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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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How to relate ceiling to space? #2368

Closed matentzn closed 2 years ago

matentzn commented 2 years ago

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 https://github.com/obophenotype/uberon/issues/2364#issuecomment-1079520940

matentzn commented 2 years ago

See https://github.com/obophenotype/uberon/commit/0f9c44d6635a0734d42ee3a076f3d752003623e1

This may be wrong

shawntanzk commented 2 years ago

I would have just done part of lymph node - do we need to formalise the ceiling part?

shawntanzk commented 2 years ago

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: 'part of' some 'lymph node' 'upper side' (BSPO:0000001)/'superior side' (BSPO:0000022)* some 'subcapsular sinus lymph node' 'adjacent to' some 'subcapsular sinus lymph node'

shawntanzk commented 2 years ago

'upper side' (BSPO:0000001)/'superior side' (BSPO:0000022)* some 'subcapsular sinus lymph node'

ok realised upper side is a class not an object property so not quite sure how to use it

paolaroncaglia commented 2 years ago

For the specific case that gave rise to this ticket, see discussion in https://github.com/obophenotype/uberon/pull/2371#issuecomment-1080627577 and following comments

uberon commented 2 years ago

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) https://github.com/obophenotype/uberon/pull/2364#issuecomment-1079520940

— Reply to this email directly, view it on GitHub https://github.com/obophenotype/uberon/issues/2368, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGZRCEBPFRSCMM6DJZ45L3VB4CILANCNFSM5RXA5RAA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

RDruzinsky commented 2 years ago

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) < https://github.com/obophenotype/uberon/pull/2364#issuecomment-1079520940>

— Reply to this email directly, view it on GitHub https://github.com/obophenotype/uberon/issues/2368, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AAGZRCEBPFRSCMM6DJZ45L3VB4CILANCNFSM5RXA5RAA

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sbello commented 2 years ago

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.

matentzn commented 2 years ago

Fixed by #2371