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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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'skeletal muscle tissue' develops_from some myotome - applicability across taxa? #324

Closed cmungall closed 3 years ago

cmungall commented 11 years ago

See: muscle

cmungall commented 11 years ago

See also: https://code.google.com/p/cell-ontology/issues/detail?id=91

dosumis commented 11 years ago

Notes for a cleanup of muscle representation in Uberon.

  1. Current structure seems to have semi-random distribution between muscle organ and muscle tissue. Much of what is under the latter (e.g. 'skeletal muscle of arm') should probably be under the former.
  2. Primary classification should be based on the relation of muscles to external anatomy. Suggested defs should be considered first draft. skeletal muscle: A muscle with insertion and/or (?) origin in a bone. comment: Having and/or includes extrinsic muscles of tongue. Excludes intrinsic muscles of tongue.

somatic muscle: A muscle with insertion and/or (?) origin in the underside of the epidermis, or its specialisations comment: and/or added as a hedge. Might be sufficient to simply have 'and' here. Need advice.. This def works for many different invertebrates (nematodes, arthropods), but does it actually include some vertebrate muscles?

cardiac muscle: A muscle whose contraction drives pumping of the heart. comment: if arthropods have a heart, then this means 'cardiac muscle' will encompass very different types as judged by internal anatomy. Might be best to add

visceral muscle: A muscle associated with the gut or other internal organs. comment: 'associated with' seems very vague. Note - this will encompass arthropod visceral muscle, which is striated. Potential edge cases includes gut and heart suspensor muscles in insects (one end inserted in epithelium - the other in the gut or hear - so could certainly say associated with these).

  1. A further classification can be made on the basis of cellular composition, with reference to [cell types in CL](See: https://code.google.com/p/cell-ontology/issues/detail?id=92):

    striated muscle cell ( % transversely striated muscle cell (examples include vertebrate skeletal & caridiac muscles and arthropod somatic & visceral muscles) % obliquely striated muscle cell (examples include nematode somatic muscle smooth muscle cell

cmungall commented 11 years ago

Tackling muscle organ vs muscle tissue first. Yes, needs cleaned up. There is also some possible confusion with musculature vs muscle.

Agreed that the grouping classes for axial muscles should be muscle organs. Note we currently have duplication such as "muscle of arm" (currently an organ) and "skeletal muscle of arm" (a tissue). The latter can be merged into the former. As a general rule, I think that muscle organs defined by a skeletally supported structures should all be composed of skeletal muscle tissue (smooth muscle organs tend to be sphincters?). What do you think of using hidden GCIs here? I will make an example edit to illustrate.

cmungall commented 11 years ago

I intended to tag this commit, see the commit notes: https://github.com/obophenotype/uberon/commit/ba762f5f2153549aced940d728c852fd97384855

cmungall commented 11 years ago

Also not clear that part_of is best for "muscle of X", the organs don't always neatly stay within boundaries.

dosumis commented 11 years ago

On 11 Sep 2013, at 21:23, Chris Mungall notifications@github.com wrote:

Also not clear that part_of is best for "muscle of X", the organs don't always neatly stay within boundaries.

True for arthropods too. Would overlaps be sufficient?

— Reply to this email directly or view it on GitHub.

cmungall commented 11 years ago

If you look at FMA then each limb muscle organ 'belongs' to a single limb subdivision. I think this reflects how people would want to see these classified. If we use overlaps then they will span categories.

dosumis commented 11 years ago

Proposed new terms. Will add by end of this week if no objections:

name: somatic muscle def: "A muscle organ (structure?) of invertebrates whose origin and insertion sites are in basal side of the epidermis or structures derived from it. The simplest somatic muscles consist of a single cell and associated extracellular structures." is_a: muscle structure relationship: attached_to epidermis

name: transversely striated somatic muscle def: "A somatic muscle that consists of one or more somatic muscle myotubes and any associated extracellular structures." [] intersection_of: somatic muscle intersection_of: composed_primarily_of somatic muscle myotube

name: obliquely striated somatic muscle def: "A somatic muscle that consists of one ore more obliquely striated muscle cells and any associated extracellular structures." [] intersection_of: somatic muscle intersection_of: composed_primarily_of 'obliquely striated somatic muscle cell'

mellybelly commented 11 years ago

Would be great to come up with a labeling scheme here. XXX-somatic-muscle could easily be confused with early chordate somite muscles.

dosumis commented 11 years ago

Proposal - split skeletal muscle tissue into tissue and organ terms:

(apologies for mega-entry. May come back to this and try to split it.)

Add 'skeletal muscle organ'

! (kind of amazing we still don't have this)!!

name: skeletal muscle organ def: "A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles). intersection_of: muscle organ intersection_of: develops_from myotome intersection_of: consists_predominantly_of skeletal muscle tissue intersection_of: synapsed_by somatic motor neuron intersection_of: surrounded_by some epimysium

Review 'skeletal muscle tissue':

Existing term for ref:

[Term] id: UBERON:0001134 name: skeletal muscle tissue def: "Striated muscle tissue under control of the somatic nervous system. It is one of three major muscle types, the others being cardiac and smooth muscle. As its name suggests, most skeletal muscle is attached to bones by bundles of collagen fibers known as tendons. Skeletal muscle is made up of individual components known as muscle fibers. These fibers are formed from the fusion of developmental myoblasts. The myofibers are long, cylindrical, multinucleated cells composed of actin and myosin myofibrils repeated as a sarcomere, the basic functional unit of the cell and responsible for skeletal muscle's striated appearance and forming the basic machinery necessary for muscle contraction. The term muscle refers to multiple bundles of muscle fibers held together by connective tissue[WP]." [Wikipedia:Skeletal_striated_muscle] xref: Wikipedia:Skeletal_striated_muscle comment: TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle. subset: uberon_slim subset: vertebrate_core synonym: "skeletal muscle" EXACT [] synonym: "skeletal muscle organ" RELATED [] synonym: "skeletal muscle system" RELATED [BTO:0001103] synonym: "somatic muscle" RELATED [BTO:0001103] xref: BTO:0001103 ! skeletal muscle xref: EFO:0000888 ! skeletal muscle xref: EHDAA:2923 ! skeletal muscle (also: UBERON:0003269 'skeletal muscle of eye') xref: EHDAA:5035 ! skeletal muscle xref: EHDAA:5043 ! skeletal muscle xref: EHDAA:5978 ! skeletal muscle xref: EHDAA:5984 ! skeletal muscle xref: FMA:14069 ! Skeletal muscle tissue xref: VHOG:0000319 ! skeletal muscle xref: MA:0002439 ! skeletal muscle tissue xref: MAT:0000302 ! skeletal muscle xref: MIAA:0000302 ! skeletal muscle xref: OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA xref: XAO:0000174 ! skeletal muscle xref: ncithesaurus:Skeletal_Muscle_Tissue ! Skeletal Muscle Tissue xref: ZFA:0005277 ! skeletal muscle xref: GAID:141 ! skeletal muscle xref: OpenCyc:Mx4rv2kf-5wpEbGdrcN5Y29ycA ! skeletal muscle xref: MESH:A02.633.567 ! skeletal muscle xref: EV:0100377 ! skeletal muscle xref: EHDAA2:0001842 ! skeletal muscle system intersection_of: UBERON:0002036 ! striated muscle tissue intersection_of: has_part CL:0000188 ! skeletal muscle cell relationship: composed_primarily_of CL:0000188 ! skeletal muscle cell disjoint_from: UBERON:0001133 ! cardiac muscle tissue relationship: develops_from UBERON:0003082 ! myotome xref: AAO:0011099 ! skeletal muscle xref: SCTID:426215008 ! Skeletal muscle tissue xref: TAO:0005277 ! skeletal muscle xref: http://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal\_muscle.jpg property_value: external_definition "Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]" xsd:string {ontology="TAO", external_class="TAO:0005277", date_retrieved="2012-08-14", source="ZFIN:curator"} property_value: external_definition "Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]" xsd:string {ontology="FMA", external_class="FMA:14069"} property_value: homology_notes "This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]" xsd:string {external_class="VHOG:0000319", ontology="VHOG", source="PMID:10368962 Oota S\, Saitou N\, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999)", source="http://bgee.unil.ch/", date_retrieved="2012-09-17"} relationship: homologous_in NCBITaxon:7742 {source="VHOG:0000319"} ! Vertebrata xref: CALOHA:TS-0933 xref: UMLS:C0242692 {source="ncithesaurus:Skeletal_Muscle_Tissue"} xref: EMAPA:32716 ! skeletal muscle

intersection_of: UBERON:0002036 ! striated muscle tissue intersection_of: has_part CL:0000188 ! skeletal muscle cell relationship: composed_primarily_of CL:0000188 ! skeletal muscle cell => intersection_of: muscle tissue intersection_of: consists_primarily_of CL:'skeletal muscle fiber'

We may be able to automate classification of striated muscle tissues as

striated muscle tissue intersection_of: muscle tissue ! (or perhaps just tissue) intersection_of: consists_primarily_of CL:striated muscle cell

General patterns

<SubClassOf 'muscle organ'> Equivalent To organ that composed_primarily_of some and ....

<SubClassOf 'muscle tissue'> EquivalentTo tissue that composed_primarily_of some

<SubClassOf 'muscle cell' EquivalentTo 'muscle cell' that part_of some <SubClassOf 'muscle organ/structure'> ??? - is circularity here problematic?

The key issue here is that specific muscle cell types require a combination of differentia based on ultrastructure and differentia based on what they part of - coming from Uberon. It makes most sense to use an organ term for this as this links it to the broader anatomical context whereas tissue terms are defined primarily by their composition. But we can't use 'skeletal muscle organ' for this because branchiomeric muscles because have essentially the same cellular and tissue composition (check!), but are not classified as skeletal due to their different developmental origin. Can we define a parent term for both branchiomeric and skeletal muscle organs?

Review definition of branchomeric muscle

Currently we have:

[Term] id: UBERON:0004164 name: branchiomeric muscle def: "A jaw muscle that arises from cranial mesenchyme and is innervated by cranial nerves." [ISBN10:0073040584] xref: Wikipedia:Branchiomeric_musculature synonym: "branchiomeric skeletal muscle" EXACT [GO:0014707] is_a: UBERON:0001630 ! muscle organ relationship: develops_from UBERON:0010360 {source="PMID:21610022"} ! pharyngeal arch mesenchyme from head mesenchyme relationship: innervated_by UBERON:0001785 {source="ISBN10:0073040584"} ! cranial nerve relationship: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue property_value: external_definition "The branchiomeric muscle is derived from cranial mesoderm and controls facial expression, pharyngeal and laryngeal function, operating the jaw. Branchiomeric muscles of mammals correspond to theproperty_value external_definitionmusculature of fish[GO][GO:0014707]." xsd:string {source="GO:0014707"}

Based on the Wikipedia entry, the external textual definition looks rather better than the regular one. The most important differentium seems to be developmental origin.

relationship: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue

as long as the develops_from clause is on skeletal muscle structure, not skeletal muscle tissue, I think we're fine.

cmungall commented 11 years ago

@RDruzinsky - opinions on branchiomeric muscle? ISBN10:0073040584 is Kardong, which is our usual fallback.

cmungall commented 11 years ago

Skeletal muscle organ

Added. See: https://github.com/obophenotype/uberon/commit/c0d65a04af215e5091af7eb27b39698748e076b5

David, will you add 'somatic motor neuron' to CL?

We should experiment with clauses in and out of the ECA vs SCA/hidden GCIs to see effects on autoclassification.

cmungall commented 11 years ago

somatic muscle notes:

cmungall commented 11 years ago

Melissa - is the possible confusion due to the lexical proximity of somatic and somitic? Are the taxon constraints sufficient? It's much easier now to produce taxon specific views. We can also add an extra redundant but explicit-for-humans disjointness axiom

RDruzinsky commented 11 years ago

I think that the def "A jaw muscle that arises from cranial mesenchyme and is innervated by cranial nerves" is not quite precise enough. Melissa should weigh-in on this. A better term that I think would be a synonym is probably "cranial paraxial mesoderm." Unfortunately, neither of those terms distinguishes between branchiomeric muscles and extra-ocular muscles. I think that to differentiate between branchiomeric and extra-ocular muscles there must be some reference to the branchial/pharyngeal arches in the def for branchiomeric muscles. The cranial paraxial mesoderm migrates into the precursors that become the pharyngeal arches. I don't know whether there is any distinguishing feature other than that. There may be genetic markers that allow one to identify those cells before they are in the pharyngeal arches but I don't know that literature.

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 Tue, Oct 29, 2013 at 3:37 PM, Chris Mungall notifications@github.comwrote:

@RDruzinsky https://github.com/RDruzinsky - opinions on branchiomeric muscle? ISBN10:0073040584 is Kardong, which is our usual fallback.

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/324#issuecomment-27341082 .

dosumis commented 11 years ago

Hi Robert,

Agree that getting the developmental differentium right is critical here. My other major concern was that 'jaw muscle' was too narrow a genus term for the text def. I got the impression from the wikipedia article that this class covers a broader range of facial muscles that just those of the jaw. Is this correct?

It seems to be backed up this article on the branchiomotor neurons, which are defined as motor neurons that innervate branchiomeric muscles: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2219919&tool=pmcentrez&rendertype=abstract

Cheers, David

RDruzinsky commented 10 years ago

David, you are absolutely correct. A branchial or pharyngeal muscle is one that is one that develops from a pharyngeal arch structure. In chordates with jaws, some of those are "jaw muscles." But, for example, facial muscles are branchial muscles (innervated by CN VII) but not jaw muscles. The term "jaw muscle" is often used as a synonym for trigeminal muscle, but the term is used loosely. Tongue muscles are innervated by a cranial nerve (hypoglossal, CN XII) but they are not branchial muscles. They derive from "head somites."

In the FEED project we have settled on the term oro-pharyngeal or oral-pharyngeal muscle, which we define (again, quite loosely) as a muscle that participates in feeding and other oral/pharyngeal behaviors. We use this term because it is a narrower category than "muscles of the head and neck" but much broader than "jaw muscles" or even "branchial muscles."

Hope this is helpful,

Robert

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, Oct 30, 2013 at 6:41 AM, David Osumi-Sutherland < notifications@github.com> wrote:

Hi Robert,

Agree that getting the developmental differentium right is critical here. My other major concern was that 'jaw muscle' was too narrow a genus term for the text def. I got the impression from the wikipedia article that this class covers a broader range of facial muscles that just those of the jaw. Is this correct?

Cheers, David

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/324#issuecomment-27382229 .

cmungall commented 10 years ago

It will take some effort to coordinate this proposed developmental definition of pharyngeal/branchial muscle across ontologies.

ZFA has "branchial muscle" which is undefined, and has part_of to PA3-7 (i.e. the "branchial" arches, in this sense of "branchial")

WP says "A muscle that acts on the pharynx"

GO says "A pharyngeal muscle is any muscle that forms part of the pharynx"

FMA has

(not defined)

These obviously overlap with but are not identical to the developmental definition.

I don't like awkward names, but it seems that using a label such as "pharyngeal arch-derived muscle" avoids confusion.

dosumis commented 10 years ago

Thanks Robert. Just what I needed to know.

Couple more questions:

  1. Do you have any suggestion for what to call a general classification of muscles covering both skeletal and branchiomeric?
  2. Is the structure of branchiomeric muscle tissue and constituent myotubes basically the same as that of skeletal muscle? If not, do you have any good suggestions for references describing the differences?

Cheers, David

On 31 Oct 2013, at 15:51, RDruzinsky notifications@github.com wrote:

David, you are absolutely correct. A branchial or pharyngeal muscle is one that is one that develops from a pharyngeal arch structure. In chordates with jaws, some of those are "jaw muscles." But, for example, facial muscles are branchial muscles (innervated by CN VII) but not jaw muscles. The term "jaw muscle" is often used as a synonym for trigeminal muscle, but the term is used loosely. Tongue muscles are innervated by a cranial nerve (hypoglossal, CN XII) but they are not branchial muscles. They derive from "head somites."

In the FEED project we have settled on the term oro-pharyngeal or oral-pharyngeal muscle, which we define (again, quite loosely) as a muscle that participates in feeding and other oral/pharyngeal behaviors. We use this term because it is a narrower category than "muscles of the head and neck" but much broader than "jaw muscles" or even "branchial muscles."

Hope this is helpful,

Robert

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, Oct 30, 2013 at 6:41 AM, David Osumi-Sutherland < notifications@github.com> wrote:

Hi Robert,

Agree that getting the developmental differentium right is critical here. My other major concern was that 'jaw muscle' was too narrow a genus term for the text def. I got the impression from the wikipedia article that this class covers a broader range of facial muscles that just those of the jaw. Is this correct?

Cheers, David

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/324#issuecomment-27382229 .

— Reply to this email directly or view it on GitHub.

dosumis commented 10 years ago

On 31 Oct 2013, at 20:21, Chris Mungall notifications@github.com wrote:

It will take some effort to coordinate this proposed developmental definition of pharyngeal/branchial muscle across ontologies.

ZFA has "branchial muscle" which is undefined, and has part_of to PA3-7 (i.e. the "branchial" arches, in this sense of "branchial")

Could be the same thing. WP says "A muscle that acts on the pharynx"

Worms are irrelevant to this. The key differentium is development from the branchial/pharyngeal arch. Only makes sense for vertebrates. part relationships to any structure called a pharynx are irrelevant.

GO says "A pharyngeal muscle is any muscle that forms part of the pharynx"

That's fine. This is structurally, rather than developmentally defined.
FMA has

FMA:5022 ! Muscle organ FMA:9617 ! Muscle of neck FMA:46619 ! Muscle of pharynx FMA:46620 ! Constrictor muscle of pharynx FMA:46664 ! Stylopharyngeus FMA:46665 ! Salpingopharyngeus FMA:46666 ! Palatopharyngeus (not defined)

These obviously overlap with but are not identical to the developmental definition.

Again, structurally defined. Probably all are pharyngeal, but in the end, the only reliable mapping will come from assertion of developmental origin. I don't like awkward names, but it seems that using a label such as "pharyngeal arch-derived muscle" avoids confusion.

Seems like a reasonable name. Although branchiomeric doesn't seem particularly confusing to me. — Reply to this email directly or view it on GitHub.

RDruzinsky commented 10 years ago

Hi,

I think of branchial muscles as a type of skeletal muscles. I'll have to do a bit of research to figure out whether others think of them the same way. Certainly "muscles innervated by alpha motor neurons" works.

As far as I know, the basic structure is the same. There is some evidence that there are some differences in the combinations of fiber types in adult muscles, but I don't know if anyone has looked at this carefully. I think that most people would say that the basic structure is the same.

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, Oct 31, 2013 at 5:12 PM, David Osumi-Sutherland < notifications@github.com> wrote:

Thanks Robert. Just what I needed to know.

Couple more questions:

  1. Do you have any suggestion for what to call a general classification of muscles covering both skeletal and branchiomeric?
  2. Is the structure of branchiomeric muscle tissue and constituent myotubes basically the same as that of skeletal muscle? If not, do you have any good suggestions for references describing the differences?

Cheers, David

On 31 Oct 2013, at 15:51, RDruzinsky notifications@github.com wrote:

David, you are absolutely correct. A branchial or pharyngeal muscle is one that is one that develops from a pharyngeal arch structure. In chordates with jaws, some of those are "jaw muscles." But, for example, facial muscles are branchial muscles (innervated by CN VII) but not jaw muscles. The term "jaw muscle" is often used as a synonym for trigeminal muscle, but the term is used loosely. Tongue muscles are innervated by a cranial nerve (hypoglossal, CN XII) but they are not branchial muscles. They derive from "head somites."

In the FEED project we have settled on the term oro-pharyngeal or oral-pharyngeal muscle, which we define (again, quite loosely) as a muscle that participates in feeding and other oral/pharyngeal behaviors. We use this term because it is a narrower category than "muscles of the head and neck" but much broader than "jaw muscles" or even "branchial muscles."

Hope this is helpful,

Robert

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, Oct 30, 2013 at 6:41 AM, David Osumi-Sutherland < notifications@github.com> wrote:

Hi Robert,

Agree that getting the developmental differentium right is critical here. My other major concern was that 'jaw muscle' was too narrow a genus term for the text def. I got the impression from the wikipedia article that this class covers a broader range of facial muscles that just those of the jaw. Is this correct?

Cheers, David

— Reply to this email directly or view it on GitHub< https://github.com/obophenotype/uberon/issues/324#issuecomment-27382229> .

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/324#issuecomment-27533717 .

cmungall commented 10 years ago

On Fri, Nov 1, 2013 at 2:26 AM, David Osumi-Sutherland < notifications@github.com> wrote:

Could be the same thing.

WP says "A muscle that acts on the pharynx"

Worms are irrelevant to this.

Sorry. I meant WP = wikipedia

cmungall commented 10 years ago

Ah OK, I think we're at cross-purposes. I was talking about the string "pharyngeal muscle", not about "branchiometric muscle"

I was responding to Robert's point "A branchial or pharyngeal muscle is one that is one that develops from a pharyngeal arch structure"

I like having a class for "muscle organ and develops_from some pharyngeal arch". My main point was that if we call this class expression "pharyngeal muscle", then we may end up with a terminological misalignment with other resources, which reserve this string for other definitions, implicitly or explicitly.

dosumis commented 10 years ago

On 3 Nov 2013, at 19:42, Chris Mungall notifications@github.com wrote:

Ah OK, I think we're at cross-purposes. I was talking about the string "pharyngeal muscle", not about "branchiometric muscle"

I was responding to Robert's point "A branchial or pharyngeal muscle is one that is one that develops from a pharyngeal arch structure"

I like having a class for "muscle organ and develops_from some pharyngeal arch". My main point was that if we call this class expression "pharyngeal muscle", then we may end up with a terminological misalignment with other resources, which reserve this string for other definitions, implicitly or explicitly.

So presumably branchiomeric is a better name for "muscle organ and develops_from some pharyngeal arch", as pharyngeal could refer to partonomy or developmental origin.

I'd still like a general name that covers both skeletal and branchiomeric, as I'd like to use this to define skeletal muscle fiber in CL as something ditinct from somatic muscle myotubes. I guess basically what we need though is a way to define (& name?) vertebrate myotubes.

Reply to this email directly or view it on GitHub.

RDruzinsky commented 10 years ago

I should have been more careful and said "pharyngeal arch muscle." Sorry.

I'd still like a general name that covers both skeletal and branchiomeric, as I'd like to use this to define skeletal muscle fiber in CL as something ditinct from somatic muscle myotubes. I guess basically what we need though is a way to define (& name?) vertebrate myotubes . -- This is problematic. What does one do with facial muscles? They are branchiomeric muscles that attach to skin and 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 Sun, Nov 3, 2013 at 1:52 PM, David Osumi-Sutherland < notifications@github.com> wrote:

On 3 Nov 2013, at 19:42, Chris Mungall notifications@github.com wrote:

Ah OK, I think we're at cross-purposes. I was talking about the string "pharyngeal muscle", not about "branchiometric muscle"

I was responding to Robert's point "A branchial or pharyngeal muscle is one that is one that develops from a pharyngeal arch structure"

I like having a class for "muscle organ and develops_from some pharyngeal arch". My main point was that if we call this class expression "pharyngeal muscle", then we may end up with a terminological misalignment with other resources, which reserve this string for other definitions, implicitly or explicitly.

So presumably branchiomeric is a better name for "muscle organ and develops_from some pharyngeal arch", as pharyngeal could refer to partonomy or developmental origin.

I'd still like a general name that covers both skeletal and branchiomeric, as I'd like to use this to define skeletal muscle fiber in CL as something ditinct from somatic muscle myotubes. I guess basically what we need though is a way to define (& name?) vertebrate myotubes.

Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/324#issuecomment-27652476 .

dosumis commented 10 years ago

Just to be clear - when I talk about somatic muscle myotubes, I'm referring to invertebrate somatic muscles myotubes (e.g. those of arthropods).

RDruzinsky commented 10 years ago

If that is a part of the definition that excludes chordates, then is your problem just coming up with a name for the class that includes skeletal and branchiomeric muscles in chordates?

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 Sun, Nov 3, 2013 at 2:21 PM, David Osumi-Sutherland < notifications@github.com> wrote:

Just to be clear - when I talk about somatic muscle myotubes, I'm referring to invertebrate somatic muscles myotubes (e.g. those of arthropods).

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/324#issuecomment-27653136 .

dosumis commented 10 years ago

On 3 Nov 2013, at 20:33, RDruzinsky notifications@github.com wrote:

If that is a part of the definition that excludes chordates, then is your problem just coming up with a name for the class that includes skeletal and branchiomeric muscles in chordates?

Yes

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 Sun, Nov 3, 2013 at 2:21 PM, David Osumi-Sutherland < notifications@github.com> wrote:

Just to be clear - when I talk about somatic muscle myotubes, I'm referring to invertebrate somatic muscles myotubes (e.g. those of arthropods).

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/324#issuecomment-27653136 .

— Reply to this email directly or view it on GitHub.

RDruzinsky commented 10 years ago

What about something like "chordate striated muscle" or something like that? Or just striated muscle that develops from some somite or somitomere?

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 Sun, Nov 3, 2013 at 2:45 PM, David Osumi-Sutherland < notifications@github.com> wrote:

On 3 Nov 2013, at 20:33, RDruzinsky notifications@github.com wrote:

If that is a part of the definition that excludes chordates, then is your problem just coming up with a name for the class that includes skeletal and branchiomeric muscles in chordates?

Yes

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 Sun, Nov 3, 2013 at 2:21 PM, David Osumi-Sutherland < notifications@github.com> wrote:

Just to be clear - when I talk about somatic muscle myotubes, I'm referring to invertebrate somatic muscles myotubes (e.g. those of arthropods).

— Reply to this email directly or view it on GitHub< https://github.com/obophenotype/uberon/issues/324#issuecomment-27653136> .

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/324#issuecomment-27653793 .

cmungall commented 10 years ago

This thread could probably be broken out into individual tickets...

Some additional notes for now:

Extra-ocular muscles. As I understand these are traditionally classified as skeletal and derive from cranial mesenchyme, not somites. I'm not sure about similarities to branchiomeric. So these muscles would also appear to break our axiom that skeletal muscles derive from somites.

More on distinction between extra-ocular and trunk somitic muscle: http://www.ncbi.nlm.nih.gov/pubmed/16638982

This paper was used to make this distinction in GO:

[Term]
id: GO:0002074
name: extraocular skeletal muscle development
namespace: biological_process
def: "The process whose specific outcome is the progression of the extraocular skeletal muscle over time, from its formation to the mature structure. The extraocular muscle is derived from cranial mesoderm and controls eye movements. The muscle begins its development with the differentiation of the muscle cells and ends with the mature muscle. An example of this process is found in Mus musculus." [GOC:dph, GOC:mtg_muscle, GOC:mtg_sensu, MA:0001271, PMID:16638982]
is_a: GO:0007519 ! skeletal muscle tissue development
relationship: part_of GO:0043010 ! camera-type eye development

[Term]
id: GO:0002075
name: somitomeric trunk muscle development
namespace: biological_process
def: "The process whose specific outcome is the progression of the somitomeric trunk muscle over time, from its formation to the mature structure. The somitomeric trunk muscle is derived from somitomeric mesoderm. The muscle begins its development with the differentiation of the muscle cells and ends with the mature muscle. An example of this process is found in Mus musculus." [GOC:dph, PMID:16638982]
is_a: GO:0007519 ! skeletal muscle tissue development
cmungall commented 10 years ago

Note that GO:0002075 has no annotations and child terms in GO, which I believe is an error of omission

cewall commented 10 years ago

The extra-ocular muscles derive from head paraxial mesoderm (aka somitomeres). Not sure if neural crest cells are incorporated into the connective tissue of these muscles as in branchial arch skeletal muscle. Noden in his papers refers to the extraocular muscles as "skeletal muscles", e.g., here is an image I copied from Noden and Trainor, 2005, J Anatomy 207

[http://onlinelibrary.wiley.com/store/10.1111/j.1469-7580.2005.00473.x/asset/image_n/JOA_473_f3.gif?v=1&t=hx97vg2u&s=fff60d7de2e41948b7a82b7df3b17101906640de]

From: Chris Mungall notifications@github.com Sent: Friday, July 04, 2014 8:26 PM To: obophenotype/uberon Subject: Re: [uberon] 'skeletal muscle tissue' develops_from some myotome - applicability across taxa? (#324)

This thread could probably be broken out into individual tickets...

Some additional notes for now:

Extra-ocular muscles. As I understand these are traditionally classified as skeletal and derive from cranial mesenchyme, not somites. I'm not sure about similarities to branchiomeric. So these muscles would also appear to break our axiom that skeletal muscles derive from somites.

More on distinction between extra-ocular and trunk somitic muscle: http://www.ncbi.nlm.nih.gov/pubmed/16638982

This paper was used to make this distinction in GO:

[Term] id: GO:0002074 name: extraocular skeletal muscle development namespace: biological_process def: "The process whose specific outcome is the progression of the extraocular skeletal muscle over time, from its formation to the mature structure. The extraocular muscle is derived from cranial mesoderm and controls eye movements. The muscle begins its development with the differentiation of the muscle cells and ends with the mature muscle. An example of this process is found in Mus musculus." [GOC:dph, GOC:mtg_muscle, GOC:mtg_sensu, MA:0001271, PMID:16638982] is_a: GO:0007519 ! skeletal muscle tissue development relationship: part_of GO:0043010 ! camera-type eye development

[Term] id: GO:0002075 name: somitomeric trunk muscle development namespace: biological_process def: "The process whose specific outcome is the progression of the somitomeric trunk muscle over time, from its formation to the mature structure. The somitomeric trunk muscle is derived from somitomeric mesoderm. The muscle begins its development with the differentiation of the muscle cells and ends with the mature muscle. An example of this process is found in Mus musculus." [GOC:dph, PMID:16638982] is_a: GO:0007519 ! skeletal muscle tissue development

Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/324#issuecomment-48075274.

gouttegd commented 3 years ago

WARNING: This issue has been automatically closed because it has not been updated in more than 3 years. Please re-open it if you still need this to be addressed addressed addressed – we are now getting some resources to deal with such issues.