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

From GO Wiki
Jump to: navigation, search
Line 155: Line 155:
 
===Muscle Plasticity===
 
===Muscle Plasticity===
  
Alex and I discussed the proposal above, first by e-mail and then on skype.  
+
*Alex and I discussed the proposal above, first by e-mail and then on skype.  
  
 
This was Alex's initial e-mail response:
 
This was Alex's initial e-mail response:
Line 163: Line 163:
 
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? "
 
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.  
+
*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.  
+
*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 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:
+
*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
+
[i]regulation of [the quality of] muscle plasticity
---[i]muscle plasticity process
+
---[i]muscle plasticity process
  
 
Jen did not really agree but did not have a clear idea of how else to relate them. <br>
 
Jen did not really agree but did not have a clear idea of how else to relate them. <br>
 
We decided to read a review that Erika has recommended to try to get a better idea.  
 
We decided to read a review that Erika has recommended to try to get a better idea.  
  
Alex pointed out that the idea if plasticity as a quality did not make much sense. He pointed out that there is quantity and quality, where quality might be the color of a chameleon, and quantity might be the speed with which it changes color. He wanted to explore the idea that perhaps plasticity was a quantity rather than a quality.  
+
*Alex pointed out that the idea if plasticity as a quality did not make much sense. He pointed out that there is quantity and quality, where quality might be the color of a chameleon, and quantity might be the speed with which it changes color. He wanted to explore the idea that perhaps plasticity was a quantity rather than a quality.  
  
 
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.
 
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.

Revision as of 05:12, 3 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
---[i]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.

  • Alex pointed out that the idea if plasticity as a quality did not make much sense. He pointed out that there is quantity and quality, where quality might be the color of a chameleon, and quantity might be the speed with which it changes color. He wanted to explore the idea that perhaps plasticity was a quantity rather than a quality.

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.