Unlink 'late embryonic stage' from chordate-specific terms. #3479
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The pharyngula and neurula stages are both specific to chordates. We
explicitly mark them as such (updating the existing -- and very broad --
taxon restrictiom from 'Eumetazoa' to 'Chordata') and amend their
definition accordingly.
'late embryonic stage', on the other hand, should not be restricted to
chordates. Therefore, we change the existing relation
'late embryonic stage' SubClassOf 'preceded by' some 'pharyngula stage'
to a GCI
('late embryonic stage' and ('occurs in' some Chordata))
SubClassOf 'preceded by' some 'pharyngula stage'
closes #3478
cmungall
approved these changes
Feb 12, 2025
| @@ -119536,7 +119536,7 @@ is_a: UBERON:0000105 ! life cycle stage | |||
| relationship: part_of UBERON:0000068 ! embryo stage | |||
| relationship: preceded_by RnorDv:0000010 {gci_relation="part_of", gci_filler="NCBITaxon:10116"} | |||
| relationship: preceded_by UBERON:0000111 ! organogenesis stage | |||
| relationship: preceded_by UBERON:0004707 ! pharyngula stage | |||
| relationship: preceded_by UBERON:0004707 {gci_relation="BFO:0000066", gci_filler="NCBITaxon:7711"} ! pharyngula stage | |||
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We have the shortcut for the material entity GCIs. Not sure if this will flip on a normalize? Just curious, not a blocker
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This will not flip to a shorthand form upon normalisation, because there is currently no Typedef frame for BFO:0000066 declared in uberon-edit.obo, so the occurs_in shorthand is not available to the OBO serialiser.
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The 'pharyngula' and 'neurula' stages are both specific to chordates. This PR explicitly marks them as such (updating the existing – and very broad – taxon restriction from 'Eumetazoa' to 'Chordata') and amend their definition accordingly.
On the other hand, 'late embryonic stage' should not be restricted to chordates. Therefore, we change the existing relation
to a GCI
closes #3478 (see that issue for a detailed rationale)