tongue muscles

[cmungall]

This issue stemmed from @dosumis' suggested def in #324

What should the logical def be for extrinsic and intrinsic muscles of the tongue?

@RDruzinsky - in FEED you have only the intrinsic defined

text: "The intrinsic tongue muscles are an integral part of the tongue and completely contained within the tongue that are innervated by Cranial Nerve XII."

equivalentTo: ('innervated by' some 'hypoglossal nerve') and ('attached to' only tongue) subClassOf: part_of some tongue ## hidden GCI

The use of 'only' here excludes any muscle organ attached to both the tongue and, say, the mandibular symphysis - these would be extrinsic. Nice, this is just what we want.

However, alarm bells always ring when I see 'only' axioms. These can often be counter-intuitive.

Try this: create a subclass of this class - say inferior longitudinal - add axioms that say this attaches the apex of the tongue to the root of the tongue. Add disjointness axioms between apex and root of tongue. They become unsatisfiable.

You can get around this by saying 'attached to' only (tongue or part_of some tongue). But there still may be some odd consequences.

How about instead moving the subclass axiom in as an element of the equivalence axiom. this rules out the extrinsics, as they all have some part outside the tongue.

As a bonus, we stay in EL (and can use Elk for classification)

Defining the extrinsic in EL may be harder.

[cmungall]

Also related to #324 - I like the idea of defining skeletal muscle by attachment - by this def the tongue intrinsic defs would be non-skeletal. But is this right? EHDAA2 classifies them as skeletal.

Complicating the picture, is it not the case that some intrinsic muscles do actually have some fibers connecting to bone? Do we need a stronger def of attachment that excludes this?

[RDruzinsky]

This issue is a beautiful illustration of the poor nature of some of the categories that humans create for anatomical structures. Skeletal muscle is an old term that works most of the time but not all of the time. It really means "voluntary" muscle innervated by motor neurons in the brainstem or spinal cord. Intrinsic and extrinsic tongue muscles are derived from occipital somites (Noden and Francis-West DEVELOPMENTAL DYNAMICS 235:1194 –1218, 2006) and they are clearly "skeletal" muscles, even though the intrinsic muscles of the tongue have no direct connections to bones. Perhaps we could use the term "voluntary" and make "skeletal" a synonym so that no one will worry if there is no attachment to bone?

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: 312-996-6054 Lab: 312-996-0629

On Wed, Sep 11, 2013 at 3:58 PM, Chris Mungall notifications@github.comwrote:

Also related to #324 https://github.com/obophenotype/uberon/issues/324- I like the idea of defining skeletal muscle by attachment - by this def the tongue intrinsic defs would be non-skeletal. But is this right? EHDAA2 classifies them as skeletal.

Complicating the picture, is it not the case that some intrinsic muscles do actually have some fibers connecting to bone? Do we need a stronger def of attachment that excludes this?

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/331#issuecomment-24275824 .

[mellybelly]

I second Robert's notion here. What we really care about (e.g. aggregate by) is voluntary and type of innervation.

[dosumis]

I suspect that defining voluntary would be hard, especially if we want this to apply across a very broad range of species. Perhaps we can define structurally in terms of the type of innervation:

How about: A muscle innervated by motor neurons originating in the brainstem or spinal cord.

Or perhaps just 'A muscle innervated by somatic motor neurons' ?? (see http://en.wikipedia.org/wiki/Motor_neuron)

[RDruzinsky]

"Somatic" is problematic. Muscles derived from branchial arches are not "somatic." Traditionally, they are considered "special visceral efferent," a category I loath. I think something like "muscles innervated by alpha motor neurons" might work.

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: 312-996-6054 Lab: 312-996-0629

On Thu, Sep 12, 2013 at 8:02 AM, David Osumi-Sutherland < notifications@github.com> wrote:

I suspect that defining voluntary would be hard, especially if we want this to apply across a very broad range of species. Perhaps we can define structurally in terms of the type of innervation:

How about: A muscle innervated by motor neurons originating in the brainstem or spinal cord.

Or perhaps just 'A muscle innervated by somatic motor neurons' ?? (see http://en.wikipedia.org/wiki/Motor_neuron)

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/331#issuecomment-24316633 .

[cmungall]

We may try and set up a call to discuss this.

As an interim step, it seems like a conservative step forward would be avoid hardcoding any assumptions about "skeletal" or not in uberon for any subclasses of 'muscle organ' - we specify some combo of innervations, attachments etc and then infer the rest based on what we decide here.

[gouttegd]

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