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tongue muscles #331

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cmungall opened this Issue Sep 11, 2013 · 6 comments

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cmungall commented Sep 11, 2013

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.

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cmungall commented Sep 11, 2013

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?

cmungall added a commit that referenced this issue Sep 11, 2013

* Various tongue muscle refactoring. Addresses issue #331
  * NT: lingual septum
  * Aligned some text defs with FEED
  * Improved some wikipedia derived defs
  * Changed equiv axioms for tongue muscle, extrinsic and intrinsic
  * Made child terms complete wrt attachments
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RDruzinsky commented Sep 12, 2013

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//issues/331#issuecomment-24275824
.

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mellybelly commented Sep 12, 2013

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

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dosumis commented Sep 12, 2013

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)

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RDruzinsky commented Sep 12, 2013

"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//issues/331#issuecomment-24316633
.

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cmungall commented Sep 12, 2013

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.

mellybelly added a commit that referenced this issue Sep 19, 2013

Merge branch 'master' of https://github.com/obophenotype/uberon
# By Chris Mungall
# Via Chris Mungall
* 'master' of https://github.com/obophenotype/uberon: (27 commits)
  * Fixed EquivClass axioms for axiom muscl(e/ature) to restrict to axial skeleton
  fixed typos
  null
  * Merged skeletal muscle tissue of leg, pelvic girdle into muscle organ classes
  * NT: Annule of Zinn  * Adding comments and relationships to eye muscles
  * Removed non-unicode character. Fixes #332
  * Applied rule for adding muscle organ part_of musculature
  * Musculature overhaul - ensured musculature complete w.r.t. muscle organs
  fix
  * Various tongue muscle refactoring. Addresses issue #331   * NT: lingual septum   * Aligned some text defs with FEED   * Improved some wikipedia derived defs   * Changed equiv axioms for tongue muscle, extrinsic and intrinsic   * Made child terms complete wrt attachments
  Merging skeletal muscle of arm into muscle of arm.
  null
  * Remapped EHDAA2, added notes on eye smooth muscle. Addresses #324
  null
  * Added contribution of umbilical cord to umbilicus
  * Changed naming convention for extraembryonic umbilical veins. Fixes issue #328
  * NTs for subdivision of umbilical vein into extraembryonic and embryonic portions. Fixes issue #328      * Removed redundant synonym. Fixes issue #329      * NTs: cloacal muscles      * Fixed typo in syn. Fixes issue #327
  typo fixed
  typo fixed
  typo fixed
  ...

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

merging 'skeletal muscle of tongue' into 'tongue muscle' as all tongu…
…e muscles are skeletal (FEED:rd)

This addresses #331
Note this also accompanies commit 1600 to phenotype ontologies
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