brain commissures, white matter and non-vertebrates #325
Comments
ghost
assigned 
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Perhaps here what we need is a generic "midline crossing white matter" class and a taxon-specific name. This is a problem with taxon-specific nomenclature, not really a different kind of entity (at least as far as I know). I agree we can break the link for now. |
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I'm not really for a new class just to represent a nomenclature change. It seems there is a logical difference here due to the presence/absence of myelin? If we associate white matter with myelin then including white matter in the generic entity keeps the logical problem. I think our previous representation was fine - we had 'commissure of neuraxis' (ugly name) which didn't have any implications of being white matter or myelin-based - then we made the grouping class 'white matter commissure' to be CUMBO compliant, then the issue arose - see #300 For now I will rename back to a generic commissure, make the association to white matter a taxon GCI. In future we can explore the notion of a generic axon sheath concept? Underscores the importance of having invert biologists at the CUMBO meetings (if CUMBO is to be used across species) |
…-myelin-axon taxa. Fixes issue #325
* nerve fiber - made disjoint union of myelinated and unmylelinated forms
* made commissure terminologically and logically appropriate for non-myelin-axon taxa. Fixes issue #325
* weakened develops_from relationship mouth -> stomodeum to contribution - some parts of tghe mouth are ectodermal. Fixes DV with ZFA
* jaw refactoring
* Fixed inverted L/R xrefs for EHDAA2 in auricular muscle tissue. Fixes issue #321
* Fixed synclash for spinal cord neuromere
* Added ambiguous_for_taxon.
* Added not_recommended_for_taxon
* editing nervous system def and adding to cumbo slim
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Note that this is currently represented as a taxon GCI: relationship: part_of UBERON:0002316 {gci_relation="part_of", gci_filler="NCBITaxon:7742", notes="myelin not present in all taxa that have a commissure"} ! white matter I don't think this was a great decision I think it better to break the taxon equivalence between uberon commissure and FBbt commissue. Unless @dosumis disagrees I suggest as action:
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Wow - this is an old one. There is a reasonable, abstract meaning of commissure as 'midline crossing tract' that works across species. Maybe it would be easier to make a new parent class for this (which would have the xref to FBbt). This issue then becomes a terminology issue for the current term. If we can't solve that easily I'm happy with just removing the mapping to FBbt for now. If we can come up with a better term for the vertebrate subclass, it would be good to have some way to add the preferred vertebrate term as synonyms and tag its taxon applicability. Do we already have a mechanism for this. (If not - this would be a good topic for an Uberon call) CC @gouttegd |
Mapping between FBbt's 'symmetrical commissure' and Uberon's 'nervous system commissure' causes some problem when applying taxon constraints, due to the Uberon term being linked to the concept of white matter. Remove the mapping as per Chris Mungall's suggestion in obophenotype/uberon#325.
Many Dmel classes become unsat when used with full taxon constraints:
The particular example is random - anything with an existential dependency on commissure in Fbbt would yield similar results.
Possibly multiple issues here.
FBbt is totally fine:
problem arises with the eq axiom to commissure in uberon, where we have brain commissure being a white matter commissure. Suggest we break the link, make it a taxon GCI.
See also:
http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html
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