ZFA/Uberon issues: inferior raphe nucleus #3356
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gouttegd
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Sep 12, 2024
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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@AvolaAmg If you could have a look at this issue and tell me whether I am completely wrong, that’d be much appreciated. :) |
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Some background here: Although this doesn't really explain what I think is overzealous lumping. I think either a split or simply dropping the xrefs is warranted here |
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In ZFA, 'inferior raphe nucleus' is a 'hindbrain nucleus' and therefore part_of the hindbrain.
The ZFA term is mapped to Uberon’s 'dorsal raphe nucleus', which is ultimately part_of the midbrain (through several independent relationships).
This is a direct contradiction, and a violation of the disjointness between hindbrain and midbrain in Uberon.
I believe this may be a mapping error. According to Beecher, Beamer & Bartlett 2019, the “raphe nuclei” are
So it seems dubious that ZFA’s 'inferior raphe nucleus' should be mapped to 'dorsal raphe nucleus' which is (according to the classification above) a superior raphe nucleus.
In Uberon, 'nucleus raphe obscurus', 'nucleus raphe pallidus', and 'nucleus raphe magnus' are the three parts making up the 'medullay raphe nuclear complex'. So assuming that what ZFA calls the inferior raphe nucleus is the set of three nuclei that Beecher, Beamer & Bartlett call the inferior raphe nuclei, the ZFA term should be mapped to 'medullay raphe nuclear complex' instead.
Of note, if the above is true, that is, if inferior raphe nucleus is not the same thing as dorsal raphe nucleus, then there is an also a similar error in GO: 'inferior raphe nucleus development' is said to 'results in development of the 'dorsal raphe nucleus'.
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