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Fix some ZFA mapping errors #3361

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Fix some ZFA mapping errors #3361

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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
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    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
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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
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