[Msi-workgroups-board] MSI teleconference Thursday, October 11, 7-9 a.m. Pacific (10-12 a.m. EST)

SourceForge Headquarters 1320 Columbia Street Suite 310 San Diego, CA 92101 +1 (858) 422-6466

Dear all,

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I have received responses from most of you, thanks for that. Anybody who =
is
on that list is invited to join =96 we are an inclusive discussion =
forum, not
an exclusive elite club. So, if you think somebody else would really be
interested to actively steer discussions (apart from being member in one =
of
the working groups), please tell me.

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The best time for a TC on =91how to proceed with the MSI=92 is on=20

Thursday, October 11, 7-9 a.m. Pacific=20
(10-12 a.m. US east coast, 15:00-17:00 UK time, 16:00-18:00 central =
Europe
time).=20

I will try to get a free dial-in number, so you=92ll receive another =
email
tomorrow or latest on Wednesday.

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I propose we start at 7 a.m. PST (10 am EST, 16:00 central Europe) and =
aim
at a one hour discussion but could potentially extend it, if needed and
useful.

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Those of you who can=92t make it on Thursday (e.g. Teresa and Rima), it =
would
be great if you could write a short email on how you feel the MSI =
initiative
should or might realistically go forward.=20

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Thanks so far,=20

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Please bookmark your calendars!

=20

Oliver

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Oliver Fiehn, Assoc. Prof. MCB

- Metabolomics -

UC Davis Genome Center

GBSF Building room 1315=20

451 East Health Sciences Drive

Davis (CA) 95616-8816

=20

email    of...@uc...

URL     http://fiehnlab.ucdavis.edu/

tel         +1-530-754-8258

fax        +1-530-754-9658

=20

  _____ =20

From: msi...@li...
[mailto:msi...@li...] On Behalf Of
Oliver Fiehn
Sent: Dienstag, 2. Oktober 2007 09:53
To: 'Susanna'; msi...@li...;
rim...@du...
Cc: 'Goodsaid, Federico'
Subject: [Msi-workgroups-board] Availability October 08-12 for TC with
MSIchairs - please respond

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Dear Susanna, dear all,

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Now that all MSI documents are available online at the Metabolomics =
journal
site
(http://www.springerlink.com/content/j85g85483103/?p=3D69c352ecf23641afa1=
0a372
c251b9cf7
<http://www.springerlink.com/content/j85g85483103/?p=3D69c352ecf23641afa1=
0a372
c251b9cf7&pi=3D0> &pi=3D0 ), we should discuss how to move forward. The =
view may
be different for different groups, so I would like to see opinions =
expressed
from each group chair. We will set up a date and time for a telephone
conference, but by experience, it may happen that not every WG chair can
join the discussion. In this case I would like to get input by email =
from
those chairs who eventually will not be able to join the TC.=20

=20

As for dates/time of the TC, we have a 9-hour time difference between =
the
U.S. pacific coast and central Europe. So, the time seems to be fixed
somewhere around=20
7-9 a.m. Pacific (10-12 a.m. US east coast, 15:00-17:00 UK time, =
16:00-18:00
central Europe time).=20

With respect to the dates, please=20
tell me your availability for these times next week, i.e. Monday October =
08
to Friday October 12.

=20

A one hour TC should be fine. Please respond to me, no need to respond =
to
all on the list in order to reduce email traffic.

=20

Best

Oliver

=20

=20

Oliver Fiehn, Assoc. Prof. MCB

- Metabolomics -

UC Davis Genome Center

GBSF Building room 1315=20

451 East Health Sciences Drive

Davis (CA) 95616-8816

=20

email    of...@uc...

URL     http://fiehnlab.ucdavis.edu/

tel         +1-530-754-8258

fax        +1-530-754-9658

=20

  _____ =20

From: Susanna [mailto:sa...@eb...]=20
Sent: Mittwoch, 26. September 2007 12:17
To: msi...@li...; =
rim...@du...;
of...@uc...
Cc: Goodsaid, Federico
Subject: FDA's request for teleconference with MSI chairs
Importance: High

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Dear Rima, Oliver and WGs' chairs,

In the light of our latest papers, Federico Goodsaid* (FDA's CDER and =
here
cc-e) suggests having a Webex meeting to discuss the MSI activities.
As you can see from our communication -copied below- I have suggested
inviting the working groups' chairs (or alternative leading people), a =
total
of 5 people.

I reckon this is a great opportunity, what do you think?

If your positive, Federico will provide a Webex link from their/FDA end. =
 To
start identifying possible date and time I have set up a doodle page:
Go to http://www.doodle.ch/xsv4ur7h43bxvune and enter your availability
(Federico, please, you too).
Please, let me know if you cannot make any of the proposed dates (approx
last 2 weeks of October and early Nov).

Best regards,
Susanna

* Federico is also responsible for the "Guidance for Industry -
Pharmacogenomic Data Submissions" just released by FDA:
<http://www.fda.gov/CBER/gdlns/pharmdtasubcomp.pdf>
http://www.fda.gov/CBER/gdlns/pharmdtasubcomp.pdf

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-------- Original Message --------=20

Subject:=20

RE: Metabolomics standards' papers- Nature Biotechnology and =
Metabolomics
journal

Date:=20

Wed, 26 Sep 2007 13:08:31 -0400

From:=20

"Goodsaid, Federico"  <mailto:Fed...@fd...>
<Fed...@fd...>

To:=20

"Susanna"  <mailto:sa...@eb...> <sa...@eb...>

References:=20

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=20

Susanna,

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Go ahead. Let me know of possible dates and times to do this.

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Thanks,

=20

Federico

=20

Federico Goodsaid, Ph.D.

Genomics Group

Office of Clinical Pharmacology

Office of Translational Science

Center for Drug Evaluation and Research

U.S. Food and Drug Administration

10903 New Hampshire Avenue, Building 21, Room 3663

Silver Spring, MD 20903-0002

phone:  301-796-1535

email: <email: >    <mailto:Fed...@fd...>
Fed...@fd...

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  _____ =20

From: Susanna [mailto:sa...@eb...]=20
Sent: Wednesday, September 26, 2007 12:44 PM
To: Goodsaid, Federico
Subject: Re: Metabolomics standards' papers- Nature Biotechnology and
Metabolomics journal

=20

Hi Federico,

I would be happy to help.
Actually, I should report this to the rest of the MSI Board.

I lead the ontology working group and provide links with MGED and =
proteomics
standard groups. To provide you with a summary overview of the MSI
activities, my suggestion would be to invite the other working groups'
leaders or other key people (4-5 people max?) .=20

If you wish I can write to the MSI Board and cc to you. Please, let me =
know.

Thanks,
Susanna

Goodsaid, Federico wrote:

Susanna,

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Would you be ale to give us a Webex presentation about these standards? =
We
could provide a Webex link from this end.

=20

Thanks,

=20

Federico

=20

Federico Goodsaid, Ph.D.

Genomics Group

Office of Clinical Pharmacology

Office of Translational Science

Center for Drug Evaluation and Research

U.S. Food and Drug Administration

10903 New Hampshire Avenue, Building 21, Room 3663

Silver Spring, MD 20903-0002

phone:  301-796-1535

email: <email:%A0>    <mailto:Fed...@fd...>
Fed...@fd...

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=20

  _____ =20

From: Susanna [mailto:sa...@eb...]=20
Sent: Wednesday, September 26, 2007 10:16 AM
To: Lord, Peter [PRDUS]
Cc: Hattan, David G; Jacobson-Kram, David; 'Dix. David (E-mail); =
Goodsaid,
Federico; Eshete, Feleke; Frueh, Felix; Frank Sistare; Friedlieb =
Pfannkuch
(E-mail); Gregory Akerman (E-mail); 'Haymes. Kenneth (E-mail); Elayan,
Ikram; Fuscoe, James; Jean-Charles. Gautier (E-mail); Jennifer Fostel
(E-mail); Jim Stevens (E-mail); Leighton, John K; John. N. Haselden
(E-mail); Jonathan. Tugwood (E-mail); Joseph F. Sina (E-mail); KDaniels
(E-mail); Laura Suter-Dick {PRBN~Basel} (E-mail); Freed, Lois M; =
McCarroll.
Nancy (E-mail); Michael Lawton (E-mail); Orr, Michael; Mike Waters =
(E-mail);
Nie, Alex [PRDUS]; Pine, P Scott; Roger Ulrich (E-mail); Ronald Snyder
(E-mail); Francke, Sabine; Thurmond, Scott; Spanhaak, Steven [PRDBE];
Choudhuri, Supratim; Syril Pettit; Papoian, Thomas; Tong, Weida; William
Mattes (E-mail); Ying Jiang (E-mail)
Subject: Metabolomics standards' papers- Nature Biotechnology and
Metabolomics journal

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Dear All,

several open access papers from the Metabolomics Standards Initiative =
(MSI)
are now available.
We look forward to your comments and participation in the future =
activities.

Best regards,
Susanna

********

Correspondence in Nature Biotechnology=20
(http://www.nature.com/nbt/journal/v25/n8/full/nbt0807-846b.html)

Sansone SA, Fan T, Goodacre R, Griffin JL, Hardy NW, Kaddurah-Daouk R,
Kristal BS, Lindon J, Mendes P, Morrison N, Nikolau B, Robertson D, =
Sumner
LW, Taylor C, van der Werf M, van Ommen B, Fiehn O. (2007) The =
Metabolomics
Standards Initiative. Nat Biotechnol. 2007 Aug;25(8):846-8.

Special issue papers in Metabolomics Journal
(http://springerlink.metapress.com/content/j85g85483103/?p=3Dc2b8952a7cdb=
44398
c0c4f2f7291c0c6
<http://springerlink.metapress.com/content/j85g85483103/?p=3Dc2b8952a7cdb=
44398
c0c4f2f7291c0c6&pi=3D0> &pi=3D0)

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Fiehn, O., Robertson, D., Griffin, J., van der Werf, M., Nikolau, B.,
Morrison, N., Sumner, L.W., Goodacre, R., Hardy, N.W., Taylor, C., =
Fostel,
J., Kristal, B. Kaddurah-Daouk, R., Mendes, P., van Ommen, B., Lindon, =
J.C.
& Sansone, S.-A. (2007) The metabolomics standards initiative (MSI).
Metabolomics 3, 175-178.

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Griffin, J.L., Nicholls, A.W., Daykin, C., Heald, S., Keun, H.,
Schuppe-Koistinen, I., Griffiths, J.R., Cheng, L., Rocca-Serra, P., =
Rubtsov,
D.V. & Robertson, D. (2007) Standard reporting requirements for =
biological
samples in metabolomics experiments: mammalian/in vivo experiments.
Metabolomics 3, 179-188.

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van der Werf, M.J., Takors, R., Smedsgaard, J., Nielsen, J., Ferenci, =
T.,
Portais. J.C., Wittmann, C., Hooks, M., Tomassini, A., Oldiges, M., =
Fostel,
J. & Sauer, U. (2007) Standard reporting requirements for biological =
samples
in metabolomics experiments: microbial and in vitro biology experiments.
Metabolomics 3, 189-194.

=20

Fiehn, O., Sumner, L.W., Rhee, S.Y., Ward, J., Dickerson, J., Lange, =
B.M.,
Lane, G., Roessner, U., Last, R. & Nikolau1, B. (2007) Minimum reporting
standards for plant biology context information in metabolomic studies.
Metabolomics 3, 195-201.

=20

Morrison, N., Bearden, D., Bundy, J.G., Collette, T., Currie, F., Davey,
M.P., Haigh, N.S., Hancock, D., Jones, O.A.H., Rochfort, S., Sansone, =
S.-A.,
=A9tys, D., Teng, Q., Field, D. & Viant, M.R. (2007) Standard reporting
requirements for biological samples in metabolomics experiments:
environmental context. Metabolomics 3, 203-210.

=20

Sumner, L.W., Amberg, A., Barrett, D., Beger, R., Beale, M.H., Daykin, =
C.,
Fan, T.W.-M., Fiehn, O., Goodacre, R., Griffin, J.L., Hardy, N., =
Higashi,
R., Kopka, J., Lindon, J.C., Lane, A.N., Marriott, P., Nicholls, A.W.,
Reily, M.D. & Viant, M. (2007) Proposed minimum reporting standards for
chemical analysis. Metabolomics 3, 211-221.

=20

Rubtsov, D.V., Jenkins, H., Ludwig, C., Easton, J., Viant, M.R., =
G=FCnther,
U., Griffin, J.L. & Hardy, N. (2007) Proposed reporting requirements for =
the
description of NMR-based metabolomics experiments. Metabolomics 3, =
223-229.

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Goodacre, R., Broadhurst, D., Smilde, A., Kristal, B.S., Baker, J.D., =
Beger,
R., Bessant, C., Connor, S., Capuani, G., Craig, A., Ebbels, T., Kell, =
D.B.,
Manetti, C., Newton, J., Paternostro, G., Somorjai, R., Sj=F6str=F6m, =
M., Trygg,
J. & Wulfert, F. (2007) Proposed minimum reporting standards for data
analysis in metabolomics. Metabolomics 3, 231-241.

=20

Hardy, N.W. & Taylor, C.F. (2007) A roadmap for the establishment of
standard data exchange structures for metabolomics. Metabolomics 3, =
243-248.

=20

Sansone, S.-A., Schober, D., Atherton, H.J., Fiehn, O., Jenkins, H.,
Rocca-Serra, P., Rubtsov, D.V., Spasic, I., Soldatova, L., Taylor, C.,
Tseng, A., Viant, M.R. & The Ontology Working Group Members (2007)
Metabolomics standards initiative - ontology working group - work in
progress. Metabolomics 3, 249-256.

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--=20
Susanna-Assunta Sansone, PhD
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Project - Coordinator
www.ebi.ac.uk/net-project
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--=20
Susanna-Assunta Sansone, PhD
=20
NET Project - Coordinator
=20
www.ebi.ac.uk/net-project
 =20
The European Bioinformatics Institute   email: <email: >   =
sa...@eb...
EMBL Outstation - Hinxton               direct: +44 (0)1223 494 691
Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK                  room: A229           =20
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 =20

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--=20
Susanna-Assunta Sansone, PhD
=20
NET Project - Coordinator
=20
www.ebi.ac.uk/net-project
       =20
The European Bioinformatics Institute   email:  sa...@eb...
EMBL Outstation - Hinxton               direct: +44 (0)1223 494 691
Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK                  room: A229           =20
=20
 =20