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

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*Reggiani said that Elastic Filament should be deleted.
 
*Reggiani said that Elastic Filament should be deleted.
 
*We have added new terms:<br>EF:0014728 regulation of force of skeletal muscle contraction<br>EF:0014729 regulation of shortening velocity of skeletal muscle contraction<br>
 
*We have added new terms:<br>EF:0014728 regulation of force of skeletal muscle contraction<br>EF:0014729 regulation of shortening velocity of skeletal muscle contraction<br>
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==24th September, 2007==
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* 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)
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* Ehler's suggestions:<br>GO:0043034 inserte New definition<br>

Revision as of 00:47, 24 September 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)
  • Ehler's suggestions:
    GO:0043034 inserte New definition