Re: [Msi-workgroups-board] Availability October 08-12 for TC with MSIchairs - please respond

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

I am only available Wednesday & Thursday (Oct 10-11).  Several next =
steps could include

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1) Assemble MSI metadata templates

2) Distribute templates and alert journal editors of MSI pubs=20

3) Implement the consensus standards at the Metabolomics Journal (this =
would most likely increase the rejection rate)

4) Obtain greater community input and support

5) Discuss and establish time lines

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Cheers

Lloyd=20

________________________________

From: msi...@li... =
[mailto:msi...@li...] On Behalf Of =
Oliver Fiehn
Sent: Tuesday, October 02, 2007 11:53 AM
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=
0a372c251b9cf7&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

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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.

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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.

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Best

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

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email    of...@uc...

URL     http://fiehnlab.ucdavis.edu/

tel         +1-530-754-8258

fax        +1-530-754-9658

=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>=20

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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" <Fed...@fd...> =
<mailto:Fed...@fd...>=20

To:=20

"Susanna" <sa...@eb...> <mailto:sa...@eb...>=20

References:=20

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Susanna,

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

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Thanks,

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Federico

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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>  Fed...@fd... =
<mailto:Fed...@fd...>=20

=20

=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

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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.

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Thanks,

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Federico

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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>  Fed...@fd... =
<mailto:Fed...@fd...>=20

=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=
44398c0c4f2f7291c0c6&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.

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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.

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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.

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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.

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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.

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

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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
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NET Project - Coordinator
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www.ebi.ac.uk/net-project
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The European Bioinformatics Institute   email:  <email:=A0>  =
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
Susanna-Assunta Sansone, PhD
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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
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