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Fix some ZFA mapping errors #3361
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Commits on Sep 12, 2024
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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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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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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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Commits on Oct 21, 2024
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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.
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Commits on Oct 22, 2024
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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.
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