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'skeletal muscle tissue' develops_from some myotome - applicability across taxa? #324
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Notes for a cleanup of muscle representation in Uberon.
somatic muscle: A muscle with insertion and/or (?) origin in the underside of the epidermis, or its specialisations cardiac muscle: A muscle whose contraction drives pumping of the heart. visceral muscle: A muscle associated with the gut or other internal organs.
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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. |
I intended to tag this commit, see the commit notes: ba762f5 |
Also not clear that part_of is best for "muscle of X", the organs don't always neatly stay within boundaries. |
On 11 Sep 2013, at 21:23, Chris Mungall notifications@github.com wrote:
True for arthropods too. Would overlaps be sufficient?
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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. |
# 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 ...
Proposed new terms. Will add by end of this week if no objections:name: somatic muscle
name: transversely striated somatic muscle name: obliquely striated somatic muscle |
Would be great to come up with a labeling scheme here. XXX-somatic-muscle could easily be confused with early chordate somite muscles. |
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
Review 'skeletal muscle tissue':Existing term for ref: [Term]
intersection_of: UBERON:0002036 ! striated muscle tissue We may be able to automate classification of striated muscle tissues as striated muscle tissue 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 muscleCurrently we have: [Term] 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. |
@RDruzinsky - opinions on branchiomeric muscle? ISBN10:0073040584 is Kardong, which is our usual fallback. |
Skeletal muscle organAdded. See: 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. |
somatic muscle notes:
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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 |
I think that the def "A jaw muscle that arises from cranial mesenchyme and Robert E. Druzinsky, Ph.D. Office: 312-996-6054 On Tue, Oct 29, 2013 at 3:37 PM, Chris Mungall notifications@github.comwrote:
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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, you are absolutely correct. A branchial or pharyngeal muscle is one In the FEED project we have settled on the term oro-pharyngeal or Hope this is helpful, Robert Robert E. Druzinsky, Ph.D. Office: 312-996-6054 On Wed, Oct 30, 2013 at 6:41 AM, David Osumi-Sutherland <
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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. |
Thanks Robert. Just what I needed to know. Couple more questions:
Cheers, On 31 Oct 2013, at 15:51, RDruzinsky notifications@github.com wrote:
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On 31 Oct 2013, at 20:21, Chris Mungall notifications@github.com wrote:
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Hi, I think of branchial muscles as a type of skeletal muscles. I'll have to As far as I know, the basic structure is the same. There is some evidence Robert E. Druzinsky, Ph.D. Office: 312-996-6054 On Thu, Oct 31, 2013 at 5:12 PM, David Osumi-Sutherland <
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On Fri, Nov 1, 2013 at 2:26 AM, David Osumi-Sutherland <
Sorry. I meant WP = wikipedia |
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 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. |
On 3 Nov 2013, at 19:42, Chris Mungall notifications@github.com wrote:
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.
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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, Robert E. Druzinsky, Ph.D. Office: 312-996-6054 On Sun, Nov 3, 2013 at 1:52 PM, David Osumi-Sutherland <
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Just to be clear - when I talk about somatic muscle myotubes, I'm referring to invertebrate somatic muscles myotubes (e.g. those of arthropods). |
If that is a part of the definition that excludes chordates, then is your Robert E. Druzinsky, Ph.D. Office: 312-996-6054 On Sun, Nov 3, 2013 at 2:21 PM, David Osumi-Sutherland <
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On 3 Nov 2013, at 20:33, RDruzinsky notifications@github.com wrote:
Yes
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What about something like "chordate striated muscle" or something like Robert E. Druzinsky, Ph.D. Office: 312-996-6054 On Sun, Nov 3, 2013 at 2:45 PM, David Osumi-Sutherland <
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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: This paper was used to make this distinction in GO:
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Note that GO:0002075 has no annotations and child terms in GO, which I believe is an error of omission |
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 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: This paper was used to make this distinction in GO: [Term] [Term] Reply to this email directly or view it on GitHubhttps://github.com//issues/324#issuecomment-48075274. |
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