muscle

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I wrote to David to ask this:

Hi David,

Do you think that

myogenesis ; GO:0007519 def: The developmental sequence of events leading to the formation of adult muscle that occurs in the animal and in cultured cells. In vertebrate skeletal muscle the main events are: the fusion of myoblasts to form myotubes that increase in size by further fusion to them of myoblasts, the formation of myofibrils within their cytoplasm and the establishment of functional neuromuscular junctions with motor neurons. At this stage they can be regarded as mature muscle fibers.

is meant to be the same as

muscle development ; GO:0007517 def: The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.

The definitions seem the same but I wondered whether myogenesis might be more like development of a muscle fibre rather than a whole muscle or something.

If they are the same I could merge them.

Jen

Reported by: jenclark

Original Ticket: "geneontology/ontology-requests/2757":https://sourceforge.net/p/geneontology/ontology-requests/2757

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response:

Hi Jen,

I didn't merge them because from the definition of myogenesis it does not include the development of all types of muscle. It seems to refer to the development of striated muscle. In vertebrates this would correspond to skeletal muscle, but in invertebrates, I think it would certainly include things like flight mucles. I don't think it should be redefined as development of a muscle fiber, because striated muscles are made up of many fibers that are organized in a particular way. Unfortunately I don't know enough about the lingo in the muscle field to describe all of these things and whether or not tendons and muscle attachment points would be considered part of the muscle. In the adult anatomical dictionary, the tendons are considered separate structures. In time I think we should have a number of is_a children of muscle development: myogenesis, cardiac muscle development and smooth muscle development. I am not sure if visceral and somatic muscle correspond to smooth and striated (myogenesis), but I suspect that they might. If you want I can look into this more closely a bit later.

David

Original comment by: jenclark

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Just logging in so I can monitor this

David

Original comment by: ukemi

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Hi Jen,

About the terms myogenesis and muscle development I think that you are right,they aren't the same and they couldn't merge because myogenesis is used for muscle fibers rather than a whole muscle structure. The myogenesis is usually referred to striated muscle fibers, skeletal and cardiac, but not smooth muscle fibers.The development of skeletal muscle fibers and cardiac muscle fibers is, generally, similar,instead the smooth muscle fibers development is more different from two other and not much known. Smooth muscle is a significant portion of many organs including those of the gastrointestinal, urogenital and respiratory tracts, and the vascular system. I think that you may assume that visceral muscle correspond to smooth muscle.

Lorenza

Original comment by: lorimitt80

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Hi Lorenza,

Thanks for clarifying that. I'll make an improved definition of myogenesis and post it here for you and David to check.

Thanks,

Jen

Original comment by: jenclark

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From looking again at the comments below it sounds like you two have a different view of myogenesis. It seems as though David views it as defining striated muscle development and Lorenzo sees it as being to do with striated muscle fibre development.

Conveniently my two favourite online dictionaries have exactly the same problem:

Stedman's: myogenesis (m--jen-sis) Embryonic formation of muscle cells or fibers. http://216.251.232.159/semdweb/internetsomd/ASP/1542345.asp

on-line medical: myogenesis <physiology> The developmental sequence of events leading to the formation of adult muscle that occurs in the animal and in cultured cells. In vertebrate skeletal muscle the main events are: the fusion of myoblasts to form myotubes that increase in size by further fusion to them of myoblasts, the formation of myofibrils within their cytoplasm and the establishment of functional neuromuscular junctions with motoneurons. at this stage they can be regarded as mature muscle fibres. http://cancerweb.ncl.ac.uk/cgi-bin/omd?myogenesis

Is the term often used ambiguously in the literature?

Jen

Original comment by: jenclark

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This term is used in literature to indicate also generally the development of skeletal muscle but I think that it is more correct to use "myogenesis" as development skeletal muscle fibers. The difference between development skeletal muscle fibers and development skeletal muscle, in literature,it isn't often so definite.

Original comment by: lorimitt80

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In the past, we have solved these issues by the inclusion of synonyms. I think we can address this the same way. We should choose a term myogenesis as the primary term for the most common usage and then create new terms for the less common usage and make myogenesis a synonym.

David

Original comment by: ukemi

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I have written to a myogenesis expert that I met at a recent conference to get a third opinion on this.

Jen

Original comment by: jenclark

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Here is the reply:

Dear Jennifer,

Myogenesis is a developmental terminology. Muscle consists of muscle (myo) fibres. Therefore, the terminology "myogenesis" relates typically to the development of the cells of the muscle tissue. Thus it should be: muscle fibre development.

Best Regards,

Marinus

Dr. Marinus F.W. te Pas Animal Sciences Group (Institute for Animal Science and Health (ID-Lelystad)) Division of Animal Resources Development Animal Genomics Group

Would it be okay if I just go with the muscle fibre development definition that seems to be the concensus?

Thanks,

Jen

Original comment by: jenclark

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I prefer muscle fiber development (american spelling). So, to get around the issue of having a primary term as a synonym for another term, we should make two different primary terms each with a synonym that is the same. I think we should do this whenever we run into a case like this.

David

Original comment by: ukemi

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Yes that's an idea. So two terms:

striated muscle fiber development broad_synonym: myogenesis

striated muscle development broad_synonym: myogenesis

I think there we're basically taking what I'd call a GO structured syonym and putting it in as the primary term name to avoid conflict. Sounds like it will solve the problem.

I've noticed often that conflict arises when we have to choose a single term name when there are several equally good names. I do wonder whether that is an artificial distinction, but if I asked to get rid of primary term strings and just have various classes of synonym instead that might not be too popular. :-)

Jen

Original comment by: jenclark

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Here's a proposal:

We want terms as follows:

striated muscle fiber development Def: The process aimed at the progression of striated muscle fibers over time, from formation to the mature structures. Striated muscle includes skeletal and cardiac muscle but not smooth muscle. broad_synonym: myogenesis

smooth muscle fiber development def: The process aimed at the progression of smooth muscle fibers over time, from formation to the mature structures. Smooth muscle is a significant part of many organs including those of the gastrointestinal, urogenital and respiratory tracts, and the vascular system.

muscle development def: The process aimed at the progression of muscle over time, from formation to the mature structure.

striated muscle development def: The process aimed at the progression of muscle over time, from formation to the mature structure. broad_synonym: myogenesis

smooth muscle development def: The process aimed at the progression of smooth muscle over time, from formation to the mature structures.

[i]muscle development ---[i]striated muscle development ------[p]striated muscle fiber development ---[i]smooth muscle development ------[p]smooth muscle fiber development

Below are the two terms I was looking at originally that need somehow to be clarified. Shall I make 1 become striated muscle development and 2 become muscle development?

1) myogenesis ; GO:0007519 def: The developmental sequence of events leading to the formation of adult muscle that occurs in the animal and in cultured cells. In vertebrate skeletal muscle the main events are: the fusion of myoblasts to form myotubes that increase in size by further fusion to them of myoblasts, the formation of myofibrils within their cytoplasm and the establishment of functional neuromuscular junctions with motor neurons. At this stage they can be regarded as mature muscle fibers.

2) muscle development ; GO:0007517 def: The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.

Original comment by: jenclark

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Hi Jen,

I think this reflects the consensus, but I'd let the muscle folks weigh in.

David

Original comment by: ukemi

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I have written to my other expert to get feedback.

Thanks,

jen

Original comment by: jenclark

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Hi Jen! In my opinion the new terms that you requested and their DAG structure are right; so the difference between muscle development and fiber muscle development is more clear and it would not exist confusion about these concepts. I think also that your purpose about the term GO:0007519 (myogenesis) is proper: it is better that you modify it in "striated muscle development".

Lorenza

Original comment by: lorimitt80

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Thanks. :-)

Jen

Original comment by: jenclark

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Here is some feedback from my other muscle expert:

striated muscle fiber development Def: The process aimed at the progression of striated muscle fibers over time, from formation to the mature structures.

*Suggestion: The process aimed at the amplification and progression of myoblasts (muscle precursor cells) into terminally differentiated multinucleated muscle fibers.

Striated muscle includes skeletal and cardiac muscle but not smooth muscle.

*Please note: Cardiac muscle fiber development is very different from striated muscle fiber development - not even the central genetic regulators of striated muscle fiber development (the MRF genes) are included in cardiac muscle fiber development!

*I am not an expert in smooth muscle fiber development, but I know that the process is under very different genetic regulation [from that of striated muscle development].

muscle development broad_synonym: myogenesis

*No, this is not named myogenesis

Original comment by: jenclark

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Hi Jen! I would suggest an other solution:

• striated muscle development (the process aimed at the progression of striated muscle over time, from formation to the mature structure)
• skeletal muscle development, GO:0048637 (the process whose specific outcome is the progression of the skeletal muscle over time, from its formation to the mature structure)
• skeletal muscle fiber development, GO:0007519, synonym: myogenesis (the developmental sequence of events leading to the formation of mature skeletal fiber. In vertebrate skeletal muscle fiber the main events are: the fusion of myoblasts to form myotubes that increase in size by further fusion to them of myoblasts, the formation of myofibrils within their cytoplasm and the establishment of functional neuromuscular junctions with motor neurons. At this stage they can be regarded as mature muscle fiber)
• cardiac muscle development (the process whose specific outcome is the progression of the cardiac muscle over time, from its formation to the mature structure)
• cardiac muscle fiber development (the developmental sequence of events leading to the formation of mature cardiac fiber)

also the graph could be: [i]muscle development ---[i]striated muscle development ------[i] cardiac muscle development --------[p] cardiac muscle fiber development ------[i] skeletal muscle development --------[p]skeletal muscle fiber development -----------[p] myoblast differentiation -----------[p] myoblast migration -----------[p] neuromuscular junction development -----------[p] regulation of skeletal muscle fiber development ------[p]striated muscle fiber development ---[i]smooth muscle development ------[p]smooth muscle fiber development

Original comment by: lorimitt80

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Original comment by: jenclark

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Original comment by: jenclark

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I have implemented this:

id: GO:0048738 name: cardiac muscle development namespace: biological_process def: "The process whose specific outcome is the progression of cardiac muscle over time\, from its formation to the mature structure." [GO:jic "", TRAIT:lm "", MGI:dph ""] is_a: GO:0007517 ! muscle development

[Term] id: GO:0048739 name: cardiac muscle fiber development namespace: biological_process def: "The process whose specific outcome is the progression of cardiac muscle fiber over time\, from its formation to the mature structure." [GO:jic "", TRAIT:lm "", MGI:dph ""] exact_synonym: "cardiac muscle fibre development" [] relationship: part_of GO:0048738 ! cardiac muscle development

[Term] id: GO:0048740 name: striated muscle fiber development namespace: biological_process def: "The process whose specific outcome is the amplification and progression of myoblasts (muscle precursor cells) into terminally differentiated multinucleated muscle fibers." [GO:jic "", MGI:dph "", TRAIT:lm] exact_synonym: "myogenesis" [] exact_synonym: "striated muscle fibre development" [] is_a: GO:0048747 ! muscle fiber development relationship: part_of GO:0007519 ! striated muscle development

[Term] id: GO:0048741 name: skeletal muscle fiber development namespace: biological_process def: "The process whose specific outcome is the progression of the skeletal muscle fiber over time\, from its formation to the mature structure." [TRAIT:lm "", GO:jic "", MGI:dph ""] exact_synonym: "skeletal muscle fibre development" [] is_a: GO:0048747 ! muscle fiber development relationship: part_of GO:0048637 ! skeletal muscle development

[Term] id: GO:0048742 name: regulation of skeletal muscle fiber development namespace: biological_process def: "Any process that modulates the frequency\, rate or extent of skeletal muscle fiber development." [GO:jic "", MGI:dph "", TAIR:sm ""] exact_synonym: "regulation of skeletal muscle fibre development" [] is_a: GO:0048641 ! regulation of skeletal muscle development relationship: part_of GO:0048741 ! skeletal muscle fiber development

[Term] id: GO:0048743 name: positive regulation of skeletal muscle fiber development namespace: biological_process def: "Any process that activates\, maintains or increases the rate of skeletal muscle fiber development." [GO:jic "", MGI:dph "", TRAIT:lm ""] exact_synonym: "positive regulation of skeletal muscle fibre development" [] is_a: GO:0048643 ! positive regulation of skeletal muscle development is_a: GO:0048742 ! regulation of skeletal muscle fiber development

[Term] id: GO:0048744 name: negative regulation of skeletal muscle fiber development namespace: biological_process def: "Any process that stops\, prevents or reduces the rate of skeletal muscle fiber development." [GO:jic "", MGI:dph "", TRAIT:lm ""] exact_synonym: "negative regulation of skeletal muscle fibre development" [] is_a: GO:0048642 ! negative regulation of skeletal muscle development is_a: GO:0048742 ! regulation of skeletal muscle fiber development

[Term] id: GO:0048745 name: smooth muscle development namespace: biological_process def: "The process whose specific outcome is the progression of smooth muscle over time\, from its formation to the mature structure." [GO:jic "", TRAIT:lm "", MGI:dph ""] is_a: GO:0007517 ! muscle development

[Term] id: GO:0048746 name: smooth muscle fiber development namespace: biological_process def: "The process whose specific outcome is the progression of smooth muscle fiber over time\, from its formation to the mature structure." [MGI:dph "", GO:jic "", TRAIT:lm ""] exact_synonym: "smooth muscle fibre development" [] is_a: GO:0048747 ! muscle fiber development relationship: part_of GO:0048745 ! smooth muscle development

[Term] id: GO:0048747 name: muscle fiber development namespace: biological_process def: "The process whose specific outcome is the progression of the muscle fiber over time\, from its formation to the mature structure." [TRAIT:lm "", MGI:dph "", GO:jic ""] exact_synonym: "muscle fibre development" [] relationship: part_of GO:0007517 ! muscle development

I think it reflects all the views here. Let me know if you find any problems.

Thanks for all the help in working all this out.

Jen

Original comment by: jenclark

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Original comment by: cooperl09