search

obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
Other
134 stars 29 forks source link

Subarachnoid space should not be part of brain #2006

Closed dosumis closed 2 years ago

dosumis commented 3 years ago

Uberon term

subarachnoid space http://purl.obolibrary.org/obo/UBERON_0000315

Bug description

image

The meninges and the various membranes and spaces that comprise it are the outer part of both the brain and spinal cord. They therefore should be part_of the CNS, not the brain.

https://en.wikipedia.org/wiki/Meninges#Subarachnoid_space

For optimum partonomy, it might make more sense for the space(s) to be part of the meninges (AKA meningeal cluster) or meninx image

dosumis commented 3 years ago

@tgbugs - any opinion on the optimal/correct partonomy here?

tgbugs commented 3 years ago

I wonder if there isn't a deeper issue here. Should the meninges be part of the nervous system at all? Looking at the language used in the wiki articles and e.g. https://pubmed.ncbi.nlm.nih.gov/30801905/, it seems that they probably are not?

With that in mind, given that the subarachnoid space sits between the meninges which surround more or less the entirety of the CSN and the CNS proper (?), I would say that under the current scheme the subarachnoid space would be a direct part of the CNS with no intervening parts.

If the meninges are not part of the CNS then I would suggest a set of new classes which would be equivalent to CNS + ensheathing parts, and possibly also NS + ensheathing parts. Alternately we could forgoe creating those classes and create some other relationship between meninges + subarachnoid space and the CNS (and NS and its equivalents).

Thoughts?

RDruzinsky commented 3 years ago

I agree, and to complicate things even more, the subarachnoid space is an anatomical space rather than an entity, right?

Robert E. Druzinsky, Ph.D. Clinical Associate Professor Dept. of Oral Biology College of Dentistry University of Illinois at Chicago 801 S. Paulina Chicago, IL 60612 @.***

Office: 312-996-0406 Lab: 312-996-0629 Website: www.peerj.com/RobertDruzinsky

On Thu, Jul 29, 2021 at 4:43 PM Tom Gillespie @.***> wrote:

I wonder if there isn't a deeper issue here. Should the meninges be part of the nervous system at all? Looking at the language used in the wiki articles and e.g. https://pubmed.ncbi.nlm.nih.gov/30801905/, it seems that they probably are not?

With that in mind, given that the subarachnoid space sits between the meninges which surround more or less the entirety of the CSN and the CNS proper (?), I would say that under the current scheme the subarachnoid space would be a direct part of the CNS with no intervening parts.

If the meninges are not part of the CNS then I would suggest a set of new classes which would be equivalent to CNS + ensheathing parts, and possibly also NS + ensheathing parts. Alternately we could forgoe creating those classes and create some other relationship between meninges + subarachnoid space and the CNS (and NS and its equivalents).

Thoughts?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/obophenotype/uberon/issues/2006#issuecomment-889480709, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABASAOAWLSM2YGTRT66G2BLT2HDQXANCNFSM5BHBUY7A .

cmungall commented 3 years ago

Should the meninges be part of the nervous system at all?

1261 discusses this and also compares how it is done in other ontologies. Whatever decision is made, this will need coordinated. Note all other ontologies treat meninges as part of the nervous system

I think drawing partonomies on the slide of inclusivity is easier for maintenance, and still allows people to draw their own more restricted concepts

cmungall commented 3 years ago

the subarachnoid space is an anatomical space rather than an entity,

yep but spaces can beparts of material entities so all good

cmungall commented 3 years ago

I agree with @dosumis's assessment

Furthermore we should have consistent patterns and regularized lattices for meningeal structures. We already implement {brain,forebrain,spinal} x {pia, dura, etc} so we should continue this for subarachnoid space

in fact if we had implemented this structure then our existing placement would be correctly detected as incoherent.

here is fma for comparison:

image

tgbugs commented 3 years ago

I think drawing partonomies on the slide of inclusivity is easier for maintenance, and still allows people to draw their own more restricted concepts

Agree. It is also easier to discard parts of an inclusive hierarchy than it is to pull in additional specific parts, and removing the meninges from the CNS partonomy would multiply universals if we wanted to talk about "everything inside the skull" (for example).

cmungall commented 3 years ago

sorry @rays22 I couldn't resist doing this one ticket. I did a mini-slurp, we still need an SOP for that

rays22 commented 3 years ago

sorry @rays22 I couldn't resist doing this one ticket. I did a mini-slurp, we still need an SOP for that

No problem.

dosumis commented 2 years ago

@rays22 - please check that this has fixed the inference problem in MP - MP:0009037 abnormal subarachnoid space development should not be under MP:0000913 abnormal brain development. Ticket can then be closed and tracking spreadsheet updated.