View source for Muscle biology- Muscle Implementation after Content Meeting

==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:<br>regulation of satellite cell activation involved in skeletal muscle regeneration<br>positive regualtion of satellite cell activation involved in skeletal muscle regeneration<br>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:<br>myoblast cell fate commitment in head<br>myoblast cell fate commitment in trunk<br>regulation of branchiomeric skeletal muscle development<br>negative regulation of branchiomeric skeletal muscle development<br>positive regulation of branchiomeric skeletal muscle development<br>regulation of somitomeric trunk muscle development<br>negative regulation of somitomeric trunk muscle development<br>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).<br> We have made these changes:<br>
*added or changed definitions for: muscle contraction<br>voluntary and involuntary skeletal muscle contraction<br>smooth muscle contraction<br>phasic and tonic smooth muscle contraction<br>striated muscle contraction<br>diaphragm contraction<br>skeletal muscle contraction<br>fast/twitch and slow/twitch skeletal muscle contraction<br>
*Added new terms:<br>twitch skeletal muscle contraction<br>oscillatory skeletal muscle contraction<br>
*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:<br>EF:0014728 regulation of force of skeletal muscle contraction<br>EF:0014729 regulation of shortening velocity of skeletal muscle contraction<br>

==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:<br>costamere GO:0043034 inserted New definition<br>
* 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.
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