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NTR: submandibular region #1137

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nicolevasilevsky opened this Issue Aug 11, 2015 · 15 comments

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nicolevasilevsky commented Aug 11, 2015

NTR: submandibular region
Parent: Anatomical space (Mark- do you think this is the appropriate parent?)
Definition: The region between the mandible and the hyoid bone contains the submandibular and sublingual glands, suprahyoid muscles, submandibular ganglion, and lingual artery.
syn: submandibular space
Ref: https://www.dartmouth.edu/~humananatomy/part_8/chapter_49.html

needed for HPO term: HP_0410013 Abnormality of the submandibular region

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I don't think you want a space; this is a subdivision of the face I think

@RDruzinsky look OK from a comparative POV?

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cmungall commented Aug 11, 2015

I don't think you want a space; this is a subdivision of the face I think

@RDruzinsky look OK from a comparative POV?

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This would potentially be useful for axiomatizing

or would that be too simplistic? Does the gland or node ever migrate phylogenetically but retain the same name?

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cmungall commented Aug 11, 2015

This would potentially be useful for axiomatizing

or would that be too simplistic? Does the gland or node ever migrate phylogenetically but retain the same name?

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RDruzinsky Aug 11, 2015

I agree, Chris. I was going to ask whether region and space are synonymous.
I don't think that they are.
Yes, I think that it is a subdivision of the neck. E.g. submandibular
triangle

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
druzinsk@uic.edu

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

On Tue, Aug 11, 2015 at 6:40 PM, Chris Mungall notifications@github.com
wrote:

I don't think you want a space; this is a subdivision of the face I think

@RDruzinsky https://github.com/RDruzinsky look OK from a comparative
POV?


Reply to this email directly or view it on GitHub
#1137 (comment)
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RDruzinsky commented Aug 11, 2015

I agree, Chris. I was going to ask whether region and space are synonymous.
I don't think that they are.
Yes, I think that it is a subdivision of the neck. E.g. submandibular
triangle

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
druzinsk@uic.edu

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

On Tue, Aug 11, 2015 at 6:40 PM, Chris Mungall notifications@github.com
wrote:

I don't think you want a space; this is a subdivision of the face I think

@RDruzinsky https://github.com/RDruzinsky look OK from a comparative
POV?


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#1137 (comment)
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cewall Aug 12, 2015

I agree that it is in the neck and is submandibular triangle. Not sure about whether the salivary gland can occupy different positions in different species...

Chris Wall

On Aug 11, 2015, at 7:42 PM, Robert Druzinsky notifications@github.com wrote:

I agree, Chris. I was going to ask whether region and space are synonymous.
I don't think that they are.
Yes, I think that it is a subdivision of the neck. E.g. submandibular
triangle

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
druzinsk@uic.edu

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

On Tue, Aug 11, 2015 at 6:40 PM, Chris Mungall notifications@github.com
wrote:

I don't think you want a space; this is a subdivision of the face I think

@RDruzinsky https://github.com/RDruzinsky look OK from a comparative
POV?


Reply to this email directly or view it on GitHub
#1137 (comment)
.


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cewall commented Aug 12, 2015

I agree that it is in the neck and is submandibular triangle. Not sure about whether the salivary gland can occupy different positions in different species...

Chris Wall

On Aug 11, 2015, at 7:42 PM, Robert Druzinsky notifications@github.com wrote:

I agree, Chris. I was going to ask whether region and space are synonymous.
I don't think that they are.
Yes, I think that it is a subdivision of the neck. E.g. submandibular
triangle

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
druzinsk@uic.edu

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

On Tue, Aug 11, 2015 at 6:40 PM, Chris Mungall notifications@github.com
wrote:

I don't think you want a space; this is a subdivision of the face I think

@RDruzinsky https://github.com/RDruzinsky look OK from a comparative
POV?


Reply to this email directly or view it on GitHub
#1137 (comment)
.


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RDruzinsky Aug 12, 2015

Interesting question, @cwall

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
druzinsk@uic.edu

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

On Tue, Aug 11, 2015 at 7:04 PM, Chris Wall notifications@github.com
wrote:

I agree that it is in the neck and is submandibular triangle. Not sure
about whether the salivary gland can occupy different positions in
different species...

Chris Wall

On Aug 11, 2015, at 7:42 PM, Robert Druzinsky notifications@github.com
wrote:

I agree, Chris. I was going to ask whether region and space are
synonymous.
I don't think that they are.
Yes, I think that it is a subdivision of the neck. E.g. submandibular
triangle

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
druzinsk@uic.edu

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

On Tue, Aug 11, 2015 at 6:40 PM, Chris Mungall <notifications@github.com

wrote:

I don't think you want a space; this is a subdivision of the face I
think

@RDruzinsky https://github.com/RDruzinsky look OK from a comparative
POV?


Reply to this email directly or view it on GitHub
<
https://github.com/obophenotype/uberon/issues/1137#issuecomment-130112589>
.


Reply to this email directly or view it on GitHub.


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#1137 (comment)
.

RDruzinsky commented Aug 12, 2015

Interesting question, @cwall

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
druzinsk@uic.edu

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

On Tue, Aug 11, 2015 at 7:04 PM, Chris Wall notifications@github.com
wrote:

I agree that it is in the neck and is submandibular triangle. Not sure
about whether the salivary gland can occupy different positions in
different species...

Chris Wall

On Aug 11, 2015, at 7:42 PM, Robert Druzinsky notifications@github.com
wrote:

I agree, Chris. I was going to ask whether region and space are
synonymous.
I don't think that they are.
Yes, I think that it is a subdivision of the neck. E.g. submandibular
triangle

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
druzinsk@uic.edu

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

On Tue, Aug 11, 2015 at 6:40 PM, Chris Mungall <notifications@github.com

wrote:

I don't think you want a space; this is a subdivision of the face I
think

@RDruzinsky https://github.com/RDruzinsky look OK from a comparative
POV?


Reply to this email directly or view it on GitHub
<
https://github.com/obophenotype/uberon/issues/1137#issuecomment-130112589>
.


Reply to this email directly or view it on GitHub.


Reply to this email directly or view it on GitHub
#1137 (comment)
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1178px-musculi_coli_base _my_edits_for_tringles _labeled_triangles _submandib svg

"Musculi coli base, my edits for tringles, labeled triangles, Submandib" by Olek Remesz (wiki-pl: Orem, commons: Orem) Modified by user:madhero88 - original image File:Musculi coli base.svg. Licensed under CC BY 3.0 via Wikimedia Commons - https://commons.wikimedia.org/wiki/File:Musculi_coli_base,_my_edits_for_tringles,_labeled_triangles,_Submandib.svg#/media/File:Musculi_coli_base,_my_edits_for_tringles,_labeled_triangles,_Submandib.svg

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cmungall commented Aug 12, 2015

1178px-musculi_coli_base _my_edits_for_tringles _labeled_triangles _submandib svg

"Musculi coli base, my edits for tringles, labeled triangles, Submandib" by Olek Remesz (wiki-pl: Orem, commons: Orem) Modified by user:madhero88 - original image File:Musculi coli base.svg. Licensed under CC BY 3.0 via Wikimedia Commons - https://commons.wikimedia.org/wiki/File:Musculi_coli_base,_my_edits_for_tringles,_labeled_triangles,_Submandib.svg#/media/File:Musculi_coli_base,_my_edits_for_tringles,_labeled_triangles,_Submandib.svg

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human specific?
https://en.wikipedia.org/wiki/Submandibular_triangle#Boundaries_and_coverings

The hyoid/mandible boundaries are clear for external portions; internally sticking with the Mylohyoideus anteriorly, and by the hyoglossus posteriorly makes sense across mammals?

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cmungall commented Aug 12, 2015

human specific?
https://en.wikipedia.org/wiki/Submandibular_triangle#Boundaries_and_coverings

The hyoid/mandible boundaries are clear for external portions; internally sticking with the Mylohyoideus anteriorly, and by the hyoglossus posteriorly makes sense across mammals?

cmungall added a commit that referenced this issue Aug 12, 2015

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RDruzinsky Aug 12, 2015

Probably true, but Chris W. and I are just not sure if the contents of the
triangle are the same across mammals.

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
druzinsk@uic.edu

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

On Tue, Aug 11, 2015 at 7:36 PM, Chris Mungall notifications@github.com
wrote:

human specific?

https://en.wikipedia.org/wiki/Submandibular_triangle#Boundaries_and_coverings

The hyoid/mandible boundaries are clear for external portions; internally
sticking with the Mylohyoideus anteriorly, and by the hyoglossus
posteriorly makes sense across mammals?


Reply to this email directly or view it on GitHub
#1137 (comment)
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RDruzinsky commented Aug 12, 2015

Probably true, but Chris W. and I are just not sure if the contents of the
triangle are the same across mammals.

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
druzinsk@uic.edu

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

On Tue, Aug 11, 2015 at 7:36 PM, Chris Mungall notifications@github.com
wrote:

human specific?

https://en.wikipedia.org/wiki/Submandibular_triangle#Boundaries_and_coverings

The hyoid/mandible boundaries are clear for external portions; internally
sticking with the Mylohyoideus anteriorly, and by the hyoglossus
posteriorly makes sense across mammals?


Reply to this email directly or view it on GitHub
#1137 (comment)
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markengelstad Aug 12, 2015

surgically, in humans, the submandibular triangle (an anatomic construct, bound by specific structures) submandibular region (part of the neck, less distinct than the triangle and broader in content), and submandibular space (potential space lined w/ cervical fascia and communicating with other fascial spaces of the head and neck) are all distinct concepts.

submandibular classes are neck classes-- the inferior border of the mandible is the transition line from face to neck.

the submandibular triangle (anatomic concept) and submandibular space (a fascial space) seem both subclasses of the submandibular region, itself a subclass of the neck.

i was uncertain how specific to get ... since this all only applies to humans (as far as i know) .

markengelstad commented Aug 12, 2015

surgically, in humans, the submandibular triangle (an anatomic construct, bound by specific structures) submandibular region (part of the neck, less distinct than the triangle and broader in content), and submandibular space (potential space lined w/ cervical fascia and communicating with other fascial spaces of the head and neck) are all distinct concepts.

submandibular classes are neck classes-- the inferior border of the mandible is the transition line from face to neck.

the submandibular triangle (anatomic concept) and submandibular space (a fascial space) seem both subclasses of the submandibular region, itself a subclass of the neck.

i was uncertain how specific to get ... since this all only applies to humans (as far as i know) .

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markengelstad Aug 12, 2015

for a functionally useful classification (in humans especially for cancer/ malignant disease), we would axiomatize to the very commonly utilized "Neck Dissection classification".
In which case, the submandibular region is known as "level IB"

the 6 levels of the neck with sublevels

markengelstad commented Aug 12, 2015

for a functionally useful classification (in humans especially for cancer/ malignant disease), we would axiomatize to the very commonly utilized "Neck Dissection classification".
In which case, the submandibular region is known as "level IB"

the 6 levels of the neck with sublevels

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markengelstad Aug 12, 2015

in fact, if were were going to "ontologize" the widely used neck dissection classification (a group of anatomical classes used in most head/ neck cancer surgeries/ diagnostics/ staging/ imaging), what would be the ontology to do it in?

markengelstad commented Aug 12, 2015

in fact, if were were going to "ontologize" the widely used neck dissection classification (a group of anatomical classes used in most head/ neck cancer surgeries/ diagnostics/ staging/ imaging), what would be the ontology to do it in?

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The neck dissection classification feels like it's getting away from uberon. FMA may be better for human-specific surgical divisions (but we could easily place them in uberon and clearly mark as human).

This is analogous to brain atlases. I think ultimately the correct representation here is an instance-level representation of a canonical organism, using the appropriate coordinate-oriented formalism. There are probably better tools than Protege for doing this, and any ontologization of the map should be an automatic transform.

We should discuss what the appropriate level of specificity for HPO is on the HPO tracker

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cmungall commented Aug 12, 2015

The neck dissection classification feels like it's getting away from uberon. FMA may be better for human-specific surgical divisions (but we could easily place them in uberon and clearly mark as human).

This is analogous to brain atlases. I think ultimately the correct representation here is an instance-level representation of a canonical organism, using the appropriate coordinate-oriented formalism. There are probably better tools than Protege for doing this, and any ontologization of the map should be an automatic transform.

We should discuss what the appropriate level of specificity for HPO is on the HPO tracker

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So I may have conflated triangle and region. I'm not sure we really need both classes in uberon. I would propose Uberon keeps region, and keeps the FMA class as a subclass, even though it's not strictly subclass.

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cmungall commented Aug 12, 2015

So I may have conflated triangle and region. I'm not sure we really need both classes in uberon. I would propose Uberon keeps region, and keeps the FMA class as a subclass, even though it's not strictly subclass.

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markengelstad Aug 12, 2015

i agree with that:

So I may have conflated triangle and region. I'm not sure we really need both classes in uberon. I would propose Uberon keeps region, and keeps the FMA class as a subclass, even though it's not strictly subclass.

markengelstad commented Aug 12, 2015

i agree with that:

So I may have conflated triangle and region. I'm not sure we really need both classes in uberon. I would propose Uberon keeps region, and keeps the FMA class as a subclass, even though it's not strictly subclass.

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Answering my own question about glands:

Domestic animals have a “mandibular gland” (or “mandibular salivary gland”) and a “mandibular lymph node”. The term "submandibular," as used in humans, is incorrect due the difference in topography of these structures.  Reference(s):  Anonymous. 
Nomina anatomica veterinaria. 4th ed. Zurich and Ithaca: World Association of Veterinary Anatomists, 1994. 
Evans HE. 
Miller's anatomy of the dog. 3rd ed. Philadelphia: WB Saunders Co, 1993

Source: http://www.avdc.org/Nomenclature.pdf

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cmungall commented Aug 12, 2015

Answering my own question about glands:

Domestic animals have a “mandibular gland” (or “mandibular salivary gland”) and a “mandibular lymph node”. The term "submandibular," as used in humans, is incorrect due the difference in topography of these structures.  Reference(s):  Anonymous. 
Nomina anatomica veterinaria. 4th ed. Zurich and Ithaca: World Association of Veterinary Anatomists, 1994. 
Evans HE. 
Miller's anatomy of the dog. 3rd ed. Philadelphia: WB Saunders Co, 1993

Source: http://www.avdc.org/Nomenclature.pdf

cmungall added a commit that referenced this issue Aug 13, 2015

* Branching structures
    * NTs for veins
    * Axiomatized spinal plexuses and ganglia using innervates relationships
 * Ontolology alignment
    * Brought in select synonyms from ZFA
    * aligned with FMA 4.0.1 - this version of FMA has many more embryonic structures
    * Generalized classes from EHDAA2: embryonic capillary plexus, yolk sac cavities
 * Other
    * NT: submandibular region. Issue #1137
    * added logical definition for endothelium
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