Fix some ZFA mapping errors #3361
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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
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
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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This PR fixes a handful of “simple” mapping errors¹ between ZFA and Uberon:
See the linked issues (or the individual commit messages) for the rationale behind each remapping.
closes #3353
closes #3356
¹ What I mean by “simple mapping error”: the error is simply that a ZFA term is mapped to the wrong Uberon term, but none of the term on either side is otherwise incorrect.