 ('medullary
    raphe nuclear complex'), which seemed a better match.
    
    However, for lack of certainty about what the ZFA term really
    represents, it is better to drop the mapping entirely.
    gouttegd committed Oct 21, 2024
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Commits on Oct 22, 2024

  1. Remove mapping with ZFA:0000518.

    There are conflicting statements in the available literature regarding
    the mammalian equivalent of ZFA's 'griseum centrale'.
    
    Candidates include:
    
    * the 'central gray substance of midbrain' (aka the 'periaqueductal
      gray'), according to Olson et al. 2024
      (doi:10.1016/j.ibror.2017.01.001);
    * the 'nucleus incertus', according to Spikol et al. 2024
      (doi:10.7554/eLife.89516.3);
    * and the 'central gray substance of medulla', based on the
      classification of the ZFA term.
    
    It is better to simply remove the mapping for now.
    gouttegd committed Oct 22, 2024
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