-
Notifications
You must be signed in to change notification settings - Fork 29
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
UBERON:0002726 cervical spinal cord, subclass to create? for GTex annotation #725
Comments
note we have:
I prefer the Cn nomenclature, rather than spelling out the ordinal How should these be related to the vertebral segments? On 29 Jun 2015, at 10:16, ANiknejad wrote:
|
Can you suggest a definition pattern for Cn segments? Remember we have a C8. This makes sense for the nerves (C8 nerve goes under vertebra 7), maybe the segments are defined in terms of nerves, which are themselves defined in terms of vertebrae (over for C1-7, under for C8). But what about dermatomes? |
Dermatomes, by definition, are regions innervated by the sensory neurons of Robert E. Druzinsky, Ph.D. Office: 312-996-0406 On Wed, Jul 1, 2015 at 4:23 PM, Chris Mungall notifications@github.com
|
The nerves (C1-C8) are defined with respect to both spinal cord segments and somites (i.e., an anatomical and a developmental reason). On each side of the body, each somite is innervated by a segment of the spinal cord and a segmental (spinal) nerve. There are 8 cervical somites, therefore 8 spinal cord segments and 8 segmental nerves. Vertebrae are defined as "intersegmental" because they are formed by the fusion of neighboring parts of somites (i.e., they form from more than one somite). The upper part of the first cervical somite that becomes bone fuses to the base of the skull (the details of this pattern probably vary some across major taxonomic groups) and ossifies as part of the occipital bone, and so the C1 nerve travels between the base of the skull and the C1 vertebra. Dermatomes (the skin that is innervated by a particular segmental nerve) will also correspond to somites. Not sure if that helps. Chris W. From: Chris Mungall notifications@github.com Can you suggest a definition pattern for Cn segments? Remember we have a C8. This makes sense for the nerves (C8 nerve goes under vertebra 7), maybe the segments are defined in terms of nerves, which are themselves defined in terms of vertebrae (over for C1-7, under for C8). But what about dermatomes? Reply to this email directly or view it on GitHubhttps://github.com//issues/725#issuecomment-117828264. |
Thanks both! I realize my comment about dermatomes was confusing and not strictly relevant. There are actually two senses of this term: UBERON:0004016 ! dermatome A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells @RDruzinsky is of course correct. Dermatomes (sensu skin nerve fields) don't pose any particular problem here, and the number of these necessarily corresponds to the number of spinal nerve pairs. I think when I mentioned dermatomes it was a brain fart, and I was thinking of the somite lineage to the vertebral elements (which is more relevant than those leading to the dermis), and @cewalls's comments get at the heart of the matter here. We need to choose the appropriate axis (anatomical vs developmental) for definitions and make sure things align (including the off-by-1/2 for vertebral elements and somites). As an aside, I was looking at EHDAA2, which is usually very precise for lineage in humans, but I think there are some problems here (if you are reading this in email you may need to switch to the ticket on the github website). See image: |
I will close this, as we already have UBERON:0006469 However, I will link to this ticket from the ontology so any further discussion on improving representation welcome here |
Hi Chris,
What do you think, creating
'C1 cervical spinal cord'
relationship: is_a UBERON:0002726 {gci_filler="NCBITaxon:9606", gci_relation="part_of"} ! cervical spinal cord
for mapping GTex Brain - Spinal cord (cervical c-1)' ?
Thank you for comments and help
Cheers,
Anne
The text was updated successfully, but these errors were encountered: