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

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 > letter goes out (from this working group)and to our metabolomics 
community to explain what was done so far
Presentation to meetings ( e.g. next Metabolomics Society meeting) with 
dedicated slots for discussions and workgroups is also helpful to engage 
with others.
Susanna

Rima Kaddurah-Daouk wrote:

>
> Excellent ideas Don and congratulations on new job with BMS. Would it 
> also help if a letter goes out (from this working group)and to our 
> metabolomics community to explain what was done so far, point them to 
> publications, ask them for their input and participation for next 
> phase and solicit ideas as to what next phase should achieve? reaching 
> editors is key and working with regulatory agencies a must. best rima
>
>
>
>
> Don Robertson <don...@bm...>
> Sent by: don...@bm...
>
> 10/02/2007 01:47 PM
>
> 	
> To
> 	Oliver Fiehn <of...@uc...>
> cc
> 	"'Susanna'" <sa...@eb...>, 
> msi...@li..., 
> rim...@du..., "'Goodsaid, Federico'" 
> <Fed...@fd...>
> Subject
> 	Re: [Msi-workgroups-board] Availability October 08-12 for TC with MSI 
>        chairs - please respond
>
>
>
> 	
>
>
>
>
>
> Oliver/All,
>
> I think an important next step will be to gain feedback from the 
> consumers of standards (not necessarily the users).  I think users 
> (those generating data) have had and continue to have the opportunity 
> for feedback, but my impression is that such feedback has been minimal 
> so far (though as I've been out of touch for a few months - maybe I've 
> missed a groundswell of interest?).  By consumers, I mean journal 
> editors and regulators who might incorporate our standards  into their 
> requirements for submissions (either manuscripts or regulatory 
> submissions).  Maybe this is happening already??? If not, our telecon 
> with Federico may be a good first step so we can see how consumer 
> friendly the standards are in their present form and where we need to 
> expand or clarify things. I think we should also think about 
> contacting editors and/or editorial boards of relevant journals to 
> solicit feedback.  I'm not sure how best to do that , but I hope you 
> or some of your academic colleagues might have suggestions for a 
> mechanism to accomplish that.  
>
> My thoughts for what they are worth...
>
> BTW - from 10 -12 USEDT next week works for me Tuesday through 
> Thursday with no problem.  Monday is doable but not ideal and Friday 
> is not very good at all.    
>
> Don
>
>
>
> Oliver Fiehn wrote:
> Dear Susanna, dear all,
>  
> Now that all MSI documents are available online at the Metabolomics 
> journal site 
> (http://www.springerlink.com/content/j85g85483103/?p=69c352ecf23641afa10a372c251b9cf7&pi=0 
> <http://www.springerlink.com/content/j85g85483103/?p=69c352ecf23641afa10a372c251b9cf7&pi=0> 
> ), 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.
>  
> 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
> 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).
> With respect to the dates, please
> tell me your availability for these times next week, i.e. Monday 
> October 08 to Friday October 12.
>  
> 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.
>  
> Best
> Oliver
>  
>  
> Oliver Fiehn, Assoc. Prof. MCB
> - Metabolomics -
> UC Davis Genome Center
> GBSF Building room 1315
> 451 East Health Sciences Drive
> Davis (CA) 95616-8816
>  
> email    of...@uc... <mailto:of...@uc...>
> URL     http://fiehnlab.ucdavis.edu/
> tel         +1-530-754-8258
> fax        +1-530-754-9658
>  
>
> ------------------------------------------------------------------------
>
> From: Susanna [mailto:sa...@eb...]
> Sent: Mittwoch, 26. September 2007 12:17
> To: msi...@li... 
> <mailto:msi...@li...>; 
> rim...@du... <mailto:rim...@du...>; 
> of...@uc... <mailto:of...@uc...>
> Cc: Goodsaid, Federico
> Subject: FDA's request for teleconference with MSI chairs
> Importance: High
>  
> 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
>
>  
>
> -------- Original Message --------
>
> Subject:
> 	RE: Metabolomics standards' papers- Nature Biotechnology and 
> Metabolomics journal
> Date:
> 	Wed, 26 Sep 2007 13:08:31 -0400
> From:
> 	"Goodsaid, Federico" <Fed...@fd...> 
> <mailto:Fed...@fd...>
> To:
> 	"Susanna" <sa...@eb...> <mailto:sa...@eb...>
> References:
> 	 
>
>
>  
> Susanna,
>  
> Go ahead. Let me know of possible dates and times to do this.
>  
> Thanks,
>  
> Federico
>  
> 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...>
>  
>  
>
>
> ------------------------------------------------------------------------
>
> From: Susanna [mailto:sa...@eb...]
> Sent: Wednesday, September 26, 2007 12:44 PM
> To: Goodsaid, Federico
> Subject: Re: Metabolomics standards' papers- Nature Biotechnology and 
> Metabolomics journal
>  
> 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?) .
>
> If you wish I can write to the MSI Board and cc to you. Please, let me 
> know.
>
> Thanks,
> Susanna
>
>
> Goodsaid, Federico wrote:
> Susanna,
>  
> Would you be ale to give us a Webex presentation about these 
> standards? We could provide a Webex link from this end.
>  
> Thanks,
>  
> Federico
>  
>
> 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...>
>
>  
>
>  
>
>
> ------------------------------------------------------------------------
>
> From: Susanna [mailto:sa...@eb...]
> 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
>  
> 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
> (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=c2b8952a7cdb44398c0c4f2f7291c0c6&pi=0 
> <http://springerlink.metapress.com/content/j85g85483103/?p=c2b8952a7cdb44398c0c4f2f7291c0c6&pi=0>)
>
>  
> 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.
>  
> 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.
>  
> 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.
>  
> 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.
>  
> 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., ©tys, D., Teng, Q., Field, D. & Viant, M.R. (2007) 
> Standard reporting requirements for biological samples in metabolomics 
> experiments: environmental context. Metabolomics 3, 203-210.
>  
> 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.
>  
> Rubtsov, D.V., Jenkins, H., Ludwig, C., Easton, J., Viant, M.R., 
> Günther, U., Griffin, J.L. & Hardy, N. (2007) Proposed reporting 
> requirements for the description of NMR-based metabolomics 
> experiments. Metabolomics 3, 223-229.
>  
> 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., Sjöström, M., Trygg, J. & Wulfert, F. (2007) Proposed minimum 
> reporting standards for data analysis in metabolomics. Metabolomics 3, 
> 231-241.
>  
> Hardy, N.W. & Taylor, C.F. (2007) A roadmap for the establishment of 
> standard data exchange structures for metabolomics. Metabolomics 3, 
> 243-248.
>  
> 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.
>  
>  
> -- 
> Susanna-Assunta Sansone, PhD
>  
> Project - Coordinator
> www.ebi.ac.uk/net-project <http://www.ebi.ac.uk/net-project>
>  
>  
>  
>  
>  
>  
> -- 
> Susanna-Assunta Sansone, PhD
>  
> NET Project - Coordinator
>  
> www.ebi.ac.uk/net-project <http://www.ebi.ac.uk/net-project>
>  
> The European Bioinformatics Institute   email: 
> <email:%A0> sa...@eb... <mailto: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            
>  
>  
>  
>
>
> -- 
> Susanna-Assunta Sansone, PhD
>  
> NET Project - Coordinator
>  
> www.ebi.ac.uk/net-project <http://www.ebi.ac.uk/net-project>
>        
> The European Bioinformatics Institute   email:  sa...@eb... 
> <mailto: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            
>  
>  
>
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