Difference between revisions of "Muscle biology- Muscle Implementation after Content Meeting"

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We decided to destroy the terms to do with longer sustained or strenuous muscle contractions as they were too difficult to define for now.  
 
We decided to destroy the terms to do with longer sustained or strenuous muscle contractions as they were too difficult to define for now.  
  
We fixed the parentage of the 'response to stimulus' and 'detection of stimulus' terms and they are ready to be sent off to Alex Deihl to be checked.
+
We fixed the parentage of the 'response to stimulus' and 'detection of stimulus' terms and they are ready to be sent off to Alex Diehl to be checked.

Revision as of 06:53, 9 October 2007

12th September, 2007

Participants: Erika Feltrin, Jennifer Deegan

We went through about two thirds of the list on the google spreadsheet and figured out what to do about each item.


13th September, 2007

Participants: Erika Feltrin, Jennifer Deegan

We went through the descendants of skeletal muscle regeneration and fixed the graph and definitions. We made the terms is_a complete as we went along.

We made a new term called cell-cell fusion as an is_a parent for the myoblast fusion term. Cell-cell fusion has been placed as a cellular process.

14th September, 2007

Participants: Erika Feltrin, Jennifer Deegan

We worked on:

  • descendents of contractile fiber part
  • descendents of sarcoplasmic reticulum terms
  • descendents of muscle regeneration terms
  • cell fusion

We have now checked all the definitions and graphs for all of these terms and they are correct apart for 2 or 3 small outstanding questions. The questions are listed on the google spreadsheet and Erika and I have identified experts who can help us with them.

18th September, 2007

Participants: Erika Feltrin, Jennifer Deegan

  • Terms with myotube, myoblast or myofibre in the name were given cell definitions and synonyms.
  • We moved myotube development under muscle fibre development.
  • Inserted def for satellite cell in all terms covering satellite cell.
  • Checked defs for muscle regeneration terms except for EF:0014815 (a term covering growth factor in muscle regeneration.)
  • Wrote to David to ask about a skype call to cover striated muscle grouping.

Erika in the afternoon

  • EF:0014815 has a definition
  • ADDED two new terms:
    regulation of satellite cell activation involved in skeletal muscle regeneration
    positive regualtion of satellite cell activation involved in skeletal muscle regeneration
    MOVED EF:0014815 as a is_a of positive regulation of satellite cell activation involved in skeletal muscle regeneration
  • MOVED myblast migration involved in skeletal muscle regeneration is_a child of myoblast migration
  • ADDED a new term: satellite cell activation is_a cell activation
  • MOVED satellite cell activation involved in skeletal muscle regeneration is_a child satellite cell activation

HOMEWORKS:

  • WHAT IS A MUSCLE CELL? Check the muscle cell development structure
  • We need definitions for:
    myoblast cell fate commitment in head
    myoblast cell fate commitment in trunk
    regulation of branchiomeric skeletal muscle development
    negative regulation of branchiomeric skeletal muscle development
    positive regulation of branchiomeric skeletal muscle development
    regulation of somitomeric trunk muscle development
    negative regulation of somitomeric trunk muscle development
    positive regulation of somitomeric trunk muscle development

19th September, 2007

prof. Reggiani came and helped for definition of muscle contraction terms. We have defined almost all "muscle contraction" terms (he will come on Friday to get the work finished).
We have made these changes:

  • added or changed definitions for: muscle contraction
    voluntary and involuntary skeletal muscle contraction
    smooth muscle contraction
    phasic and tonic smooth muscle contraction
    striated muscle contraction
    diaphragm contraction
    skeletal muscle contraction
    fast/twitch and slow/twitch skeletal muscle contraction
  • Added new terms:
    twitch skeletal muscle contraction
    oscillatory skeletal muscle contraction
  • changed definition for GO:0031446, 0031447, 0031448 from striated to fast-twitch

QUESTIONS:

  • Reggiani said that he does not know for sure if there is differences at the molecular level between "urinary system type smooth muscle contraction" and "artery type smooth muscle contraction" but He said that these type of muscle might have a difference expresion profiles, for instance they express different kind of receptors for hormons or different channels. Should I delete these muscle type contraction terms? I saw that there is already a term GO:0003056 contraction of vascular smooth muscle which has been added by cardio_mtg.DONE

CHAT WITH DAVID HILL

  • We need to get rid of all terms with type inside the term name
  • We consider plasticity a quality
  • Muscle cell (see CL) is a MATURE muscle cell and instead myoblast, myotube are precursors.
  • oscillatory skeletal muscle contraction should be "striated" Ask Reggiani for this!
  • we can do cross references between CL and GO (asked to Chris Mungall)
  • striated muscle development. To be asked to muscle experts. We can take it if it is too complicate.

20th September, 2007

  • Check almost all the relationships and definitions under muscle contraction and skeletal muscle development.
  • Create a new spreadsheet with the list of the terms that should be defined called terms_to_define
  • Erika will write to muscle experts asking for definition for atrophy, hyperatrophy and other plasticity terms
  • Inserted MA and CL dbxrefs in the muscle contraction terms

22st September, 2007

  • Reggiani defined all terms under muscle contraction
  • We have copied peristalsis also under phasic smooth muscle contraction EF:0014821
  • Reggiani said that Elastic Filament should be deleted.
  • We have added new terms:
    EF:0014728 regulation of force of skeletal muscle contraction
    EF:0014729 regulation of shortening velocity of skeletal muscle contraction

24th September, 2007

  • Made some changes at the "muscle plasticity" structure: moved terms under "regulation of muscle plasticity" and added definitions of atrophy , hypertrophy and hyperplasia form cancer web dictionary (TO BE CHECKED)
  • I have destroy "elastic filament" that was under contratile fiber part and also sarcomere since it is made by just the portein titin Definition was: Non-contractile elastic cytoskeletal filaments in the sarcomere.
  • Ehler's suggestions:
    costamere GO:0043034 inserted New definition
  • modified definition for T-tubule and copied it also under sarcolemma as part_of.
  • Deleted the synonym of "intercaleted disc" from GO:0005916 and create a new term: EF:0014704 intercalated disc using Elisabeth's definition. Moved GO:0005916, 0030057 and 0005921 as part_of children of EF:0014704.
  • New term: EF0014731 spectrin-associated cytoskeleton PMID:15970557 but this citoskeleton is membrane-bounded but now it is under non -membrane bounded???

2nd October, 2007

Partecipants: Erika and Jennifer

We have discussed about muscle plasticity terms. Correct the definition of costamere and muscle plasticity. We need to ask about merging between muscle plasticity and regulation of muscle plasticity.

Erika in the afternoon have done some editing. Definitions of:
EF:0014882 definition of myofibrill from GO:0030016
EF:0014881 definition of myofibrill from GO:0030016

EF:0014732 NEW TERM skeletal muscle atrophy
EF:0014733 NEW TERM regulation of skeletal muscle plasticity
EF:0014734 NEW TERM skeletal muscle hypertrophy

EF:0014899 cardiac muscle atrophy
EF:0014898 cardiac muscle hypertrophy
EF:0014887 regulation of cardiac muscle plasticity
EF:0014890 smooth muscle atrophy
EF:0014895 smooth muscle hypertrophy
EF:0014805 regulation of skeletal muscle plasticity
EF:0014733 regulation of smooth muscle plasticity
EF:0014732 skeletal muscle atrophy
EF:0014891 striated muscle atrophy
EF:0014734 striated muscle hypertrophy
EF:0014898 skeletal muscle hypertrophy
EF:0014888 regulation of striated muscle plasticity
EF:0014889 muscle atrophy
EF:0014900 muscle hyperplasia
EF:0014896 muscle hypertrophy

3rd October

Participants: Erika Feltrin, Jennifer Deegan

Muscle Plasticity

We have a plan for muscle plasticity. We have written to Alex Deihl to ask for his thoughts. This is the plan:

Plan

Erika has spoken to experts on the muscle plasticity question. They have told us that for muscle plasticity the line between quality and process is so blurred as to be meaningless. We wondered if we might make the following structures. The whole thing is paraphrased, as we don't have rigorously thought out definitions and are just giving an idea of how we might do it to get feedback. However the term names with a * are our actual intended term names. Here's our idea:

[i]regulation of a biological quality
---[i]regulation of the biological quality of muscle plasticity* 
      (Something like: The process by which the ability of muscle to change its structure and activity is increased or decreased.)
------[i]positive regulation of the biological quality of muscle plasticity 
         (A process that makes muscles more able to adapt their structure and activity.)
------[i]negative regulation of the biological quality of muscle plasticity 
         (A process that makes muscles less able to adapt their structure and activity.)

Then to accommodate the language problem we thought about adding:

[i]muscle plasticity process* 
    (The process by which the structure and activity of muscle is actually changed.) This could have helpful synonyms.
---[i]muscle atrophy
---[i]muscle hypertrophy

We hope this might accommodate the really subtle use of language in the community, but help keep the concepts clearly apart in a useful way in the GO.


3rd October

Participants: Alex Deihl, Jennifer Deegan

Muscle Plasticity

  • Alex and I discussed the proposal above, first by e-mail and then on skype.

This was Alex's initial e-mail response:

"I am a strong supporter of reflecting the language of biologists in the formation and organization of GO terms, although in this case I think the biologists have abused the language a bit. While I can live with the approach you have outlined, I have to admit that I find "regulation of the biological quality of muscle plasticity" needlessly wordy, and indeed sounding rather jargony. I think it would be less confusing just to say "regulation of muscle plasticity," with the definition you provide, since the placement of the term in the ontology would indicate that that we are referring to muscle plasticity as a biological quality in this case. We could even add a comment or extend the definition to say specifically that we are referring to muscle plasticity as a biological quality for this term.

I do like the "muscle plasticity process" term. Will it be a part_of to the "regulation of [the biological quality of] muscle plasticity" term? "

  • On the skype call we discussed the names of terms and then graph placement.
  • Jen agreed with Alex's points in his first paragraph above.
  • We agreed that muscle plasticity process might be well placed as a child of muscle development but that we should check with David.
  • We tried to work out how the two terms 'muscle plasticity process' and 'regulation of [the quality of] muscle plasticity' might be related to one another. Alex thought perhaps this would be good:
[i]regulation of [the quality of] muscle plasticity
---[p]muscle plasticity process

Jen did not really agree but did not have a clear idea of how else to relate them.
We decided to read a review that Erika has recommended to try to get a better idea.

In proposing this relationship, Alex suggested looking at the relationships between various blood pressure terms as a guide, although without much success. Alex also pointed out the distinction that for a biological quality such as blood pressure, negative and positive regulation terms were possible, since blood pressure is a quality which can be quantified, whereas for a biological quality such as muscle plasticity, negative and positive regulation terms may not be appropriate, depending on how one interprets the term. Alex gave a weak analogy to the skin color of a chameleon as a biological quality, where one could imagine having a "regulation of skin color" term, but not have negative and positive regulation terms.

In the end of the discussion we had some good new avenues to explore and we are going to read on with an open mind and get back together on Friday or Monday to discuss further.

I HAVE FOUND SOME DEFINITIONS FOR MUSCLE PLASTICITY:

Muscle Plasticity:

the ability of striated muscle tissue to adapt to changes in activity or in working conditions is extremely high. In some ways it is comparable to the ability of the brain to learn. The interest in muscle adaptation is increasing in relation to the idea that physical fitness helps in the prevention of disease, may counteract the loss of physical performance and generally improves wellbeing. Plasticity is the word used since the late 1970’s to indicate collectively all the processes and mechanisms which form the background of muscle adaptation. http://www.springer.com/west/home/new+&+forthcoming+titles+(default)?SGWID=4-40356-22-173664756-0

Skeletal muscle is the single most abundant tissue in higher animals. Thus, in order to minimize the expenditure for maintenance and maximize functionality, skeletal muscle has an enormous capacity to adapt to various stimuli, e.g., motor nerve activation and contractile activity, nutrient supply, temperature and hypoxia [1]. Altered signaling pathways and changes in metabolic and contractile properties contribute to the phenotypic plasticity of skeletal muscle. http://www.researchportal.ch/unizh/p7970.htm

In this report,we will be dealing with the concept of muscle plasticity, which is the ability of a given muscle cell to alter either the quantity (amount) of protein or the type of protein (i.e., phenotype or isoform) comprising its different sub-cellular components in response to any stimulus that disrupts its normal homeostasis. For example, a given muscle fiber may respond to chronic increases in mechanical stress (physical activity) by increasing its crosssectional area such that all of the subcellular components remain in normal proportion to one another and the same specific protein pheno-types are maintained in normal expression. In this case, the muscle expands both its protein mass and mechanical strength without qualitatively changing any other inherent functional property such as endurance or contractile speed. On the other hand, a given fiber may respond o the same perturbation by both increasing its mass and altering the type of MHC isoform that it expresses in the myofilaments. In this situation, as the muscle becomes both larger and stronger because of the increase in contractile protein accumulation, its intrinsic contractile properties also become transformed due to the altered myosin phenotype that is expressed. Thus, the muscle’s plasticity potential may involve (1) a change in the amount of protein, (2)the type of protein isoform it expresses, and (3) a combination of the two. However, the derived functional consequences of such a transformation will depend on which component or components of the cell are altered in terms of the quantity and quality of protein expression. http://www.nmdinfo.net/Publications/Consensus%20Conf%202002%20Papers/Baldwin.pdf

8th October

  • Webex/skype chat about plasticity: Erika Feltrin, Jennifer Deegan, Alex Diehl

We all did some reading over the last few days and came back to discuss muscle plasticity again. Just before the call started Alex sent out a proposed structure shown below:

[i]muscle adaptation -- synonym (related):muscle plasticity
--[i]muscle atrophy
----[p]regulation of muscle atrophy
------[i]negative regulation of muscle atrophy
------[i]positive regulation of muscle atrophy
--[i]muscle hypertrophy
----[p]regulation of muscle hypertrophy
------[i]negative regulation of muscle hypertrophy
------[i]positive regulation of muscle hypertrophy
--[p]regulation of muscle adaptation  ; related syn: regulation of muscle plasticity
----[i]negative regulation of muscle adaptation  ; related syn: negative regulation of muscle plasticity
------[i]negative regulation of muscle atrophy
------[i]negative regulation of muscle hypertrophy
----[i]positive regulation of muscle adaptation  ; related syn: positive regulation of muscle plasticity
------[i]positive regulation of muscle atrophy
------[i]positive regulation of muscle hypertrophy
----[i]regulation of muscle atrophy
------[i]negative regulation of muscle atrophy
------[i]positive regulation of muscle atrophy
----[i]regulation of muscle hypertrophy
------[i]negative regulation of muscle hypertrophy
------[i]positive regulation of muscle hypertrophy 
--[i]muscle hyperplasia
----[p]regulation of muscle hyperplasia
------[i]negative regulation of muscle hyperplasia
------[i]positive regulation of muscle hyperplasia

He suggests that as the ambiguous community use of the word plasticity is what causes all the problems we might relegate it to the synonym field and only use unambiguous phrases in the term names. He further proposes that since the terms that we actually want to capture are things like hyperplasia, atrophy and hypertrophy, which are processes that adapt muscle, we might be best just to have the top term muscle adaptation to cover such processes, and forget about the quality term altogether. This way we can finish the edits that we are doing now, and if anyone ever wants a term to cover the meaning of plasticity that we think might require a regulation of quality term then we can deal with that when the time comes.

Erika and I agreed entirely with this approach and so Erika is implementing it immediately. We had previously merged the terms muscle plasticity and regulation of muscle plasticity but we went back and reverted this change before Erika started to implement the new plan.

8th October

Erika Feltrin's progress on mappings to cell type ontology.

  • Cell ontology request

SF request for new terms about muscle cell in the cell ontology
http://sourceforge.net/tracker/index.php?func=detail&aid=1809468&group_id=76834&atid=925065


  • CL:0000056 myoblast added as Dbxref in these terms:

EF:0014714 myoblast cell fate commitment in head
EF:0014715 myoblast cell fate commitment in trunk
EF:0014835 myoblast cell differentiation involved in skeletal muscle regeneration
EF:0014836 myoblast cell fate commitment involved in skeletal muscle regeneration
EF:0014837 myoblast cell fate determination involved in skeletal muscle regeneration
EF:0014838 myoblast cell fate specification involved in skeletal muscle regeneration
EF:0014839 myoblast migration involved in skeletal muscle regeneration
EF:0014844 myoblast cell proliferation involved in skeletal muscle regeneration
EF:0014872 myoblast cell division
EF:0014905 myoblast fusion involved in skeletal muscle regeneration
EF:0014914 myoblast maturation involved in muscle regeneration
GO:0007518 myoblast cell fate determination
GO:0007520 myoblast fusion
GO:0045445 myoblast differentiation
GO:0045661 regulation of myoblast differentiation
GO:0045662 negative regulation of myoblast differentiation
GO:0045663 positive regulation of myoblast differentiation
GO:0048625 myoblast cell fate commitment
GO:0048626 myoblast cell fate specification
GO:0048627 myoblast development
GO:0048628 myoblast maturation
GO:0051450 myoblast proliferation
GO:0051451 myoblast migration

  • CL:0000187 muscle cell added as Dbxref in these terms:

EF:0014812 muscle cell migration
GO:0007521 muscle cell fate determination
GO:0033002 muscle cell proliferation
GO:0042692 muscle cell differentiation
GO:0042693 muscle cell fate commitment
GO:0042694 muscle cell fate specification
GO:0051147 regulation of muscle cell differentiation
GO:0051148 negative regulation of muscle cell differentiation
GO:0051149 positive regulation of muscle cell differentiation
GO:0055001 muscle cell development

  • CL:0000188 skeletal muscle cell added as Dbxref in these terms:

EF:0014856 skeletal muscle cell proliferation
EF:0014857 regulation of skeletal muscle cell proliferation
EF:0014858 positive regulation of skeletal muscle cell proliferation
EF:0014859 negative regulation of skeletal muscle cell proliferation

  • CL:0000192 smooth muscle cell added as Dbxref in these terms:

EF:0014909 smooth muscle cell migration
EF:0014910 regulation of smooth muscle cell migration
EF:0014911 positive regulation of smooth muscle cell migration
EF:0014912 negative regulation of smooth muscle cell migration
GO:0048659 smooth muscle cell proliferation
GO:0048660 regulation of smooth muscle cell proliferation
GO:0048661 positive regulation of smooth muscle cell proliferation
GO:0048662 negative regulation of smooth muscle cell proliferation
GO:0051145 smooth muscle cell differentiation
GO:0051150 regulation of smooth muscle cell differentiation
GO:0051151 negative regulation of smooth muscle cell differentiation
GO:0051152 positive regulation of smooth muscle cell differentiation

  • CL:0000190 fast muscle cell added as Dbxref in these terms:

GO:0031443 fast-twitch skeletal muscle fiber contraction
GO:0031446 regulation of fast-twitch skeletal muscle contraction
GO:0031447 negative regulation of fast-twitch skeletal muscle contraction
GO:0031448 positive regulation of fast-twitch skeletal muscle contraction

  • CL:0000189 slow muscle cell added as Dbxref in these terms:

GO:0031444 slow-twitch skeletal muscle contraction
GO:0031449 regulation of slow-twitch skeletal muscle contraction
GO:0031450 negative regulation of slow-twitch skeletal muscle contraction
GO:0031451 positive regulation of slow-twitch skeletal muscle contraction

  • CL:0000737 striated muscle cell added as Dbxref in these terms:

EF:0014855 striated muscle cell proliferation
GO:0051145 smooth muscle cell differentiation
GO:0051146 striated muscle cell differentiation
GO:0051153 regulation of striated muscle cell differentiation
GO:0051154 negative regulation of striated muscle cell differentiation
GO:0051155 positive regulation of striated muscle cell differentiation
GO:0055002 striated muscle cell development


9th October

  • Participants: Erika Feltrin, Jennifer Deegan

We looked through the remaining to do items and made sure they were all assigned.

We redefined contraction, which sounds like a function term just because some very detailed information was given about individual steps in the process. The def is now much more processy and Erika is going to reapply the standard definition accross the board.

We decided to destroy the terms to do with longer sustained or strenuous muscle contractions as they were too difficult to define for now.

We fixed the parentage of the 'response to stimulus' and 'detection of stimulus' terms and they are ready to be sent off to Alex Diehl to be checked.