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Remap ZFA's 'inferior raphe nucleus'.
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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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gouttegd committed Sep 12, 2024
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Showing 1 changed file with 2 additions and 1 deletion.
3 changes: 2 additions & 1 deletion src/ontology/uberon-edit.obo
Original file line number Diff line number Diff line change
Expand Up @@ -39384,7 +39384,6 @@ xref: neuronames:512 {source="BIRNLEX:982"}
xref: TAO:0000366
xref: UMLS:C0175392 {source="BIRNLEX:982"}
xref: Wikipedia:Dorsal_raphe_nucleus
xref: ZFA:0000366
is_a: UBERON:0002308 ! nucleus of brain
relationship: mutually_spatially_disjoint_with UBERON:0002145 {source="ABA"} ! interpeduncular nucleus
relationship: part_of UBERON:0002639 {source="Wikipedia"} ! midbrain reticular formation
Expand Down Expand Up @@ -57219,6 +57218,7 @@ property_value: external_definition "Region of the mesencephalon that arises fro
[Term]
id: UBERON:0002692
name: medullary raphe nuclear complex
synonym: "inferior raphe nuclei" RELATED [doi:10.1016/B978-0-12-800050-2.00006-1]
synonym: "nuclei raphe (myelencephali)" RELATED OMO:0003011 [NeuroNames:738]
synonym: "raphe medullae oblongatae" EXACT OMO:0003011 [FMA:68874, FMA:TA]
synonym: "raphe nuclei of medulla" EXACT [FMA:68874]
Expand All @@ -57231,6 +57231,7 @@ xref: HBA:9642
xref: neuronames:738 {source="BIRNLEX:1420"}
xref: SCTID:362420006
xref: UMLS:C0175514 {source="BIRNLEX:1420"}
xref: ZFA:0000366
is_a: UBERON:0007245 ! nuclear complex of neuraxis
relationship: part_of UBERON:0001896 {source="FMA"} ! medulla oblongata
relationship: part_of UBERON:0004684 {source="Wikipedia"} ! raphe nuclei
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