2007 Muscle Meeting Report

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Muscle Gene Ontology Content Meeting

CRIBI - Department of Biology
25-26 July 2007 Padua (Italy)

Participants

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 Knöll (University of Goettingen)
Vincenzo Sorrentino (University of Siena)

and from Padua University
Stefano Campanaro (researcher)
Erika Feltrin (PhD student)
Chiara Gardin (PhD student)
Paolo Laveder (researcher)
Lorenza Mittempergher (PhD student)
Alessandra Nori (researcher)
Marco Sandri (researcher)
Giorgio Valle (professor)
Pompeo Volpe (professor)

Agenda for Content Meeting


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 at PePen, Italian pizza bar and restaurant in the town center.

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)

Introduction


Since GO people are very interesting in improving the GO in several areas of specific interest, they often
organize meeting called GO Content Meeting in which together GO group members and a few domain experts
in person usually discuss about GO categories concerning the focused domain.
In 2004 GO consortium organized the GO Immunology Content meeting held at the Institute for Genomic
Research (TIGR) and in 2006 the GO Neurobiology Content Meeting held at MGI at Bar Harbor (Maine, US)
in which I was actively involved and during which about 500 new terms have been added.

Purpose


Purpose of this content meeting is to bring together experts in muscle biology and physiology to review and
discuss interesting areas in the GO process ontology and GO cellular component. The aim is to come up with
suggestions and comments on existing GO muscle terms but also to propose new GO muscle-specific terms
and specific action items to resolve doubts come to mind during the meeting.
It has been noticed noticed that GO is poor of muscle specific terms so me and prof. Valle have decided to
organise a Muscle Gene Ontology Content Meeting in Padua to improve the representation of. Muscle
Biology in GO and to make some new GO terms about muscle.
Since here in Padua there are several groups working on muscle biology which would provide a good starting
point, there is no doubt that a better definition of the GO related to muscle biology would be very useful,
particularly in microarray and proteomic studies but also for annotate genes involved in neuromuscular
disease. Since Prof. Valle has a grant from the Telethon Foundation to work on GO, first we got in contact
with muscle experts here in Padua and then with external muscle biologists All of them were very enthusiastic
to collaborate and contribute to GO.
The working plan is summarized at
http://wiki.geneontology.org/index.php/Muscle_Development.

Links


Gene Ontology Home page
http://www.geneontlogy.org

Gene Ontology Wiki Page
http://wiki.geneontology.org/index.php/Content_Meeting_Participants_Information

AmiGO home page
http://amigo.geneontology.org/cgi-bin/amigo/go.cgi

Gene Ontology cardio file
http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/gene_ontology_cardio.obo

Tutorial in Italian
http://www.geneontology.org/teaching_resources/tutorials/2007-08_italian_oboedit_tutorial.pdf

Wiki page for Muscle meting
http://wiki.geneontology.org/index.php/Content_Meeting_Participants_Information
username: MuscleMeeting
password: sarcomere


Discussion


The main goal of the meeting was to introduce changes in the representation of the muscle biology in the GO:

  • adding new muscle GO terms and new defintions;
  • checking the existing muscle terms
  • defining action items for improving the description of "muscle" biological processes in the GO.


Sarcoplasmic reticulum and membrane delimited compartments



Prof. Pompeo Volpe and Dr. Alessandra Nori are experts in membrane delimeted compartements and in
particular in sarcoplasmic reticulum.
They suggested to introduce terms that describe the two different portion of sarcoplasmic reticul because they
are morphologically and at molecular level different one form each other.
So new GO terms have been implemented:


EF:0014701 ; junctional sarcoplasmic reticulum membrane
EF:0014702 ; free sarcoplasmic reticulum membrane
EF:0014801 ; longitudinal sarcoplasmic reticulum
EF:0014802 ; terminal cisternae
EF:0014803 ; longitudinal sarcoplasmic reticulum lumen
EF:0014804 ; terminal cisternae lumen

and some definitions have been changed:

GO:0016529 ; sarcoplasmic reticulum
GO:0033017 ; sarcoplasmic reticulum membrane
GO:0033018 ; sarcoplasmic reticulum lumen

Muscle contraction


Prior to the meeting, prof. Carlo Reggiani, a muscle physiologist with a vast knowledge in muscle contraction
had prepared a DAGs showing revised portions on the biological process of muscle contraction. The new
DAG structure contained new GO terms about different kind of muscle contraction (e.g. phasic and rhythmic)
but also several regulation terms of this process.
Unfortunately prof. Reggiani could not come to the meeting due to a family problem but we will contact him
for further help in defining all the new GO terms.
There is still a doubt about some terms of muscle contraction. Do we really need to specify all type of
"muscle contraction" (e.g. artery type muscle contraction)?

EF:0014820 ; tonic smooth muscle contraction
EF:0014821 ; phasic smooth muscle contraction
EF:0014822 ; rhythmic phasic smooth muscle contraction
EF:0014823 ; non-rhythmic smooth muscle contraction
EF:0014824 ; artery type smooth muscle contraction
EF:0014825 ; stomach fundus type smooth muscle contraction
EF:0014826 ; vein type smooth muscle contraction
EF:0014827 ; intestine type smooth muscle contraction
EF:0014828 ; distal stomach type smooth muscle contraction
EF:0014829 ; vascular type smooth muscular contraction
EF:0014830 ; arteriole type smooth muscle contraction
EF:0014831 ; gastro-intestinal system type smooth muscle contraction
EF:0014832 ; urinary bladder type smooth muscle contraction
EF:0014845 ; stomach body type smooth muscle contraction
EF:0014846 ; esophagus type smooth muscle contraction
EF:0014847 ; proximal stomach type smooth muscle contraction
EF:0014848 ; urinary system type smooth muscle contraction
EF:0014849 ; ureter type smooth muscle contraction
EF:0014850 ; vagina type smooth muscle contraction
EF:0014851 ; regulation of voluntary skeletal muscle contraction
EF:0014852 ; regulation of skeletal muscle contraction by neural stimulation via neuromuscular junction
EF:0014853 ; end plate depolarization involved in skeletal muscle contraction
EF:0014854 ; synaptic vesicle docking involved in skeletal muscle contraction
EF:0014860 ; neurotransmitter secretion involved in skeletal muscle contraction
EF:0014861 ; regulation of skeletal muscle contraction by membrane action potential
EF:0014862 ; chemo-mechanical energy conversion involved in skeletal muscle contraction
EF:0014863 ; power generation by chemo-mechanical energy conversion involved in skeletal muscle contraction
EF:0014864 ; force generation by chemo-mechanical energy conversion involved in skeletal muscle contraction
EF:0014865 ; ATP splitting by chemo-mechanical energy conversion involved in skeletal muscle contraction
EF:0014867 ; acto-myosin interaction process
EF:0014868 ; cross bridge cycling
EF:0014869 ; sarcomere shortening
EF:0014871 ; cross bridge formation
GO:0006936 ; muscle contraction
GO:0006939 ; smooth muscle contraction

Sarcomere


It has been discussed also about the "costamere" GO:0043034 but the experts did not have the same opinion
and so they did not come to an agreement.
We would need more time to discuss about it.

All muscle experts agree that the specialised membranes of muscle are still underrepresented at present in the

GO. So they suggested to add new other terms useful to cover specialized areas like: muscle membrane
invagination.

EF:0014704 ; elastic filament
EF:0014705 ; C zone
GO:0005863 ; striated muscle thick filament
GO:0005865 ; striated muscle thin filament
GO:0030017 ; sarcomere
GO:0030018 ; Z disc
GO:0031430 ; M band
GO:0031672 ; A band
GO:0031673 ; H zone
GO:0031674 ; I band
GO:0043034 ; costamere


Muscle Development


Dr. Paolo Laveder made changes to the "muscle development" node.
There are some doubts about "striated muscle development" EF:0014706 because we are not sure if it is
correct to use this term as a parent term for both skeletal and cardiac muscle development.

EF:0014706 ; striated muscle development
EF:0014707 ; branchiomeric skeletal muscle development
EF:0014708 ; regulation of somitomeric trunk muscle development
EF:0014709 ; positive regulation of somitomeric trunk muscle development
EF:0014710 ; negative regulation of somitomeric trunk muscle development
EF:0014711 ; regulation of branchiomeric skeletal muscle development
EF:0014712 ; positive regulation of branchiomeric skeletal muscle development
EF:0014713 ; negative regulation of branchiomeric skeletal muscle development
EF:0014714 ; myoblast cell fate commitment in head
EF:0014715 ; myoblast cell fate commitment in trunk

Muscle plasticity


We started to organize the DAG structure for muscle plasticity dividing the plasticity process by type of
muscle (smooth, striated, etc) and type of change (atrophy, hypertrophy, etc.).
We need to check all the defintions and for doing this, we are still in contact with people at King's College
(London).


Muscle regeneration


Erika had added few terms before the meeting and we had checked all of them but we are still confused about
satellite cell and myoblast. These cells are involved in different stage of muscle regeneration and we need to be
sure if the terms should refer to satellite cell or to myoblast.

Action items


This is primarily a list of things remaining to do after the meeting,
with a few comments here and there.

All three ontologies: check for is_a orphans and run all verification checks and fix accordingly.
[Jen]

A) Muscle Cell Compartments

1. Check definitions of all children of sarcoplasmic reticulum (GO:0016529), especially the part of
children we worked on.
[Erika and Pompeo Volpe]

2. Check calcium sequestration and release terms (there may be typos).
[Jen]

3. Elisabeth Ehler terms
[Erika to add]

B) Sarcomere & Muscle Contraction

B.1) Muscle contraction

1. Check with cardio meeting participants: is it OK not to retain the "voluntary contraction" and
"involuntary contraction" terms? Several of the experts at the muscle meeting (e.g. Vincenzo
Sorrentino) say that they equate voluntary contraction with skeletal muscle contraction, so it would
make more sense to use synonyms.

-- voluntary muscle contraction = skeletal muscle contraction
-- involuntary muscle contraction = cardiac or smooth muscle contraction
[Jen]

If the cardio group objects, get a discussion going to resolve this question and determine what GO
should have. Note: a bit later in the meeting, someone mentioned that the voluntary/involuntary
difference has to do with innervation.

2. Check origin of hindgut contraction term and definition; make sure new parentage under smooth muscle
contraction is OK.
[Jen]

3. Refine definition wording for smooth muscle contraction and its children.
[Erika and Reggiani]

4. Check relationship between phasic (aka peristaltic) smooth muscle contraction and peristalsis – should
there be a relationship, and if so, what? (Harold Drabkin may be able to help; he did some work on
digestion terms.)
[Jen and Harold] [Erika and Reggiani]

5. Ask Regianni to help with several definitions, including phasic contraction; search for his name in the
file!
[Erika and Reggiani]

6. Rename "artery type smooth muscle contraction" and other "x type" terms to avoid using "type" in
names.

Note: Vincenzo queries the need for these specific types of smooth muscle contraction — the
distinction comes from the muscle physiology community's usage, but on a molecular level there may
not be different gene products to annotate to the different terms.

Note re: slow- vs. fast-twitch fibers: Everyone agrees that there are no muscles composed entirely of
slow-twitch, or entirely of fast-twitch, fibers. The slow/fast distinction is relevant at the level of the
fiber, not the entire muscle. Check to make sure term names and definitions reflect this.
[Erika and Reggiani]

7. For skeletal and cardiac muscle contraction: convert to revised wording (I think this refers to the
definition we agreed upon).
[Jen]

8. Add "fibre" synonyms for all "fiber" terms.
[Jen]

9. Look into adding term(s) for the "elastic resonance" (I think that phrase got used) seen in insect fibrillar
muscle and also in other invertebrates. Multiple contractions occur per motor neuron impulse. In
cardio.obo there's a draft term provisionally named "oscillatory fibrillar muscle contraction"
(EF:0014703).
[Erika]
B.2) Sarcomere

1. Check definition wording for elastic filament (narrow synonym: titin) (EF:0014704); make sure it's
really a legit component terms, i.e. a complex, not just a single protein. The generic wording at least
allows titin, nebulin, obscurin, and possibly other proteins to be annotated. Decide whether we can
keep the term (and suggest term(s) to use for annotations if we don't keep this term).
[Erika and Pompeo Volpe]

2. Check provenance of costamere definition.
[Erika and Giorgio]

3. Work on parentage and part of children of costamere generally. For one thing, decide whether
costamere, or a part of child, should be part of sarcolemma instead of cytoplasm.

Note: if GO used has part, could say costamere has part dystroglycan complex. Can't do DGC part of
costamere because the dystroglycan complex is also found elsewhere. (There was some confusion over
part of vs. has part.).

4. Note: Membrane–cytoskeleton linkages in general need work. Jennifer Fordham has volunteered to
look at the ontology in this area.
[Erika and Giorgio]

C) Muscle development

1. Decide what to do about striated muscle development – there was some discussion about whether to
group cardiac and skeletal under striated in the muscle development branch (we have grouped them
elsewhere, e.g. in the muscle contraction branch, but the experts say the developmental paths don't
have much in common). Either obsolete striated muscle development or make it an is a parent of both
cardiac and skeletal muscle development.
[Jen]

2. Obsolete or destroy "satellite cell" (EF:0014812) – it's a cell type. Check for it in CL.
[Erika]

D) Muscle plasticity

1. Finish implementing the structure organizing muscle plasticity children by (a) type of muscle (smooth,
striated, etc.) and type of change (atrophy, hypertrophy, hyperplasia, etc.; also include change in
myofibril size and change in myofibril number where appropriate).
[Erika and Georgine]

2. Complete and correct definitions of terms in the above structure; hold Webex session with experts if
needed.
[Erika]

3. Finish filling in parts (Erika has done some).
[Erika]

4. Make sure the "response to stimulus involved in muscle plasticity" terms are OK – is there any
precedent? If they are good to GO, there are quite a few types of stimulus to fill in (both terms and
definitions).If not, figure out what names, definitions etc. to use. In any case, finish adding terms and
writing defs.

Note: Giorgio Valle would prefer "response to stimulus leading to . . . " in term names –would that
have the same meaning, or another acceptable definition? (additional note: I suggest "resulting in"
instead of "leading to").
[Midori]

5. Ask Alex Diehl for comments/advice on how to name and define terms for children of muscle plasticity
that have to do with responses to sustained activity vs. short bursts, strenuous activity, etc. It would
be very useful to be able to distinguish these, but there's the problem of what constituted (e.g.)
"sustained" or "strenuous" activity, and whether they can be defined in an objective, species-neutral
way.
[Midori]

E) Muscle regeneration

1. Check whether "activation of satellite cell . . . " should have some relationship to cell cycle — satellite
cell activation is exit from a quiescence-like state (Georgine Faulkner says it's arrested in G1 [I think],
and not exactly quiescent).
[Jen and Erika]

2. Move satellite cell differentiation out from under muscle regeneration, because satellite cells exist
before muscle regeneration begins; they differentiate as part of general muscle development.

3. Upon activation, satellite cells undergo further differentitation, becoming myoblasts that fuse into
myotubes, etc. The terms that currently have "satellite cell differentiation—development—
commitment—etc involved in muscle regeneration" probably refer to this differentiation of satellite
cells into myoblasts, and should be renamed.
[Jen and Erika]

4. Change "process during which" to "process whereby" througout (definitions).

Note: has part would also be useful for muscle regeneration has part myoblast fusion.
[Jen and Erika]

5. Jen to ask David Hill whether myotube differentiation is "like the Drosophila thing."Note added during
transcription: I'm not sure "ATP splitting by chemo-mechanical energy conversion involved in skeletal
muscle contraction" (EF:0014865) is really a process. It sounds more like a function, belonging in the
"ATPase activity, coupled" department (and if it is a process, the name should use "ATP
hydrolysis").
[Jen and Erika]

Link to Google spreadsheet:
User: geneontology
psw: goconsortium
http://spreadsheets.google.com/ccc?key=pt9OZIJ8pTRajD1K7ut9Qdw&inv=erika@cribi.unipd.it&t=879985
9578820031159&guest