Muscle Development

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Giorgio Valle and Erika Feltrin of CRIBI at the University of Padua are planning a content meeting to make some new muscle development terms. Here are some rough plans.


Technology: webex and skype.
Content meeting: Planned for the last week of July (2 days beetween July 23-27)
Erika Feltrin and Jennifer Clark will meet at 11 am GMT for skype conferences every Friday to push this work through. All welcome.


Personnel

  • Erika Feltrin (Local organizer)
  • Jennifer Clark (GO Editorial Office organizer)
  • Giorgio Valle (Funding and recruiting experts)
  • Content meeting partecipants from University of Padua;

Chiara Gardin
Paolo Laveder
Lorenza Mittempergher
Alessandra Nori
Marco Sandri
Pompeo Volpe
Stefano Campanaro

  • Content meeting external partecipants:

Jennifer Clark (GO Editorial Office, EBI)
Elisabeth Ehler (King's College, London)
Georgine Faulkner (ICGEB, Trieste)
Jennifer Fordham (King's College, London)
Midori Harris (GO Editorial Office, EBI)
Ralph Knoell (University of Goettingen)
Vincenzo Sorrentino (University of Siena)

  • David Hill and Midori Harris (Ontology Development Managers)

Muscle experts:

Erika and Giorgio met 5 local experts last week. After a brief introduction on GO, they discussed about the Content Meeting: what it is, what it is for and what they would like to achieve. The local experts who would like to contribute to this Muscle Content Meeting are:

  • prof. Pompeo Volpe
  • dr. Marco Sandri
  • dr. Paolo Laveder
  • prof. Carlo Reggiani

Implementation plan:

Get experts and money:

  • Get Telethon funding changed from salary to meeting money (Giorgio Valle) Done
  • Find local muscle people to put in initial batch of terms from reviews. (Giorgio Valle and Erika Feltrin) Done.
  • Find more widespread muscle experts to come to content meeting and check terms. (Giorgio Feltrin and Erika Feltrin)

Set up infrastructure:

  • Erika needs to be able to commit to scratch directory. Jennifer Clark to organize this.
  • Wiki page to be set up (Jennifer Clark) Done.
  • Erika and Giorgio to get GOCwiki passwords Done
  • Software to set up at Erika Feltrin's end: Webex, skype, OBO-Edit (Erika Feltrin, Jennifer Clark) Done.
  • Erika Feltrin to join OBO-Edit working group and OBO-Edit chat as required to help deal with OBO-Edit issues. (Erika Feltrin and Jennifer Clark)
  • Local Padua experts to get OBO-Edit so they can start to edit. (Erika Feltrin and Jennifer Clark) Done.
  • Set date and work out meeting details (Local experts and Erika Feltrin) Done.

The meeting is planned for the end of July (25th-26th). Erika needs to start writing up her PhD by the end of August so we need to be completely finished by then.

Rough Timeline

February - March

Find local and remote experts. (Giorgio Valle)
Choose reviews (Local Experts)
Get infrastructure set up. (Erika Feltrin and Jennifer Clark)

April - June

Read reviews and make terms.
Continuted teaching and monitoring of term addition (Jennifer Clark and Erika Feltrin with help from Ontology working group.)
Meeting organisation (Giorgio Valle and Erika Feltrin with local assistance.)

July

Content meeting
All experts and Erika Feltrin, Giorgio Valle, Midori Harris, Jennifer Clark
Jane Lomax, Amelia Ireland (it depends on money)

August

Merge and implement terms (Jennifer Clark)
Check is_a completeness (Jennifer Clark)

  • end

Content Meeting Plan

This meeting will run for two days.
This meeting will be unusual in that it will involved two languages (English and Italian) as well as expert muscle biology knowledge and ontology expertise. In addition there are no muscle experts in the GO Editorial Office. If no one with both muscle and ontology expertise is coming then extra time and perhaps extra GO Editorial office personnel should be included to allow for this.


Content Meeting Provisional Programme

Wednesday 25 July

9.00 Welcoming address
9.20 J. Clark & M. Harris. Introduction to Gene Ontology

11.00 Coffee break

11.20 Presentation of the topics to be discussed and agenda
11.30 Session 1

13.00 Lunch

14.30 Session 2

16.30 Coffee break

17.00 Session 3
18.30 End

19.30 Dinner

Thursday 26 July

9.00 Session 4

11.00 Coffee break

11.30 Session 5

13.30 Lunch

14.30 Conclusive remarks
16.30 Visit to Scrovegni Chappel (Giotto's) and Old University (Galileo's)


During the 5 sessions the following topics will be discussed:

Topic 1: Sarcoplasmic reticulum and membrane delimited compartments
Topic 2: Sarcomere and muscle contraction
Topic 3: Muscle regeneration 
Topic 4: Muscle plasticity
Topic 5: Muscle development

Details of File Management

It has been decided to use the gene_ontology_cardio.obo file. Below there is file details:

format-version: 1.2
date: 18:05:2007 21:01
saved-by: mgi
auto-generated-by: OBO-Edit 1.100
subsetdef: goslim_generic "Generic GO slim"
subsetdef: goslim_goa "GOA and proteome slim"
subsetdef: goslim_plant "Plant GO slim"
subsetdef: goslim_yeast "Yeast GO slim"
subsetdef: gosubset_prok "Prokaryotic GO subset"
default-namespace: gene_ontology
remark: cvs version: $Revision: 1.3 $

The number ranges assigned to the editors are:

GO:0014301	GO:0014999	GOE	Erika Feltrin	subrange; Muscle content meeting
GO:0014301	GO:0014400	GOE	Erika Feltrin	subrange; Muscle content meeting: Pompeo Volpe
GO:0014401	GO:0014500	GOE	Erika Feltrin	subrange; Muscle content meeting: Paolo Laveder
GO:0014501	GO:0014600	GOE	Erika Feltrin	subrange; Muscle content meeting: Marco Sandri
GO:0014601	GO:0014700	GOE	Erika Feltrin	subrange; Muscle content meeting: Carlo Reggiani
GO:0014701	GO:0014800	GOE	Erika Feltrin	subrange; Muscle content meeting: Giorgio Valle
GO:0014801	GO:0014999	GOE	Erika Feltrin	subrange; Muscle content meeting: Erika Feltrin (Before and during the live content meeting)

This information is also in the numbers file.

To Do List