How to relate ceiling to space? #2368
Comments
|
See 0f9c44d This may be wrong |
|
I would have just done part of lymph node - do we need to formalise the ceiling part? |
|
just relooking at this now, I think 'part of' some 'subcapsular sinus lymph node' is wrong too, given the sinus is a anatomical space. Can we do:
|
ok realised upper side is a class not an object property so not quite sure how to use it |
|
For the specific case that gave rise to this ticket, see discussion in #2371 (comment) and following comments |
|
I agree the ontology is inconsistent in how the string "sinus" is treated.
I think at least for the paranasal sinuses there is value in switching to
modeling as material - with the mucous membranes etc being part of the
sinus.
We can optionally make a separate class "paranasal sinus space" for the
space nerds who really want to talk about the space, and map the FMA term
to that. But this kind of duplication has some cost (maintenance, danger of
raggedness, being *too precise* about mappings such that FMA no longer
transitively maps to the other ontologies that only include a term for the
material aspect)
…On Sat, Mar 26, 2022 at 5:54 AM Nico Matentzoglu ***@***.***> wrote:
Given that the sinus = space I don't know that there is an adequate way to
relate the ceiling to the space. Even assuming adjacent_to can be used
between a material and immaterial entity it loses that this is the top
portion and we will probably need to enter a term for the floor at some
point.
You can say that this is part_of the lymph node, that much is accurate.
Note there is inconsistency in Uberon as to whether X sinus refers to the
space or the tissue surrounding the space. This is probably due to the way
biologists name things but it does make finding relevant examples tricky.
Sorry not to give you a definite answer.
*Originally posted by @sbello <https://github.com/sbello> in #2364
(comment)
<#2364 (comment)>*
—
Reply to this email directly, view it on GitHub
<#2368>, or unsubscribe
<https://github.com/notifications/unsubscribe-auth/AAGZRCEBPFRSCMM6DJZ45L3VB4CILANCNFSM5RXA5RAA>
.
You are receiving this because you are subscribed to this thread.Message
ID: ***@***.***>
|
|
I think this is a good idea. Every space has material boundaries defined by
anatomists, so it makes sense to treat spaces as material entities for the
sake of simplicity.
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 Mon, Mar 28, 2022 at 10:00 AM uberon ***@***.***> wrote:
I agree the ontology is inconsistent in how the string "sinus" is treated.
I think at least for the paranasal sinuses there is value in switching to
modeling as material - with the mucous membranes etc being part of the
sinus.
We can optionally make a separate class "paranasal sinus space" for the
space nerds who really want to talk about the space, and map the FMA term
to that. But this kind of duplication has some cost (maintenance, danger of
raggedness, being *too precise* about mappings such that FMA no longer
transitively maps to the other ontologies that only include a term for the
material aspect)
On Sat, Mar 26, 2022 at 5:54 AM Nico Matentzoglu ***@***.***>
wrote:
> Given that the sinus = space I don't know that there is an adequate way
to
> relate the ceiling to the space. Even assuming adjacent_to can be used
> between a material and immaterial entity it loses that this is the top
> portion and we will probably need to enter a term for the floor at some
> point.
> You can say that this is part_of the lymph node, that much is accurate.
> Note there is inconsistency in Uberon as to whether X sinus refers to the
> space or the tissue surrounding the space. This is probably due to the
way
> biologists name things but it does make finding relevant examples tricky.
> Sorry not to give you a definite answer.
>
> *Originally posted by @sbello <https://github.com/sbello> in #2364
> (comment)
> <
#2364 (comment)>*
>
> —
> Reply to this email directly, view it on GitHub
> <#2368>, or unsubscribe
> <
https://github.com/notifications/unsubscribe-auth/AAGZRCEBPFRSCMM6DJZ45L3VB4CILANCNFSM5RXA5RAA
>
> .
> You are receiving this because you are subscribed to this thread.Message
> ID: ***@***.***>
>
—
Reply to this email directly, view it on GitHub
<#2368 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ABASAOAV4RVDYC2VQWRAYFTVCHCRTANCNFSM5RXA5RAA>
.
You are receiving this because you are subscribed to this thread.Message
ID: ***@***.***>
|
|
The reason for the distinction between the space and the walls of the space as I understand it is that at times we want to talk about the walls of the space (the example that started this) and at other times we want to talk about the stuff within the space (e.g. lymph fluid, cerebrospinal fluid). My guess s that whether a sinus is an immaterial space or material entity was probably driven by the use case the person entering the term had in mind. |
|
Fixed by #2371 |
Given that the sinus = space I don't know that there is an adequate way to relate the ceiling to the space. Even assuming adjacent_to can be used between a material and immaterial entity it loses that this is the top portion and we will probably need to enter a term for the floor at some point.
You can say that this is part_of the lymph node, that much is accurate.
Note there is inconsistency in Uberon as to whether X sinus refers to the space or the tissue surrounding the space. This is probably due to the way biologists name things but it does make finding relevant examples tricky.
Sorry not to give you a definite answer.
Originally posted by @sbello in #2364 (comment)
The text was updated successfully, but these errors were encountered: