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Ontologies for mouse anatomy and development
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pterygoid is_a facial muscle? #12

Open cmungall opened 9 years ago

cmungall commented 9 years ago

in EMAPA, the pterygoid (grouping for lateral and medial pterygoid) as classified as facial muscles.

facial muscles are usually defined as those that control facial expression and are innervated by the facial nerve. See

cc @RDruzinsky, FEED currently has:

[Term]
id: MFMO:0000005
name: facial muscle
comment: Term in Uberon is equivalent but the definition needs revision.
xref: obo:UBERON_0001577
intersection_of: UBERON:0001630  ! muscle organ
intersection_of: develops_from UBERON:0003066 ! branchial arch 2
intersection_of: innervated_by UBERON:0001647 ! facial nerve

We could have uberon follow the pattern in feed where we name the muscles more explicitly such as 'facial nerve muscle'. That way EMAPA's facial muscle could simply be 'muscle of part of face' without confusion... but I'm guessing the intent is to have the EMAPA class align with the traditional concept and the placement of pterygoid is a mistake.

RDruzinsky commented 9 years ago

My guess is that the EMAPA categorization is just sloppy. Pterygoid muscles and other muscles of mastication are very rarely described as "facial" muscles. They are only muscles of the face in the very broadest sense.

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 Sun, Apr 12, 2015 at 3:11 PM, Chris Mungall notifications@github.com wrote:

in EMAPA, the pterygoid (grouping for lateral and medial pterygoid) as classified as facial muscles.

facial muscles are usually defined as those that control facial expression and are innervated by the facial nerve. See

cc @RDruzinsky https://github.com/RDruzinsky, FEED currently has:

[Term] id: MFMO:0000005 name: facial muscle comment: Term in Uberon is equivalent but the definition needs revision. xref: obo:UBERON_0001577 intersection_of: UBERON:0001630 ! muscle organ intersection_of: develops_from UBERON:0003066 ! branchial arch 2 intersection_of: innervated_by UBERON:0001647 ! facial nerve

We could have uberon follow the pattern in feed where we name the muscles more explicitly such as 'facial nerve muscle'. That way EMAPA's facial muscle could simply be 'muscle of part of face' without confusion... but I'm guessing the intent is to have the EMAPA class align with the traditional concept and the placement of pterygoid is a mistake.

— Reply to this email directly or view it on GitHub https://github.com/obophenotype/mouse-anatomy-ontology/issues/12.

cmungall commented 9 years ago

Others should be checked too:

      po EMAPA:25133 ! facial muscle 
       is_a EMAPA:25134 ! digastric
       is_a EMAPA:25135 ! masseter ***
       is_a EMAPA:25136 ! mylohyoid
       is_a EMAPA:25137 ! sterno-mastoid
       is_a EMAPA:25138 ! temporalis ***
       is_a EMAPA:25139 ! pterygoid ***
cmungall commented 9 years ago 
    is_a MA:0000579 ! cranial/facial muscle ***  [xref: EMAPS:3526528] <-- ? in EMAPA
        is_a MA:0003115 ! masticatory muscle
        is_a MA:0003160 ! facial muscle [xref: EMAPS:2513328] <-- facial muscle EMAPA:25133 in EMAPA

Maybe EMAPA:25133 should be associated with and relabeled as MA:0000579 ! cranial/facial muscle

RDruzinsky commented 9 years ago

I will go through all of the MFMO muscles.

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 Mon, Apr 13, 2015 at 11:22 AM, Chris Mungall notifications@github.com wrote:

is_a MA:0000579 ! cranial/facial muscle ***  [xref: EMAPS:3526528] <-- ? in EMAPA
    is_a MA:0003115 ! masticatory muscle
    is_a MA:0003160 ! facial muscle [xref: EMAPS:2513328] <-- facial muscle EMAPA:25133 in EMAPA

Maybe EMAPA:25133 should be associated with and relabeled as MA:0000579 ! cranial/facial muscle

— Reply to this email directly or view it on GitHub https://github.com/obophenotype/mouse-anatomy-ontology/issues/12#issuecomment-92415930 .

tfhayamizu commented 9 years ago

EMAPA:35265 has been merged (retained as alt.) with EMAPA:25133. I have not gotten around to making corresponding changes in the MA. I can rename as cranial/facial muscle and change the xref in MA file. I will leave MA:0003160 (without EMAPA xref) in the MA for now and further consider (renamed as "facial nerve muscle"?) for the mouse.