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Cranial nerve fixes #634

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cmungall opened this Issue Dec 30, 2014 · 2 comments

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cmungall commented Dec 30, 2014

  • merge peripheral nerve with nerve
  • deal with optic nerve (not truly a nerve)
  • deal with spinal accessory nerve (is this cranial or spinal? two components? or is 'cranial' component part of the vagus nerve?)
  • Implement standard pattern: see #298
    • nerves should have innervates relationships. See Kardong table 10-1
    • nerves and nuclei should be connected; they don't overlap, but there are fibers that overlap both
    • nerve roots should all be in CNS, with fiber extensions into nerves
    • nerves should have develops from relationships; Kardong table 10-2
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cmungall commented Dec 30, 2014

Also: NT for epiphyseal cranial nerve

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cmungall commented Dec 30, 2014

Also: align with EMAPA - obophenotype/mouse-anatomy-ontology#6

@cmungall cmungall closed this in 1855297 Dec 30, 2014

cmungall added a commit that referenced this issue Dec 30, 2014

cmungall added a commit that referenced this issue Jan 2, 2015

cmungall added a commit that referenced this issue Jan 2, 2015

This release encompasses multiple imrpovements in the representation
of the nervous system. Many wikipedia-sourced definitions have been
replaced with definitions from neurolex ([632](#632)). We have defined and
implemented a design pattern for cranial and spinal nerves, ganglia
and nuclei ([634](#634)). We made improvements to the mapping to Allen
ontologies. Additionally, we now use the numeric identifiers for all
Allen classes, rather than acronyms. Please note that the "ABA" prefix
has been superseded by "MBA" (mouse brain atlas), to be consistent
with the others (HBA, PBA, DMBA, DHBA). New terms were added from the
HarvardOxford Cortical atlas based on work by Russ Poldrack and Trish
Whetzel ([630](#630)).

This release also ensures that every class from NIF_GrossAnatomy (but
not its successor, neurolex) is represented in Uberon. Note that not
all classes will be in the bridge file. Many of the region-part-of-X
classes are present in Uberon as obsolete classes.
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