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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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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PR updated to remove entirely the mapping with ZFA’s 'inferior raphe nucleus', as suggested in the comments of #3356. |
aleixpuigb
requested changes
Oct 22, 2024
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.
aleixpuigb
approved these changes
Oct 23, 2024
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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.