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From: Susanna-Assunta S. <sa...@eb...> - 2009-09-25 14:56:07
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Apologies for cross-posting -------- Original Message -------- Subject: 1st Call for Papers: Computational Aspects of Metabolomics (CINF Symposium, ACS Spring 2010) Date: Fri, 25 Sep 2009 16:27:36 +0200 From: Christoph Steinbeck <ste...@eb...> To: Christoph Steinbeck <ste...@eb...> References: <49E...@eb...> First Call for Papers: Computational Aspects of Metabolomics 239th ACS National Meeting San Francisco, March 21-25, 2010 CINF Division Deadline for submissions: October 19, 2009 Dear Colleagues, this email is to invite papers for our symposium on computational aspects of Metabolomics at the 239th National Meeting of the American Chemical Society (ACS) in San Francisco next spring. Metabolomics studies the occurrence and change of concentrations of small molecular weight chemical compounds (metabolites) in organisms, organs, tissues, cells and ultimately cell compartments in the context of environmental changes, disease or other boundary conditions. It does this by means of spectroscopic and chromatographic techniques and by observing at once not only a few but all compounds visible to the particular technique used. As such, it is a field at the boundary between chemistry and biology, helping to answer biological questions using analytical chemistry and cheminformatics techniques. The metabolomics symposium at the 239th ACS national meeting in San Francisco invites submissions of talks about computing, informatics as well as chemical information aspects of metabolomics. Topics could include the analysis of metabolomics experiments, metabolomics databases, computer-assisted structure elucidation of metabolites and more. Abstracts may be submitted via http://abstracts.acs.org. You'll find the metabolomics session as part of the CINF division symposiums. Deadline is October 19, 2009. In case of questions, please email Christoph Steinbeck at ste...@eb.... Please distribute this call for papers as widely as possible. Cheers, Chris -- Dr. Christoph Steinbeck Head of Chemoinformatics and Metabolism European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK Phone +44 1223 49 2640 Video meliora proboque deteriora sequor. ... Ovid, Metamorphoses VII, 20/21 |
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From: Susanna-Assunta S. <sa...@eb...> - 2008-08-08 16:06:22
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Dear colleagues, We would like to inform you that the paper describing the Minimum Information for Biological and Biomedical Investigations (MIBBI) project -- http://www.mibbi.org/ -- has been published this month in Nature Biotechnology. This represents a significant step towards a comprehensive set complementary reporting guidelines for the biosciences; both by describing our work to date, and by acting as a beacon for new participants. A PDF of the paper is freely-available for download: http://www.nature.com/nbt/journal/v26/n8/pdf/nbt.1411.pdf This paper: 1. Describes the foundational work performed by the ever-growing list of participants in this project. 2. Provides analysis of the various MI specifications registered at the site (scope, conflicts, etc.), including the MSI's CIMR 3. Addresses the view of funders and publishers on the enforcement of consensual reporting guidelines. 4. Outlines our plans for future work, which all are strongly encouraged to monitor, and in which all are invited to participate. Any questions can be directed to: Chris Taylor Susanna-Assunta Sansone Dawn Field Yours Sincerely, Susanna, Chris and Dawn, on behalf of all authors. -- |
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From: Rima Kaddurah-D. <rim...@du...> - 2007-10-18 11:43:17
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From: Susanna-Assunta S. <sa...@eb...> - 2007-10-18 09:03:08
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Thanks it sounds great. >>Does anyone know of any moves towards an >> international public repository for metabolomics data? I can ask Rolf >> Apweiler (EBI).... At EBI we do have some funds to start a public repository to archive metabolomics experiments. This are not dedicate funds, however, but part of an EU research grant. We will levarage on an existing public repository for proteomics (Pride), by Rolf's group, and work closely with them. Susanna Sue Rhee wrote: > Hi: I was recently at a DOE panel discussion to examine the issue of > computational models for Genomes to Life (GTL) and how progress could be > accelerated through targeted investments in applied mathematics, > computer science and computational biology. There was a small > representation of people working on metabolic engineering and metabolic > pathway databases, but I think the metabolomics community was not > represented well, if at all. I don't know how much of the needs > articulated by Oliver and Jules would be relevant to their vision but my > impression was that they were pretty open-minded. If someone/people > (e.g. Oliver and Jules) could formulate a short executive summary with a > few most pressing/bottleneck items, I would be happy to forward it to > the panel organizers. I tried to do this with the bullet points from > Oliver but wasn't sure which of the needs were the most pressing and > thought it would be best for me to be a conduit rather than a > representative. > > Sue > > Jules Griffin wrote: >> >> Dear all, >> >> >> >> No one plans an international public repository at present -- at least >> not involving any of the funding bodies I know of. I don't think this >> would help though as much as a decent database that people could house >> their own data in using the schemes developed by MSI and /or the >> possibility of getting vendor buy-in to produce a print out of the >> standard conditions performed during a given analysis. The problem is >> this requires real (paid!) work to achieve this and I agree with >> Oliver that we've all been doing this in our spare time and for free. >> Without some investment it makes it very difficult to bring things >> together into software that would be useful for the wider community. I >> think without this it's difficult to get the wider community really >> excited in this. Ive tried to do something with people at the EBI and >> I know Oliver has also tried to get things funded but I've had no >> success convincing the UK research councils to fund this area. >> >> >> >> Best wishes, >> >> >> >> Jules >> >> >> >> ------------------------------------------------------------------------ >> >> *From:* msi...@li... >> [mailto:msi...@li...] *On Behalf >> Of *Sue Rhee >> *Sent:* 16 October 2007 17:34 >> *To:* Susanna-Assunta Sansone >> *Cc:* msi...@li...; 'Goodsaid, Federico' >> *Subject:* Re: [Msi-workgroups-board] minutes of the MSI >> teleconference Thursday, October 11, 7-9 a.m. Pacific (10-12 a.m. EST) >> >> >> >> Yes, I totally agree. Does anyone know of any moves towards an >> international public repository for metabolomics data? I can ask Rolf >> Apweiler (EBI), Jim Ostell (NCBI) and Takashi Gojobori (DDBJ) if you >> think this would be helpful. >> >> Sue >> >> Susanna-Assunta Sansone wrote: >> >> Hi Oliver, >> >> >>> The Society or the MSI is not a body .... >>> Almost every participant in the MSI process does this voluntarily... >>> No journal insists on (metabolomic) data sharing plans.... >>> So, there is simply neither a 'push' (by money [big consortia >>> projects], >>> reputation or else) nor a 'pull' (by journals, vendors, pharmaceutical >>> industries or agencies).... >>> >> >> It is also true for microarray and proteomics, and despite this but MGED >> and PSI have found reasons to go ahead. >> >> I reckon the main issue here is the lack of public repositories, willing >> to exchange datasets, the real strenght behind MGED and PSI efforts. >> >> Susanna >> >> >> >> >> Oliver Fiehn wrote: >> >>> Dear Federico, >>> >>> >>> >>> Thanks for your email. It is always very helpful to get questions that >>> seem >>> to be easy but are nevertheless difficult to be answered. There are >>> several >>> answers to your question, some more fundamental and some more practical >>> ones. >>> >>> >>> >>> * I think, discussions around standards are a little bit like >>> democracy: in order to have developing standards adopted, we cannot >>> move >>> very fast but always have to try to get feedback from researchers who >>> were >>> less actively involved. >>> >>> * The Society or the MSI is not a body that can or wants to >>> declare >>> rules and regulations. >>> >>> * Almost every participant in the MSI process does this >>> voluntarily >>> is >>> his/her spare time. That means, our salary and our reputation is >>> depending >>> on other efforts, most of all scientific work and reporting (and for >>> academic PIs, grant writing and teaching). Basically, MSI is an >>> unfunded >>> effort that just cannot gain very high priority on the agenda of most >>> people >>> who are involved. >>> >>> * Most grants we write (e.g. for NIH) have somewhere a section >>> that >>> demands we share data. However, this section is rarely critically >>> reviewed, >>> in comparison to the experimental design sections. The MSI was >>> co-initiated >>> by the NIH/NIDDK, but when the next two 'requests for applications' >>> came >>> out >>> from the NIH, these had nothing to do with data sharing but focused on >>> small >>> biochemical networks or on translational medicine. >>> >>> * No journal insists on (metabolomic) data sharing plans, neither >>> is >>> this requested by reviewers of scientific publications. >>> >>> >>> So, there is simply neither a 'push' (by money [big consortia >>> projects], >>> reputation or else) nor a 'pull' (by journals, vendors, pharmaceutical >>> industries or agencies). >>> >>> >>> In addition, there are of course also quite a few substantial >>> scientific >>> arguments. >>> >>> >>> >>> * The field is still fairly new and researchers want to explore >>> (and >>> publish) a wide variety of approaches. That means, any guideline or >>> document >>> that is too specific might hamper research, something we surely do not >>> want >>> to happen. >>> >>> * Researchers may simply disagree on topics, e.g. what are the >>> 'required' metadata compared to 'optional' metadata. >>> >>> * Metabolomics as an approach lends itself to an array of >>> different >>> biological fields and studies, each of these having its own pace of >>> discussions. >>> >>> * We lack certified reference materials. It would be beneficial if >>> there were trusted resources of standard matrices (tissue, bodyfluids) >>> that >>> have certified contents of metabolites and that could be used to >>> validate >>> novel approaches. >>> >>> * There is a lack of funding for comparison of existing >>> techniques, >>> but >>> agencies (and researchers) have the tendency to push for 'novel >>> innovations' >>> instead of solidifying and validating methods that are already >>> implemented. >>> Ring trials would be beneficial to prove that certain techniques are >>> complementary or overlapping, or even that data can be compared across >>> laboratories. >>> >>> * Metabolism is more flexible than many researchers (outside the >>> metabolomic community) tend to believe. The sheer complexity of >>> compounds >>> found in specimen makes it very difficult to chemically identify even >>> the >>> most part of the detected signals. Hence, reporting 'quantifications of >>> unknown signals' between studies in a single laboratory is >>> scientifically >>> very difficult, let alone comparisons and standardizations between >>> different >>> labs. >>> >>> * Metabolic signals cannot be 'sequenced', unlike peptides or RNA. >>> Libraries (NMR or MS) either do not comprise thousands of compounds or >>> technical differences (e.g. pH, solvent, instrument, other metadata) >>> make >>> it >>> difficult to use spectra beyond the exact conditions under which these >>> spectra were acquired. >>> >>> >>> >>> So, there we are, at least from my point of view. I truly believe we >>> need >>> metabolomic standards and databases to mature the field, and I am >>> convinced, >>> so do most participants of the MSI project. There are other points that >>> contribute to these issues (e.g. accessibility and knowledge about >>> databases, ontologies and else). However, at the current point, I tend >>> not >>> to believe that more workshops will foster or accelerate the MSI in a >>> dramatic way, although of course we will continue to discuss MSI topics >>> in >>> meetings or dedicated workshops to keep the discussions going. >>> >>> >>> >>> I am not familiar enough with the FDA to make reasonable suggestions >>> how >>> you >>> could help fostering and speeding up discussions. We can discuss this >>> further if you call me, if you like (see number below)? >>> >>> >>> >>> >>> >>> With best regards, >>> >>> Oliver Fiehn >>> >>> >>> >>> >>> >>> >>> >>> 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: Goodsaid, Federico [mailto:Fed...@fd...] >>> Sent: Montag, 15. Oktober 2007 08:05 >>> To: Oliver Fiehn; Susanna; msi...@li... >>> <mailto:msi...@li...>; >>> rim...@du... <mailto:rim...@du...> >>> Cc: Sue Rhee >>> Subject: RE: minutes of the MSI teleconference Thursday, October 11, >>> 7-9 >>> a.m. Pacific (10-12 a.m. EST) >>> >>> >>> >>> Oliver, >>> >>> >>> >>> I listened in on part of this teleconference. Why do you think there >>> continues to be hesitation in this area to commit to a systematic >>> definition >>> for data standards or to a broader set of recommendations for data >>> generation, analysis, interpretation and reporting? Please let us know >>> how >>> we can help encourage a discussion leading to a consensus around data >>> standards in this area. >>> >>> >>> >>> 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 4524 >>> >>> Silver Spring, MD 20903-0002 >>> >>> phone: 301-796-1535 >>> >>> email: <mailto:Fed...@fd...> >>> Fed...@fd... <mailto:Fed...@fd...> >>> >>> >>> >>> >>> >>> _____ >>> >>> From: Oliver Fiehn [mailto:of...@uc...] >>> Sent: Thursday, October 11, 2007 3:24 PM >>> To: 'Oliver Fiehn'; 'Susanna'; >>> msi...@li... >>> <mailto:msi...@li...>; >>> rim...@du... <mailto:rim...@du...> >>> Cc: Goodsaid, Federico; 'Sue Rhee' >>> Subject: minutes of the MSI teleconference Thursday, October 11, 7-9 >>> a.m. >>> Pacific (10-12 a.m. EST) >>> >>> >>> >>> Dear all, >>> >>> >>> >>> For those of you who could make the TC meeting today, thanks for your >>> input. >>> And I apologize to Susanna because we were unable to provide a >>> toll-free >>> dial in number - as it turned out, it was toll-free, but just within >>> the >>> U.S. >>> >>> Rima is trying to follow up for potential next meetings and see if we >>> could >>> get a provider for international toll-free dial ins. >>> >>> >>> >>> So, here are the >>> >>> >>> >>> Minutes of today's MSI TC >>> >>> >>> >>> Attendants: >>> Norman Morrison, Oliver Fiehn, Rima Kaddurah-Daouk, Roy Goodacre, Bruce >>> Kristal, Nigel Hardy, Don Robertson, Lloyd W Sumner. >>> >>> >>> >>> Teresa Fan, Mariet vd Werf, Susanna Assunta-Sansone, Basil Nikolau and >>> Jules >>> Griffin sent their apologies for being unavailable to join the TC for a >>> variety reasons. Sue Rhee from Stanford expressed interest in being >>> informed >>> on the outcome of the TC, that's why I cc' her here. >>> >>> >>> >>> Single topic of discussion was 'next steps for the MSI' >>> >>> >>> >>> * MSI documents are published freely online accessible in the >>> Metabolomics journal, thanks to Susanna and Roy for pushing that! It >>> was >>> recognized that the content published in these documents have variable >>> degree of details of information. >>> >>> * Three options of going forward were initially put into the >>> discussion: >>> (a) efforts to persuade journals and agencies to endorse the 'minimal' >>> standards >>> (b) efforts to continue group activities towards 'best practice' >>> documents >>> (c) efforts to draft instances of units and data exchange formats >>> originating from the 'minimal' standards >>> >>> * (a) efforts to persuade journals and agencies to endorse the >>> 'minimal' standards >>> The participants agreed that it was too early to actively enforce >>> journals >>> to use these 'minimal' standards in their editorial guidelines. Based >>> on >>> the >>> example of our own 'Metabolomics' journal, it was instead suggested >>> that >>> the >>> editor and reviewers will be asked to check submissions if papers are >>> MSI-compliant 'with exceptions'. The list of such exceptions might then >>> inform us on pitfalls or where researchers actually failed to >>> accumulate >>> data. In addition, the idea is to lead by example by submitting own >>> papers >>> and stating these papers to be MSI-compliant. Lloyd Sumner (for Plant >>> Phys) >>> and Oliver Fiehn (for Plant J) have submitted manuscripts that detail >>> instances of MSI-compliant reports. In order to spread the idea of MSI >>> standards, it would be important that (all) contributors of the MSI >>> documents would submit their research manuscripts along with >>> MSI-compliant >>> data sheets. The idea here would be (right now) to compile all relevant >>> MSI >>> metadata in a single document (e.g. a data table) and submit such >>> information as supplemental data in conjunction with scientific >>> reports. >>> Otherwise, method sections would become too verbose. >>> In addition, Rima Kaddurah-Daouk will send out a letter to the >>> Metabolomics >>> Society members (which will be drafted by Oliver Fiehn) that calls for >>> community feedback based on the current MSI documents. This period of >>> feedback should extend to 6 months to gather a certain amount of >>> experience. >>> >>> * (b) efforts to continue group activities towards 'best >>> practice' >>> documents >>> Currently, MSI groups are mostly dormant. Writing initial MSI papers >>> helped >>> fostering group activities but groups have not been active since. The >>> idea >>> was revitalized to unify the 'biological context' documents into a >>> single >>> 'umbrella' document that would have further details for the different >>> research areas; however, TC participants did not actively agree on >>> that. >>> A disagreement was stated on the usefulness of working towards 'best >>> practice' documents, especially for the 'data processing' working >>> group. >>> One >>> argument raised was that any official MSI 'best practice' document >>> would >>> be >>> counterproductive because such an official stamp would be easily >>> violating >>> the idea of a continuation of improving practices and methods. Instead, >>> a >>> group of individuals might publish their view of 'current best >>> practice' >>> in >>> order to lead by example which could be improved by other authors using >>> the >>> regular way of scientific discussion. Nevertheless, the point was >>> raised >>> that for 'data processing' it would be really hard to distinguish >>> between >>> 'minimal standards' and 'best practice' and that it would be >>> MSI-compliant >>> to report a wrong way to do a certain piece of research (the same would >>> of >>> course be true for all MSI-areas). So, in a way, right now >>> MSI-compliant >>> would give papers or projects a touch of validation, even if the study >>> design or the way of data acquisition and processing would be very bad. >>> This discussion was consolidated in the general agreement that >>> 'lead-by-example' papers will also serve as best practice documents. >>> One >>> of >>> such instances is a current submission to the journal Metabolomics on >>> use >>> and misuse of PLS in statistics. >>> >>> * (c) efforts to draft instances of units and data exchange >>> formats >>> originating from the 'minimal' standards >>> In practical terms, currently there are a variety of efforts underway >>> to >>> accumulate data and distribute these via websites. However, none of the >>> current efforts really embrace the need of data exchange formats in >>> order >>> to >>> standardize and compile different data sets or data sets of different >>> origins. Some cyberinfrastructure projects (e.g. NSF funded in plant >>> science) will be carried out that might yield standardized >>> repositories, >>> e.g. for biological context data. It is unclear, if other fields of >>> research >>> (e.g. clinical, biomedical) have similar efforts, but it is clear that >>> currently, there are no efforts for (U.S.) national repositories for >>> metabolomics data although in Europe, there are consortia (e.g. >>> Metafor) >>> that might be working into that direction. So, for now this topic is an >>> unsolved problem that would require active research and funding to go >>> forward. >>> >>> * other points >>> Before an email can be sent to the Metabolomics Soc members, it is >>> important >>> to ensure that the msi-sourceforge pages are up to date. Nigel will >>> contact >>> Susanna on that behalf to find out. The pages might need to be >>> revisited >>> with respect to easiness of communication and use - if we want to >>> obtain >>> feedback from members (or other researchers), there must be low-entry >>> ways >>> to do so. A wiki attached to the sourceforge pages was discussed or >>> branching out to the Metabolomics Society pages. >>> With respect to contacts to other efforts, especially the MIBBI efforts >>> led >>> by Chris Taylor, Nigel will serve as contact point (in addition to >>> Susanna's >>> continuing efforts). It is anticipated that there potentially might be >>> significant synergies that could be gathered from such unifying >>> biology-focused reporting efforts. Susanna has acquired funding for >>> workshop(s) that will foster efforts in this direction. >>> >>> >>> >>> >>> >>> Best regards to all, >>> >>> >>> >>> 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 >>> >>> >>> >> >> > > -- > Sue Rhee > Staff Scientist > Carnegie Institution, Department of Plant Biology > 260 Panama Street, Stanford, CA 94305 > Email: (650) 325-1521 x251 > Fax: (650) 325-6857 > > |
|
From: Sue R. <rh...@ac...> - 2007-10-17 22:28:10
|
Hi: I was recently at a DOE panel discussion to examine the issue of computational models for Genomes to Life (GTL) and how progress could be accelerated through targeted investments in applied mathematics, computer science and computational biology. There was a small representation of people working on metabolic engineering and metabolic pathway databases, but I think the metabolomics community was not represented well, if at all. I don't know how much of the needs articulated by Oliver and Jules would be relevant to their vision but my impression was that they were pretty open-minded. If someone/people (e.g. Oliver and Jules) could formulate a short executive summary with a few most pressing/bottleneck items, I would be happy to forward it to the panel organizers. I tried to do this with the bullet points from Oliver but wasn't sure which of the needs were the most pressing and thought it would be best for me to be a conduit rather than a representative. Sue Jules Griffin wrote: > > Dear all, > > > > No one plans an international public repository at present -- at least > not involving any of the funding bodies I know of. I don't think this > would help though as much as a decent database that people could house > their own data in using the schemes developed by MSI and /or the > possibility of getting vendor buy-in to produce a print out of the > standard conditions performed during a given analysis. The problem is > this requires real (paid!) work to achieve this and I agree with > Oliver that we've all been doing this in our spare time and for free. > Without some investment it makes it very difficult to bring things > together into software that would be useful for the wider community. I > think without this it's difficult to get the wider community really > excited in this. Ive tried to do something with people at the EBI and > I know Oliver has also tried to get things funded but I've had no > success convincing the UK research councils to fund this area. > > > > Best wishes, > > > > Jules > > > > ------------------------------------------------------------------------ > > *From:* msi...@li... > [mailto:msi...@li...] *On Behalf > Of *Sue Rhee > *Sent:* 16 October 2007 17:34 > *To:* Susanna-Assunta Sansone > *Cc:* msi...@li...; 'Goodsaid, Federico' > *Subject:* Re: [Msi-workgroups-board] minutes of the MSI > teleconference Thursday, October 11, 7-9 a.m. Pacific (10-12 a.m. EST) > > > > Yes, I totally agree. Does anyone know of any moves towards an > international public repository for metabolomics data? I can ask Rolf > Apweiler (EBI), Jim Ostell (NCBI) and Takashi Gojobori (DDBJ) if you > think this would be helpful. > > Sue > > Susanna-Assunta Sansone wrote: > > Hi Oliver, > > >> The Society or the MSI is not a body .... >> Almost every participant in the MSI process does this voluntarily... >> No journal insists on (metabolomic) data sharing plans.... >> So, there is simply neither a 'push' (by money [big consortia projects], >> reputation or else) nor a 'pull' (by journals, vendors, pharmaceutical >> industries or agencies).... >> > > It is also true for microarray and proteomics, and despite this but MGED > and PSI have found reasons to go ahead. > > I reckon the main issue here is the lack of public repositories, willing > to exchange datasets, the real strenght behind MGED and PSI efforts. > > Susanna > > > > > Oliver Fiehn wrote: > >> Dear Federico, >> >> >> >> Thanks for your email. It is always very helpful to get questions that >> seem >> to be easy but are nevertheless difficult to be answered. There are >> several >> answers to your question, some more fundamental and some more practical >> ones. >> >> >> >> * I think, discussions around standards are a little bit like >> democracy: in order to have developing standards adopted, we cannot move >> very fast but always have to try to get feedback from researchers who were >> less actively involved. >> >> * The Society or the MSI is not a body that can or wants to declare >> rules and regulations. >> >> * Almost every participant in the MSI process does this voluntarily >> is >> his/her spare time. That means, our salary and our reputation is depending >> on other efforts, most of all scientific work and reporting (and for >> academic PIs, grant writing and teaching). Basically, MSI is an unfunded >> effort that just cannot gain very high priority on the agenda of most >> people >> who are involved. >> >> * Most grants we write (e.g. for NIH) have somewhere a section that >> demands we share data. However, this section is rarely critically >> reviewed, >> in comparison to the experimental design sections. The MSI was >> co-initiated >> by the NIH/NIDDK, but when the next two 'requests for applications' came >> out >> from the NIH, these had nothing to do with data sharing but focused on >> small >> biochemical networks or on translational medicine. >> >> * No journal insists on (metabolomic) data sharing plans, neither is >> this requested by reviewers of scientific publications. >> >> >> So, there is simply neither a 'push' (by money [big consortia projects], >> reputation or else) nor a 'pull' (by journals, vendors, pharmaceutical >> industries or agencies). >> >> >> In addition, there are of course also quite a few substantial scientific >> arguments. >> >> >> >> * The field is still fairly new and researchers want to explore (and >> publish) a wide variety of approaches. That means, any guideline or >> document >> that is too specific might hamper research, something we surely do not >> want >> to happen. >> >> * Researchers may simply disagree on topics, e.g. what are the >> 'required' metadata compared to 'optional' metadata. >> >> * Metabolomics as an approach lends itself to an array of different >> biological fields and studies, each of these having its own pace of >> discussions. >> >> * We lack certified reference materials. It would be beneficial if >> there were trusted resources of standard matrices (tissue, bodyfluids) >> that >> have certified contents of metabolites and that could be used to validate >> novel approaches. >> >> * There is a lack of funding for comparison of existing techniques, >> but >> agencies (and researchers) have the tendency to push for 'novel >> innovations' >> instead of solidifying and validating methods that are already >> implemented. >> Ring trials would be beneficial to prove that certain techniques are >> complementary or overlapping, or even that data can be compared across >> laboratories. >> >> * Metabolism is more flexible than many researchers (outside the >> metabolomic community) tend to believe. The sheer complexity of compounds >> found in specimen makes it very difficult to chemically identify even the >> most part of the detected signals. Hence, reporting 'quantifications of >> unknown signals' between studies in a single laboratory is scientifically >> very difficult, let alone comparisons and standardizations between >> different >> labs. >> >> * Metabolic signals cannot be 'sequenced', unlike peptides or RNA. >> Libraries (NMR or MS) either do not comprise thousands of compounds or >> technical differences (e.g. pH, solvent, instrument, other metadata) make >> it >> difficult to use spectra beyond the exact conditions under which these >> spectra were acquired. >> >> >> >> So, there we are, at least from my point of view. I truly believe we need >> metabolomic standards and databases to mature the field, and I am >> convinced, >> so do most participants of the MSI project. There are other points that >> contribute to these issues (e.g. accessibility and knowledge about >> databases, ontologies and else). However, at the current point, I tend not >> to believe that more workshops will foster or accelerate the MSI in a >> dramatic way, although of course we will continue to discuss MSI topics in >> meetings or dedicated workshops to keep the discussions going. >> >> >> >> I am not familiar enough with the FDA to make reasonable suggestions how >> you >> could help fostering and speeding up discussions. We can discuss this >> further if you call me, if you like (see number below)? >> >> >> >> >> >> With best regards, >> >> Oliver Fiehn >> >> >> >> >> >> >> >> 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: Goodsaid, Federico [mailto:Fed...@fd...] >> Sent: Montag, 15. Oktober 2007 08:05 >> To: Oliver Fiehn; Susanna; msi...@li... <mailto:msi...@li...>; >> rim...@du... <mailto:rim...@du...> >> Cc: Sue Rhee >> Subject: RE: minutes of the MSI teleconference Thursday, October 11, 7-9 >> a.m. Pacific (10-12 a.m. EST) >> >> >> >> Oliver, >> >> >> >> I listened in on part of this teleconference. Why do you think there >> continues to be hesitation in this area to commit to a systematic >> definition >> for data standards or to a broader set of recommendations for data >> generation, analysis, interpretation and reporting? Please let us know how >> we can help encourage a discussion leading to a consensus around data >> standards in this area. >> >> >> >> 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 4524 >> >> Silver Spring, MD 20903-0002 >> >> phone: 301-796-1535 >> >> email: <mailto:Fed...@fd...> >> Fed...@fd... <mailto:Fed...@fd...> >> >> >> >> >> >> _____ >> >> From: Oliver Fiehn [mailto:of...@uc...] >> Sent: Thursday, October 11, 2007 3:24 PM >> To: 'Oliver Fiehn'; 'Susanna'; msi...@li... <mailto:msi...@li...>; >> rim...@du... <mailto:rim...@du...> >> Cc: Goodsaid, Federico; 'Sue Rhee' >> Subject: minutes of the MSI teleconference Thursday, October 11, 7-9 a.m. >> Pacific (10-12 a.m. EST) >> >> >> >> Dear all, >> >> >> >> For those of you who could make the TC meeting today, thanks for your >> input. >> And I apologize to Susanna because we were unable to provide a toll-free >> dial in number - as it turned out, it was toll-free, but just within the >> U.S. >> >> Rima is trying to follow up for potential next meetings and see if we >> could >> get a provider for international toll-free dial ins. >> >> >> >> So, here are the >> >> >> >> Minutes of today's MSI TC >> >> >> >> Attendants: >> Norman Morrison, Oliver Fiehn, Rima Kaddurah-Daouk, Roy Goodacre, Bruce >> Kristal, Nigel Hardy, Don Robertson, Lloyd W Sumner. >> >> >> >> Teresa Fan, Mariet vd Werf, Susanna Assunta-Sansone, Basil Nikolau and >> Jules >> Griffin sent their apologies for being unavailable to join the TC for a >> variety reasons. Sue Rhee from Stanford expressed interest in being >> informed >> on the outcome of the TC, that's why I cc' her here. >> >> >> >> Single topic of discussion was 'next steps for the MSI' >> >> >> >> * MSI documents are published freely online accessible in the >> Metabolomics journal, thanks to Susanna and Roy for pushing that! It was >> recognized that the content published in these documents have variable >> degree of details of information. >> >> * Three options of going forward were initially put into the >> discussion: >> (a) efforts to persuade journals and agencies to endorse the 'minimal' >> standards >> (b) efforts to continue group activities towards 'best practice' documents >> (c) efforts to draft instances of units and data exchange formats >> originating from the 'minimal' standards >> >> * (a) efforts to persuade journals and agencies to endorse the >> 'minimal' standards >> The participants agreed that it was too early to actively enforce journals >> to use these 'minimal' standards in their editorial guidelines. Based on >> the >> example of our own 'Metabolomics' journal, it was instead suggested that >> the >> editor and reviewers will be asked to check submissions if papers are >> MSI-compliant 'with exceptions'. The list of such exceptions might then >> inform us on pitfalls or where researchers actually failed to accumulate >> data. In addition, the idea is to lead by example by submitting own papers >> and stating these papers to be MSI-compliant. Lloyd Sumner (for Plant >> Phys) >> and Oliver Fiehn (for Plant J) have submitted manuscripts that detail >> instances of MSI-compliant reports. In order to spread the idea of MSI >> standards, it would be important that (all) contributors of the MSI >> documents would submit their research manuscripts along with MSI-compliant >> data sheets. The idea here would be (right now) to compile all relevant >> MSI >> metadata in a single document (e.g. a data table) and submit such >> information as supplemental data in conjunction with scientific reports. >> Otherwise, method sections would become too verbose. >> In addition, Rima Kaddurah-Daouk will send out a letter to the >> Metabolomics >> Society members (which will be drafted by Oliver Fiehn) that calls for >> community feedback based on the current MSI documents. This period of >> feedback should extend to 6 months to gather a certain amount of >> experience. >> >> * (b) efforts to continue group activities towards 'best practice' >> documents >> Currently, MSI groups are mostly dormant. Writing initial MSI papers >> helped >> fostering group activities but groups have not been active since. The idea >> was revitalized to unify the 'biological context' documents into a single >> 'umbrella' document that would have further details for the different >> research areas; however, TC participants did not actively agree on that. >> A disagreement was stated on the usefulness of working towards 'best >> practice' documents, especially for the 'data processing' working group. >> One >> argument raised was that any official MSI 'best practice' document would >> be >> counterproductive because such an official stamp would be easily violating >> the idea of a continuation of improving practices and methods. Instead, a >> group of individuals might publish their view of 'current best practice' >> in >> order to lead by example which could be improved by other authors using >> the >> regular way of scientific discussion. Nevertheless, the point was raised >> that for 'data processing' it would be really hard to distinguish between >> 'minimal standards' and 'best practice' and that it would be MSI-compliant >> to report a wrong way to do a certain piece of research (the same would of >> course be true for all MSI-areas). So, in a way, right now MSI-compliant >> would give papers or projects a touch of validation, even if the study >> design or the way of data acquisition and processing would be very bad. >> This discussion was consolidated in the general agreement that >> 'lead-by-example' papers will also serve as best practice documents. One >> of >> such instances is a current submission to the journal Metabolomics on use >> and misuse of PLS in statistics. >> >> * (c) efforts to draft instances of units and data exchange formats >> originating from the 'minimal' standards >> In practical terms, currently there are a variety of efforts underway to >> accumulate data and distribute these via websites. However, none of the >> current efforts really embrace the need of data exchange formats in order >> to >> standardize and compile different data sets or data sets of different >> origins. Some cyberinfrastructure projects (e.g. NSF funded in plant >> science) will be carried out that might yield standardized repositories, >> e.g. for biological context data. It is unclear, if other fields of >> research >> (e.g. clinical, biomedical) have similar efforts, but it is clear that >> currently, there are no efforts for (U.S.) national repositories for >> metabolomics data although in Europe, there are consortia (e.g. Metafor) >> that might be working into that direction. So, for now this topic is an >> unsolved problem that would require active research and funding to go >> forward. >> >> * other points >> Before an email can be sent to the Metabolomics Soc members, it is >> important >> to ensure that the msi-sourceforge pages are up to date. Nigel will >> contact >> Susanna on that behalf to find out. The pages might need to be revisited >> with respect to easiness of communication and use - if we want to obtain >> feedback from members (or other researchers), there must be low-entry ways >> to do so. A wiki attached to the sourceforge pages was discussed or >> branching out to the Metabolomics Society pages. >> With respect to contacts to other efforts, especially the MIBBI efforts >> led >> by Chris Taylor, Nigel will serve as contact point (in addition to >> Susanna's >> continuing efforts). It is anticipated that there potentially might be >> significant synergies that could be gathered from such unifying >> biology-focused reporting efforts. Susanna has acquired funding for >> workshop(s) that will foster efforts in this direction. >> >> >> >> >> >> Best regards to all, >> >> >> >> 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 >> >> >> > > -- Sue Rhee Staff Scientist Carnegie Institution, Department of Plant Biology 260 Panama Street, Stanford, CA 94305 Email: (650) 325-1521 x251 Fax: (650) 325-6857 |
|
From: Jules G. <jl...@mo...> - 2007-10-17 21:55:51
|
Dear all,
No one plans an international public repository at present - at least not
involving any of the funding bodies I know of. I don't think this would help
though as much as a decent database that people could house their own data
in using the schemes developed by MSI and /or the possibility of getting
vendor buy-in to produce a print out of the standard conditions performed
during a given analysis. The problem is this requires real (paid!) work to
achieve this and I agree with Oliver that we've all been doing this in our
spare time and for free. Without some investment it makes it very difficult
to bring things together into software that would be useful for the wider
community. I think without this it's difficult to get the wider community
really excited in this. Ive tried to do something with people at the EBI and
I know Oliver has also tried to get things funded but I've had no success
convincing the UK research councils to fund this area.
Best wishes,
Jules
_____
From: msi...@li...
[mailto:msi...@li...] On Behalf Of Sue
Rhee
Sent: 16 October 2007 17:34
To: Susanna-Assunta Sansone
Cc: msi...@li...; 'Goodsaid, Federico'
Subject: Re: [Msi-workgroups-board] minutes of the MSI teleconference
Thursday, October 11, 7-9 a.m. Pacific (10-12 a.m. EST)
Yes, I totally agree. Does anyone know of any moves towards an international
public repository for metabolomics data? I can ask Rolf Apweiler (EBI), Jim
Ostell (NCBI) and Takashi Gojobori (DDBJ) if you think this would be
helpful.
Sue
Susanna-Assunta Sansone wrote:
Hi Oliver,
The Society or the MSI is not a body ....
Almost every participant in the MSI process does this voluntarily...
No journal insists on (metabolomic) data sharing plans....
So, there is simply neither a 'push' (by money [big consortia projects],
reputation or else) nor a 'pull' (by journals, vendors, pharmaceutical
industries or agencies)....
It is also true for microarray and proteomics, and despite this but MGED
and PSI have found reasons to go ahead.
I reckon the main issue here is the lack of public repositories, willing
to exchange datasets, the real strenght behind MGED and PSI efforts.
Susanna
Oliver Fiehn wrote:
Dear Federico,
Thanks for your email. It is always very helpful to get questions that
seem
to be easy but are nevertheless difficult to be answered. There are
several
answers to your question, some more fundamental and some more practical
ones.
* I think, discussions around standards are a little bit like
democracy: in order to have developing standards adopted, we cannot move
very fast but always have to try to get feedback from researchers who were
less actively involved.
* The Society or the MSI is not a body that can or wants to declare
rules and regulations.
* Almost every participant in the MSI process does this voluntarily
is
his/her spare time. That means, our salary and our reputation is depending
on other efforts, most of all scientific work and reporting (and for
academic PIs, grant writing and teaching). Basically, MSI is an unfunded
effort that just cannot gain very high priority on the agenda of most
people
who are involved.
* Most grants we write (e.g. for NIH) have somewhere a section that
demands we share data. However, this section is rarely critically
reviewed,
in comparison to the experimental design sections. The MSI was
co-initiated
by the NIH/NIDDK, but when the next two 'requests for applications' came
out
from the NIH, these had nothing to do with data sharing but focused on
small
biochemical networks or on translational medicine.
* No journal insists on (metabolomic) data sharing plans, neither is
this requested by reviewers of scientific publications.
So, there is simply neither a 'push' (by money [big consortia projects],
reputation or else) nor a 'pull' (by journals, vendors, pharmaceutical
industries or agencies).
In addition, there are of course also quite a few substantial scientific
arguments.
* The field is still fairly new and researchers want to explore (and
publish) a wide variety of approaches. That means, any guideline or
document
that is too specific might hamper research, something we surely do not
want
to happen.
* Researchers may simply disagree on topics, e.g. what are the
'required' metadata compared to 'optional' metadata.
* Metabolomics as an approach lends itself to an array of different
biological fields and studies, each of these having its own pace of
discussions.
* We lack certified reference materials. It would be beneficial if
there were trusted resources of standard matrices (tissue, bodyfluids)
that
have certified contents of metabolites and that could be used to validate
novel approaches.
* There is a lack of funding for comparison of existing techniques,
but
agencies (and researchers) have the tendency to push for 'novel
innovations'
instead of solidifying and validating methods that are already
implemented.
Ring trials would be beneficial to prove that certain techniques are
complementary or overlapping, or even that data can be compared across
laboratories.
* Metabolism is more flexible than many researchers (outside the
metabolomic community) tend to believe. The sheer complexity of compounds
found in specimen makes it very difficult to chemically identify even the
most part of the detected signals. Hence, reporting 'quantifications of
unknown signals' between studies in a single laboratory is scientifically
very difficult, let alone comparisons and standardizations between
different
labs.
* Metabolic signals cannot be 'sequenced', unlike peptides or RNA.
Libraries (NMR or MS) either do not comprise thousands of compounds or
technical differences (e.g. pH, solvent, instrument, other metadata) make
it
difficult to use spectra beyond the exact conditions under which these
spectra were acquired.
So, there we are, at least from my point of view. I truly believe we need
metabolomic standards and databases to mature the field, and I am
convinced,
so do most participants of the MSI project. There are other points that
contribute to these issues (e.g. accessibility and knowledge about
databases, ontologies and else). However, at the current point, I tend not
to believe that more workshops will foster or accelerate the MSI in a
dramatic way, although of course we will continue to discuss MSI topics in
meetings or dedicated workshops to keep the discussions going.
I am not familiar enough with the FDA to make reasonable suggestions how
you
could help fostering and speeding up discussions. We can discuss this
further if you call me, if you like (see number below)?
With best regards,
Oliver Fiehn
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...
URL http://fiehnlab.ucdavis.edu/
tel +1-530-754-8258
fax +1-530-754-9658
_____
From: Goodsaid, Federico [mailto:Fed...@fd...]
Sent: Montag, 15. Oktober 2007 08:05
To: Oliver Fiehn; Susanna; msi...@li...;
rim...@du...
Cc: Sue Rhee
Subject: RE: minutes of the MSI teleconference Thursday, October 11, 7-9
a.m. Pacific (10-12 a.m. EST)
Oliver,
I listened in on part of this teleconference. Why do you think there
continues to be hesitation in this area to commit to a systematic
definition
for data standards or to a broader set of recommendations for data
generation, analysis, interpretation and reporting? Please let us know how
we can help encourage a discussion leading to a consensus around data
standards in this area.
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 4524
Silver Spring, MD 20903-0002
phone: 301-796-1535
email: <mailto:Fed...@fd...>
<mailto:Fed...@fd...>
Fed...@fd...
_____
From: Oliver Fiehn [mailto:of...@uc...]
Sent: Thursday, October 11, 2007 3:24 PM
To: 'Oliver Fiehn'; 'Susanna'; msi...@li...;
rim...@du...
Cc: Goodsaid, Federico; 'Sue Rhee'
Subject: minutes of the MSI teleconference Thursday, October 11, 7-9 a.m.
Pacific (10-12 a.m. EST)
Dear all,
For those of you who could make the TC meeting today, thanks for your
input.
And I apologize to Susanna because we were unable to provide a toll-free
dial in number - as it turned out, it was toll-free, but just within the
U.S.
Rima is trying to follow up for potential next meetings and see if we
could
get a provider for international toll-free dial ins.
So, here are the
Minutes of today's MSI TC
Attendants:
Norman Morrison, Oliver Fiehn, Rima Kaddurah-Daouk, Roy Goodacre, Bruce
Kristal, Nigel Hardy, Don Robertson, Lloyd W Sumner.
Teresa Fan, Mariet vd Werf, Susanna Assunta-Sansone, Basil Nikolau and
Jules
Griffin sent their apologies for being unavailable to join the TC for a
variety reasons. Sue Rhee from Stanford expressed interest in being
informed
on the outcome of the TC, that's why I cc' her here.
Single topic of discussion was 'next steps for the MSI'
* MSI documents are published freely online accessible in the
Metabolomics journal, thanks to Susanna and Roy for pushing that! It was
recognized that the content published in these documents have variable
degree of details of information.
* Three options of going forward were initially put into the
discussion:
(a) efforts to persuade journals and agencies to endorse the 'minimal'
standards
(b) efforts to continue group activities towards 'best practice' documents
(c) efforts to draft instances of units and data exchange formats
originating from the 'minimal' standards
* (a) efforts to persuade journals and agencies to endorse the
'minimal' standards
The participants agreed that it was too early to actively enforce journals
to use these 'minimal' standards in their editorial guidelines. Based on
the
example of our own 'Metabolomics' journal, it was instead suggested that
the
editor and reviewers will be asked to check submissions if papers are
MSI-compliant 'with exceptions'. The list of such exceptions might then
inform us on pitfalls or where researchers actually failed to accumulate
data. In addition, the idea is to lead by example by submitting own papers
and stating these papers to be MSI-compliant. Lloyd Sumner (for Plant
Phys)
and Oliver Fiehn (for Plant J) have submitted manuscripts that detail
instances of MSI-compliant reports. In order to spread the idea of MSI
standards, it would be important that (all) contributors of the MSI
documents would submit their research manuscripts along with MSI-compliant
data sheets. The idea here would be (right now) to compile all relevant
MSI
metadata in a single document (e.g. a data table) and submit such
information as supplemental data in conjunction with scientific reports.
Otherwise, method sections would become too verbose.
In addition, Rima Kaddurah-Daouk will send out a letter to the
Metabolomics
Society members (which will be drafted by Oliver Fiehn) that calls for
community feedback based on the current MSI documents. This period of
feedback should extend to 6 months to gather a certain amount of
experience.
* (b) efforts to continue group activities towards 'best practice'
documents
Currently, MSI groups are mostly dormant. Writing initial MSI papers
helped
fostering group activities but groups have not been active since. The idea
was revitalized to unify the 'biological context' documents into a single
'umbrella' document that would have further details for the different
research areas; however, TC participants did not actively agree on that.
A disagreement was stated on the usefulness of working towards 'best
practice' documents, especially for the 'data processing' working group.
One
argument raised was that any official MSI 'best practice' document would
be
counterproductive because such an official stamp would be easily violating
the idea of a continuation of improving practices and methods. Instead, a
group of individuals might publish their view of 'current best practice'
in
order to lead by example which could be improved by other authors using
the
regular way of scientific discussion. Nevertheless, the point was raised
that for 'data processing' it would be really hard to distinguish between
'minimal standards' and 'best practice' and that it would be MSI-compliant
to report a wrong way to do a certain piece of research (the same would of
course be true for all MSI-areas). So, in a way, right now MSI-compliant
would give papers or projects a touch of validation, even if the study
design or the way of data acquisition and processing would be very bad.
This discussion was consolidated in the general agreement that
'lead-by-example' papers will also serve as best practice documents. One
of
such instances is a current submission to the journal Metabolomics on use
and misuse of PLS in statistics.
* (c) efforts to draft instances of units and data exchange formats
originating from the 'minimal' standards
In practical terms, currently there are a variety of efforts underway to
accumulate data and distribute these via websites. However, none of the
current efforts really embrace the need of data exchange formats in order
to
standardize and compile different data sets or data sets of different
origins. Some cyberinfrastructure projects (e.g. NSF funded in plant
science) will be carried out that might yield standardized repositories,
e.g. for biological context data. It is unclear, if other fields of
research
(e.g. clinical, biomedical) have similar efforts, but it is clear that
currently, there are no efforts for (U.S.) national repositories for
metabolomics data although in Europe, there are consortia (e.g. Metafor)
that might be working into that direction. So, for now this topic is an
unsolved problem that would require active research and funding to go
forward.
* other points
Before an email can be sent to the Metabolomics Soc members, it is
important
to ensure that the msi-sourceforge pages are up to date. Nigel will
contact
Susanna on that behalf to find out. The pages might need to be revisited
with respect to easiness of communication and use - if we want to obtain
feedback from members (or other researchers), there must be low-entry ways
to do so. A wiki attached to the sourceforge pages was discussed or
branching out to the Metabolomics Society pages.
With respect to contacts to other efforts, especially the MIBBI efforts
led
by Chris Taylor, Nigel will serve as contact point (in addition to
Susanna's
continuing efforts). It is anticipated that there potentially might be
significant synergies that could be gathered from such unifying
biology-focused reporting efforts. Susanna has acquired funding for
workshop(s) that will foster efforts in this direction.
Best regards to all,
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...
URL http://fiehnlab.ucdavis.edu/
tel +1-530-754-8258
fax +1-530-754-9658
|
|
From: Chris T. <chr...@eb...> - 2007-10-17 09:50:12
|
Sponsored workshops with travel and subsistence support help lots, and make for nice reports/papers detailing how the world is a better place as a result... ;) Cheers, Chris. Goodsaid, Federico wrote: > Oliver, > > > > Thanks for your interpretation. Let us know if we can be of help. > > > > 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 4524** > > **Silver Spring****, MD 20903-0002** > > **phone: 301-796-1535** > > **email: *****Fed...@fd...** > <mailto:Fed...@fd...>* > > > > > > ------------------------------------------------------------------------ > > *From:* Oliver Fiehn [mailto:of...@uc...] > *Sent:* Monday, October 15, 2007 12:10 PM > *To:* Goodsaid, Federico; 'Susanna'; > msi...@li...; rim...@du... > *Cc:* 'Sue Rhee' > *Subject:* RE: minutes of the MSI teleconference Thursday, October 11, > 7-9 a.m. Pacific (10-12 a.m. EST) > > > > Dear Federico, > > > > Thanks for your email. It is always very helpful to get questions that > seem to be easy but are nevertheless difficult to be answered. There are > several answers to your question, some more fundamental and some more > practical ones. > > > > Ø I think, discussions around standards are a little bit like > democracy: in order to have developing standards adopted, we cannot move > very fast but always have to try to get feedback from researchers who > were less actively involved. > > Ø The Society or the MSI is not a body that can or wants to declare > rules and regulations. > > Ø Almost every participant in the MSI process does this voluntarily > is his/her spare time. That means, our salary and our reputation is > depending on other efforts, most of all scientific work and reporting > (and for academic PIs, grant writing and teaching). Basically, MSI is an > unfunded effort that just cannot gain very high priority on the agenda > of most people who are involved. > > Ø Most grants we write (e.g. for NIH) have somewhere a section that > demands we share data. However, this section is rarely critically > reviewed, in comparison to the experimental design sections. The MSI was > co-initiated by the NIH/NIDDK, but when the next two ‘requests for > applications’ came out from the NIH, these had nothing to do with data > sharing but focused on small biochemical networks or on translational > medicine. > > Ø No journal insists on (metabolomic) data sharing plans, neither is > this requested by reviewers of scientific publications. > > > So, there is simply neither a ‘push’ (by money [big consortia projects], > reputation or else) nor a ‘pull’ (by journals, vendors, pharmaceutical > industries or agencies). > > > In addition, there are of course also quite a few substantial scientific > arguments. > > Ø The field is still fairly new and researchers want to explore (and > publish) a wide variety of approaches. That means, any guideline or > document that is too specific might hamper research, something we surely > do not want to happen. > > Ø Researchers may simply disagree on topics, e.g. what are the > ‘required’ metadata compared to ‘optional’ metadata. > > Ø Metabolomics as an approach lends itself to an array of different > biological fields and studies, each of these having its own pace of > discussions. > > Ø We lack certified reference materials. It would be beneficial if > there were trusted resources of standard matrices (tissue, bodyfluids) > that have certified contents of metabolites and that could be used to > validate novel approaches. > > Ø There is a lack of funding for comparison of existing techniques, > but agencies (and researchers) have the tendency to push for ‘novel > innovations’ instead of solidifying and validating methods that are > already implemented. > Ring trials would be beneficial to prove that certain techniques are > complementary or overlapping, or even that data can be compared across > laboratories. > > Ø Metabolism is more flexible than many researchers (outside the > metabolomic community) tend to believe. The sheer complexity of > compounds found in specimen makes it very difficult to chemically > identify even the most part of the detected signals. Hence, reporting > ‘quantifications of unknown signals’ between studies in a single > laboratory is scientifically very difficult, let alone comparisons and > standardizations between different labs. > > Ø Metabolic signals cannot be ‘sequenced’, unlike peptides or RNA. > Libraries (NMR or MS) either do not comprise thousands of compounds or > technical differences (e.g. pH, solvent, instrument, other metadata) > make it difficult to use spectra beyond the exact conditions under which > these spectra were acquired. > > So, there we are, at least from my point of view. I truly believe we > need metabolomic standards and databases to mature the field, and I am > convinced, so do most participants of the MSI project. There are other > points that contribute to these issues (e.g. accessibility and knowledge > about databases, ontologies and else). However, at the current point, I > tend not to believe that more workshops will foster or accelerate the > MSI in a dramatic way, although of course we will continue to discuss > MSI topics in meetings or dedicated workshops to keep the discussions going. > > > > I am not familiar enough with the FDA to make reasonable suggestions how > you could help fostering and speeding up discussions. We can discuss > this further if you call me, if you like (see number below)? > > > > > > With best regards, > > Oliver Fiehn > > > > > > > > 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... > > URL http://fiehnlab.ucdavis.edu/ > > tel +1-530-754-8258 > > fax +1-530-754-9658 > > > > ------------------------------------------------------------------------ > > *From:* Goodsaid, Federico [mailto:Fed...@fd...] > *Sent:* Montag, 15. Oktober 2007 08:05 > *To:* Oliver Fiehn; Susanna; msi...@li...; > rim...@du... > *Cc:* Sue Rhee > *Subject:* RE: minutes of the MSI teleconference Thursday, October 11, > 7-9 a.m. Pacific (10-12 a.m. EST) > > > > Oliver, > > > > I listened in on part of this teleconference. Why do you think there > continues to be hesitation in this area to commit to a systematic > definition for data standards or to a broader set of recommendations for > data generation, analysis, interpretation and reporting? Please let us > know how we can help encourage a discussion leading to a consensus > around data standards in this area. > > > > 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 4524** > > **Silver Spring****, MD 20903-0002** > > **phone: 301-796-1535** > > **email: *****Fed...@fd...** > <mailto:Fed...@fd...>* > > > > > > ------------------------------------------------------------------------ > > *From:* Oliver Fiehn [mailto:of...@uc...] > *Sent:* Thursday, October 11, 2007 3:24 PM > *To:* 'Oliver Fiehn'; 'Susanna'; > msi...@li...; rim...@du... > *Cc:* Goodsaid, Federico; 'Sue Rhee' > *Subject:* minutes of the MSI teleconference Thursday, October 11, 7-9 > a.m. Pacific (10-12 a.m. EST) > > > > Dear all, > > > > For those of you who could make the TC meeting today, thanks for your > input. And I apologize to Susanna because we were unable to provide a > toll-free dial in number – as it turned out, it was toll-free, but just > within the U.S. > > Rima is trying to follow up for potential next meetings and see if we > could get a provider for international toll-free dial ins. > > > > So, here are the > > > > *_Minutes of today’s MSI TC_* > > > > _Attendants_: > Norman Morrison, Oliver Fiehn, Rima Kaddurah-Daouk, Roy Goodacre, Bruce > Kristal, Nigel Hardy, Don Robertson, Lloyd W Sumner. > > > > Teresa Fan, Mariet vd Werf, Susanna Assunta-Sansone, Basil Nikolau and > Jules Griffin sent their apologies for being unavailable to join the TC > for a variety reasons. Sue Rhee from Stanford expressed interest in > being informed on the outcome of the TC, that’s why I cc’ her here. > > > > Single _topic of discussion_ was ‘next steps for the MSI’ > > > > · MSI documents are published freely online accessible in the > Metabolomics journal, thanks to Susanna and Roy for pushing that! It was > recognized that the content published in these documents have variable > degree of details of information. > > · Three options of going forward were initially put into the > discussion: > (a) efforts to persuade journals and agencies to endorse the ‘minimal’ > standards > (b) efforts to continue group activities towards ‘best practice’ documents > (c) efforts to draft instances of units and data exchange formats > originating from the ‘minimal’ standards > > · /_(a) efforts to persuade journals and agencies to endorse the > ‘minimal’ standards > _/The participants agreed that it was too early to actively enforce > journals to use these ‘minimal’ standards in their editorial guidelines. > Based on the example of our own ‘Metabolomics’ journal, it was instead > suggested that the editor and reviewers will be asked to check > submissions if papers are MSI-compliant ‘with exceptions’. The list of > such exceptions might then inform us on pitfalls or where researchers > actually failed to accumulate data. In addition, the idea is to lead by > example by submitting own papers and stating these papers to be > MSI-compliant. Lloyd Sumner (for Plant Phys) and Oliver Fiehn (for Plant > J) have submitted manuscripts that detail instances of MSI-compliant > reports. In order to spread the idea of MSI standards, it would be > important that (all) contributors of the MSI documents would submit > their research manuscripts along with MSI-compliant data sheets. The > idea here would be (right now) to compile all relevant MSI metadata in a > single document (e.g. a data table) and submit such information as > supplemental data in conjunction with scientific reports. Otherwise, > method sections would become too verbose. > In addition, Rima Kaddurah-Daouk will send out a letter to the > Metabolomics Society members (which will be drafted by Oliver Fiehn) > that calls for community feedback based on the current MSI documents. > This period of feedback should extend to 6 months to gather a certain > amount of experience. > > · /_(b) efforts to continue group activities towards ‘best > practice’ documents_/ > Currently, MSI groups are mostly dormant. Writing initial MSI papers > helped fostering group activities but groups have not been active since. > The idea was revitalized to unify the ‘biological context’ documents > into a single ‘umbrella’ document that would have further details for > the different research areas; however, TC participants did not actively > agree on that. > A disagreement was stated on the usefulness of working towards ‘best > practice’ documents, especially for the ‘data processing’ working group. > One argument raised was that any official MSI ‘best practice’ document > would be counterproductive because such an official stamp would be > easily violating the idea of a continuation of improving practices and > methods. Instead, a group of individuals might publish their view of > ‘current best practice’ in order to lead by example which could be > improved by other authors using the regular way of scientific > discussion. Nevertheless, the point was raised that for ‘data > processing’ it would be really hard to distinguish between ‘minimal > standards’ and ‘best practice’ and that it would be MSI-compliant to > report a wrong way to do a certain piece of research (the same would of > course be true for all MSI-areas). So, in a way, right now MSI-compliant > would give papers or projects a touch of validation, even if the study > design or the way of data acquisition and processing would be very bad. > This discussion was consolidated in the general agreement that > ‘lead-by-example’ papers will also serve as best practice documents. One > of such instances is a current submission to the journal Metabolomics on > use and misuse of PLS in statistics. > > · /_(c) efforts to draft instances of units and data exchange > formats originating from the ‘minimal’ standards_ > /In practical terms, currently there are a variety of efforts underway > to accumulate data and distribute these via websites. However, none of > the current efforts really embrace the need of data exchange formats in > order to standardize and compile different data sets or data sets of > different origins. Some cyberinfrastructure projects (e.g. NSF funded in > plant science) will be carried out that might yield standardized > repositories, e.g. for biological context data. It is unclear, if other > fields of research (e.g. clinical, biomedical) have similar efforts, but > it is clear that currently, there are no efforts for (U.S.) national > repositories for metabolomics data although in Europe, there are > consortia (e.g. Metafor) that might be working into that direction. So, > for now this topic is an unsolved problem that would require active > research and funding to go forward. > > · /_other points > _/Before an email can be sent to the Metabolomics Soc members, it is > important to ensure that the *msi-sourceforge* pages are up to date. > Nigel will contact Susanna on that behalf to find out. The pages might > need to be revisited with respect to easiness of communication and use – > if we want to obtain feedback from members (or other researchers), there > must be low-entry ways to do so. A wiki attached to the sourceforge > pages was discussed or branching out to the Metabolomics Society pages. > With respect to contacts to other efforts, especially the *MIBBI* > efforts led by Chris Taylor, Nigel will serve as contact point (in > addition to Susanna’s continuing efforts). It is anticipated that there > potentially might be significant synergies that could be gathered from > such unifying biology-focused reporting efforts. Susanna has acquired > funding for workshop(s) that will foster efforts in this direction. > > / / > > / / > > /Best regards to all,/ > > > > 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... > > URL http://fiehnlab.ucdavis.edu/ > > tel +1-530-754-8258 > > fax +1-530-754-9658 > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > > > ------------------------------------------------------------------------ > > _______________________________________________ > Msi-workgroups-board mailing list > Msi...@li... > https://lists.sourceforge.net/lists/listinfo/msi-workgroups-board -- ~~~~~~~~~~~~~~~~~~~~~~~~ chr...@eb... http://mibbi.sf.net/ ~~~~~~~~~~~~~~~~~~~~~~~~ |
|
From: Chris T. <chr...@eb...> - 2007-10-17 09:35:45
|
Funny you should mention it :) There'll be one at EBI in the near(ish) future (and more than that it will be loosely integrated with existing databases for transcriptomics and proteomics experimental data to allow for meaningfully 'joined up' reporting of multi-domain work). Susanna can comment further. Cheers, Chris. Sue Rhee wrote: > Yes, I totally agree. Does anyone know of any moves towards an > international public repository for metabolomics data? I can ask Rolf > Apweiler (EBI), Jim Ostell (NCBI) and Takashi Gojobori (DDBJ) if you > think this would be helpful. > > Sue > > Susanna-Assunta Sansone wrote: >> Hi Oliver, >> >> >>> The Society or the MSI is not a body .... >>> Almost every participant in the MSI process does this voluntarily... >>> No journal insists on (metabolomic) data sharing plans.... >>> So, there is simply neither a 'push' (by money [big consortia projects], >>> reputation or else) nor a 'pull' (by journals, vendors, pharmaceutical >>> industries or agencies).... >>> >> >> It is also true for microarray and proteomics, and despite this but MGED >> and PSI have found reasons to go ahead. >> >> I reckon the main issue here is the lack of public repositories, willing >> to exchange datasets, the real strenght behind MGED and PSI efforts. >> >> Susanna >> >> >> >> >> Oliver Fiehn wrote: >> >>> Dear Federico, >>> >>> >>> >>> Thanks for your email. It is always very helpful to get questions that >>> seem >>> to be easy but are nevertheless difficult to be answered. There are >>> several >>> answers to your question, some more fundamental and some more practical >>> ones. >>> >>> >>> >>> * I think, discussions around standards are a little bit like >>> democracy: in order to have developing standards adopted, we cannot move >>> very fast but always have to try to get feedback from researchers who were >>> less actively involved. >>> >>> * The Society or the MSI is not a body that can or wants to declare >>> rules and regulations. >>> >>> * Almost every participant in the MSI process does this voluntarily >>> is >>> his/her spare time. That means, our salary and our reputation is depending >>> on other efforts, most of all scientific work and reporting (and for >>> academic PIs, grant writing and teaching). Basically, MSI is an unfunded >>> effort that just cannot gain very high priority on the agenda of most >>> people >>> who are involved. >>> >>> * Most grants we write (e.g. for NIH) have somewhere a section that >>> demands we share data. However, this section is rarely critically >>> reviewed, >>> in comparison to the experimental design sections. The MSI was >>> co-initiated >>> by the NIH/NIDDK, but when the next two 'requests for applications' came >>> out >>> from the NIH, these had nothing to do with data sharing but focused on >>> small >>> biochemical networks or on translational medicine. >>> >>> * No journal insists on (metabolomic) data sharing plans, neither is >>> this requested by reviewers of scientific publications. >>> >>> >>> So, there is simply neither a 'push' (by money [big consortia projects], >>> reputation or else) nor a 'pull' (by journals, vendors, pharmaceutical >>> industries or agencies). >>> >>> >>> In addition, there are of course also quite a few substantial scientific >>> arguments. >>> >>> >>> >>> * The field is still fairly new and researchers want to explore (and >>> publish) a wide variety of approaches. That means, any guideline or >>> document >>> that is too specific might hamper research, something we surely do not >>> want >>> to happen. >>> >>> * Researchers may simply disagree on topics, e.g. what are the >>> 'required' metadata compared to 'optional' metadata. >>> >>> * Metabolomics as an approach lends itself to an array of different >>> biological fields and studies, each of these having its own pace of >>> discussions. >>> >>> * We lack certified reference materials. It would be beneficial if >>> there were trusted resources of standard matrices (tissue, bodyfluids) >>> that >>> have certified contents of metabolites and that could be used to validate >>> novel approaches. >>> >>> * There is a lack of funding for comparison of existing techniques, >>> but >>> agencies (and researchers) have the tendency to push for 'novel >>> innovations' >>> instead of solidifying and validating methods that are already >>> implemented. >>> Ring trials would be beneficial to prove that certain techniques are >>> complementary or overlapping, or even that data can be compared across >>> laboratories. >>> >>> * Metabolism is more flexible than many researchers (outside the >>> metabolomic community) tend to believe. The sheer complexity of compounds >>> found in specimen makes it very difficult to chemically identify even the >>> most part of the detected signals. Hence, reporting 'quantifications of >>> unknown signals' between studies in a single laboratory is scientifically >>> very difficult, let alone comparisons and standardizations between >>> different >>> labs. >>> >>> * Metabolic signals cannot be 'sequenced', unlike peptides or RNA. >>> Libraries (NMR or MS) either do not comprise thousands of compounds or >>> technical differences (e.g. pH, solvent, instrument, other metadata) make >>> it >>> difficult to use spectra beyond the exact conditions under which these >>> spectra were acquired. >>> >>> >>> >>> So, there we are, at least from my point of view. I truly believe we need >>> metabolomic standards and databases to mature the field, and I am >>> convinced, >>> so do most participants of the MSI project. There are other points that >>> contribute to these issues (e.g. accessibility and knowledge about >>> databases, ontologies and else). However, at the current point, I tend not >>> to believe that more workshops will foster or accelerate the MSI in a >>> dramatic way, although of course we will continue to discuss MSI topics in >>> meetings or dedicated workshops to keep the discussions going. >>> >>> >>> >>> I am not familiar enough with the FDA to make reasonable suggestions how >>> you >>> could help fostering and speeding up discussions. We can discuss this >>> further if you call me, if you like (see number below)? >>> >>> >>> >>> >>> >>> With best regards, >>> >>> Oliver Fiehn >>> >>> >>> >>> >>> >>> >>> >>> 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... >>> >>> URL http://fiehnlab.ucdavis.edu/ >>> >>> tel +1-530-754-8258 >>> >>> fax +1-530-754-9658 >>> >>> >>> >>> _____ >>> >>> From: Goodsaid, Federico [mailto:Fed...@fd...] >>> Sent: Montag, 15. Oktober 2007 08:05 >>> To: Oliver Fiehn; Susanna; msi...@li...; >>> rim...@du... >>> Cc: Sue Rhee >>> Subject: RE: minutes of the MSI teleconference Thursday, October 11, 7-9 >>> a.m. Pacific (10-12 a.m. EST) >>> >>> >>> >>> Oliver, >>> >>> >>> >>> I listened in on part of this teleconference. Why do you think there >>> continues to be hesitation in this area to commit to a systematic >>> definition >>> for data standards or to a broader set of recommendations for data >>> generation, analysis, interpretation and reporting? Please let us know how >>> we can help encourage a discussion leading to a consensus around data >>> standards in this area. >>> >>> >>> >>> 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 4524 >>> >>> Silver Spring, MD 20903-0002 >>> >>> phone: 301-796-1535 >>> >>> email: <mailto:Fed...@fd...> >>> Fed...@fd... >>> >>> >>> >>> >>> >>> _____ >>> >>> From: Oliver Fiehn [mailto:of...@uc...] >>> Sent: Thursday, October 11, 2007 3:24 PM >>> To: 'Oliver Fiehn'; 'Susanna'; msi...@li...; >>> rim...@du... >>> Cc: Goodsaid, Federico; 'Sue Rhee' >>> Subject: minutes of the MSI teleconference Thursday, October 11, 7-9 a.m. >>> Pacific (10-12 a.m. EST) >>> >>> >>> >>> Dear all, >>> >>> >>> >>> For those of you who could make the TC meeting today, thanks for your >>> input. >>> And I apologize to Susanna because we were unable to provide a toll-free >>> dial in number - as it turned out, it was toll-free, but just within the >>> U.S. >>> >>> Rima is trying to follow up for potential next meetings and see if we >>> could >>> get a provider for international toll-free dial ins. >>> >>> >>> >>> So, here are the >>> >>> >>> >>> Minutes of today's MSI TC >>> >>> >>> >>> Attendants: >>> Norman Morrison, Oliver Fiehn, Rima Kaddurah-Daouk, Roy Goodacre, Bruce >>> Kristal, Nigel Hardy, Don Robertson, Lloyd W Sumner. >>> >>> >>> >>> Teresa Fan, Mariet vd Werf, Susanna Assunta-Sansone, Basil Nikolau and >>> Jules >>> Griffin sent their apologies for being unavailable to join the TC for a >>> variety reasons. Sue Rhee from Stanford expressed interest in being >>> informed >>> on the outcome of the TC, that's why I cc' her here. >>> >>> >>> >>> Single topic of discussion was 'next steps for the MSI' >>> >>> >>> >>> * MSI documents are published freely online accessible in the >>> Metabolomics journal, thanks to Susanna and Roy for pushing that! It was >>> recognized that the content published in these documents have variable >>> degree of details of information. >>> >>> * Three options of going forward were initially put into the >>> discussion: >>> (a) efforts to persuade journals and agencies to endorse the 'minimal' >>> standards >>> (b) efforts to continue group activities towards 'best practice' documents >>> (c) efforts to draft instances of units and data exchange formats >>> originating from the 'minimal' standards >>> >>> * (a) efforts to persuade journals and agencies to endorse the >>> 'minimal' standards >>> The participants agreed that it was too early to actively enforce journals >>> to use these 'minimal' standards in their editorial guidelines. Based on >>> the >>> example of our own 'Metabolomics' journal, it was instead suggested that >>> the >>> editor and reviewers will be asked to check submissions if papers are >>> MSI-compliant 'with exceptions'. The list of such exceptions might then >>> inform us on pitfalls or where researchers actually failed to accumulate >>> data. In addition, the idea is to lead by example by submitting own papers >>> and stating these papers to be MSI-compliant. Lloyd Sumner (for Plant >>> Phys) >>> and Oliver Fiehn (for Plant J) have submitted manuscripts that detail >>> instances of MSI-compliant reports. In order to spread the idea of MSI >>> standards, it would be important that (all) contributors of the MSI >>> documents would submit their research manuscripts along with MSI-compliant >>> data sheets. The idea here would be (right now) to compile all relevant >>> MSI >>> metadata in a single document (e.g. a data table) and submit such >>> information as supplemental data in conjunction with scientific reports. >>> Otherwise, method sections would become too verbose. >>> In addition, Rima Kaddurah-Daouk will send out a letter to the >>> Metabolomics >>> Society members (which will be drafted by Oliver Fiehn) that calls for >>> community feedback based on the current MSI documents. This period of >>> feedback should extend to 6 months to gather a certain amount of >>> experience. >>> >>> * (b) efforts to continue group activities towards 'best practice' >>> documents >>> Currently, MSI groups are mostly dormant. Writing initial MSI papers >>> helped >>> fostering group activities but groups have not been active since. The idea >>> was revitalized to unify the 'biological context' documents into a single >>> 'umbrella' document that would have further details for the different >>> research areas; however, TC participants did not actively agree on that. >>> A disagreement was stated on the usefulness of working towards 'best >>> practice' documents, especially for the 'data processing' working group. >>> One >>> argument raised was that any official MSI 'best practice' document would >>> be >>> counterproductive because such an official stamp would be easily violating >>> the idea of a continuation of improving practices and methods. Instead, a >>> group of individuals might publish their view of 'current best practice' >>> in >>> order to lead by example which could be improved by other authors using >>> the >>> regular way of scientific discussion. Nevertheless, the point was raised >>> that for 'data processing' it would be really hard to distinguish between >>> 'minimal standards' and 'best practice' and that it would be MSI-compliant >>> to report a wrong way to do a certain piece of research (the same would of >>> course be true for all MSI-areas). So, in a way, right now MSI-compliant >>> would give papers or projects a touch of validation, even if the study >>> design or the way of data acquisition and processing would be very bad. >>> This discussion was consolidated in the general agreement that >>> 'lead-by-example' papers will also serve as best practice documents. One >>> of >>> such instances is a current submission to the journal Metabolomics on use >>> and misuse of PLS in statistics. >>> >>> * (c) efforts to draft instances of units and data exchange formats >>> originating from the 'minimal' standards >>> In practical terms, currently there are a variety of efforts underway to >>> accumulate data and distribute these via websites. However, none of the >>> current efforts really embrace the need of data exchange formats in order >>> to >>> standardize and compile different data sets or data sets of different >>> origins. Some cyberinfrastructure projects (e.g. NSF funded in plant >>> science) will be carried out that might yield standardized repositories, >>> e.g. for biological context data. It is unclear, if other fields of >>> research >>> (e.g. clinical, biomedical) have similar efforts, but it is clear that >>> currently, there are no efforts for (U.S.) national repositories for >>> metabolomics data although in Europe, there are consortia (e.g. Metafor) >>> that might be working into that direction. So, for now this topic is an >>> unsolved problem that would require active research and funding to go >>> forward. >>> >>> * other points >>> Before an email can be sent to the Metabolomics Soc members, it is >>> important >>> to ensure that the msi-sourceforge pages are up to date. Nigel will >>> contact >>> Susanna on that behalf to find out. The pages might need to be revisited >>> with respect to easiness of communication and use - if we want to obtain >>> feedback from members (or other researchers), there must be low-entry ways >>> to do so. A wiki attached to the sourceforge pages was discussed or >>> branching out to the Metabolomics Society pages. >>> With respect to contacts to other efforts, especially the MIBBI efforts >>> led >>> by Chris Taylor, Nigel will serve as contact point (in addition to >>> Susanna's >>> continuing efforts). It is anticipated that there potentially might be >>> significant synergies that could be gathered from such unifying >>> biology-focused reporting efforts. Susanna has acquired funding for >>> workshop(s) that will foster efforts in this direction. >>> >>> >>> >>> >>> >>> Best regards to all, >>> >>> >>> >>> 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... >>> >>> URL http://fiehnlab.ucdavis.edu/ >>> >>> tel +1-530-754-8258 >>> >>> fax +1-530-754-9658 >>> >>> >>> >> >> > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. > Still grepping through log files to find problems? Stop. > Now Search log events and configuration files using AJAX and a browser. > Download your FREE copy of Splunk now >> http://get.splunk.com/ > > > ------------------------------------------------------------------------ > > _______________________________________________ > Msi-workgroups-board mailing list > Msi...@li... > https://lists.sourceforge.net/lists/listinfo/msi-workgroups-board -- ~~~~~~~~~~~~~~~~~~~~~~~~ chr...@eb... http://mibbi.sf.net/ ~~~~~~~~~~~~~~~~~~~~~~~~ |
|
From: Sue R. <rh...@ac...> - 2007-10-16 16:34:44
|
Yes, I totally agree. Does anyone know of any moves towards an international public repository for metabolomics data? I can ask Rolf Apweiler (EBI), Jim Ostell (NCBI) and Takashi Gojobori (DDBJ) if you think this would be helpful. Sue Susanna-Assunta Sansone wrote: > Hi Oliver, > > >> The Society or the MSI is not a body .... >> Almost every participant in the MSI process does this voluntarily... >> No journal insists on (metabolomic) data sharing plans.... >> So, there is simply neither a 'push' (by money [big consortia projects], >> reputation or else) nor a 'pull' (by journals, vendors, pharmaceutical >> industries or agencies).... >> > > It is also true for microarray and proteomics, and despite this but MGED > and PSI have found reasons to go ahead. > > I reckon the main issue here is the lack of public repositories, willing > to exchange datasets, the real strenght behind MGED and PSI efforts. > > Susanna > > > > > Oliver Fiehn wrote: > >> Dear Federico, >> >> >> >> Thanks for your email. It is always very helpful to get questions that >> seem >> to be easy but are nevertheless difficult to be answered. There are >> several >> answers to your question, some more fundamental and some more practical >> ones. >> >> >> >> * I think, discussions around standards are a little bit like >> democracy: in order to have developing standards adopted, we cannot move >> very fast but always have to try to get feedback from researchers who were >> less actively involved. >> >> * The Society or the MSI is not a body that can or wants to declare >> rules and regulations. >> >> * Almost every participant in the MSI process does this voluntarily >> is >> his/her spare time. That means, our salary and our reputation is depending >> on other efforts, most of all scientific work and reporting (and for >> academic PIs, grant writing and teaching). Basically, MSI is an unfunded >> effort that just cannot gain very high priority on the agenda of most >> people >> who are involved. >> >> * Most grants we write (e.g. for NIH) have somewhere a section that >> demands we share data. However, this section is rarely critically >> reviewed, >> in comparison to the experimental design sections. The MSI was >> co-initiated >> by the NIH/NIDDK, but when the next two 'requests for applications' came >> out >> from the NIH, these had nothing to do with data sharing but focused on >> small >> biochemical networks or on translational medicine. >> >> * No journal insists on (metabolomic) data sharing plans, neither is >> this requested by reviewers of scientific publications. >> >> >> So, there is simply neither a 'push' (by money [big consortia projects], >> reputation or else) nor a 'pull' (by journals, vendors, pharmaceutical >> industries or agencies). >> >> >> In addition, there are of course also quite a few substantial scientific >> arguments. >> >> >> >> * The field is still fairly new and researchers want to explore (and >> publish) a wide variety of approaches. That means, any guideline or >> document >> that is too specific might hamper research, something we surely do not >> want >> to happen. >> >> * Researchers may simply disagree on topics, e.g. what are the >> 'required' metadata compared to 'optional' metadata. >> >> * Metabolomics as an approach lends itself to an array of different >> biological fields and studies, each of these having its own pace of >> discussions. >> >> * We lack certified reference materials. It would be beneficial if >> there were trusted resources of standard matrices (tissue, bodyfluids) >> that >> have certified contents of metabolites and that could be used to validate >> novel approaches. >> >> * There is a lack of funding for comparison of existing techniques, >> but >> agencies (and researchers) have the tendency to push for 'novel >> innovations' >> instead of solidifying and validating methods that are already >> implemented. >> Ring trials would be beneficial to prove that certain techniques are >> complementary or overlapping, or even that data can be compared across >> laboratories. >> >> * Metabolism is more flexible than many researchers (outside the >> metabolomic community) tend to believe. The sheer complexity of compounds >> found in specimen makes it very difficult to chemically identify even the >> most part of the detected signals. Hence, reporting 'quantifications of >> unknown signals' between studies in a single laboratory is scientifically >> very difficult, let alone comparisons and standardizations between >> different >> labs. >> >> * Metabolic signals cannot be 'sequenced', unlike peptides or RNA. >> Libraries (NMR or MS) either do not comprise thousands of compounds or >> technical differences (e.g. pH, solvent, instrument, other metadata) make >> it >> difficult to use spectra beyond the exact conditions under which these >> spectra were acquired. >> >> >> >> So, there we are, at least from my point of view. I truly believe we need >> metabolomic standards and databases to mature the field, and I am >> convinced, >> so do most participants of the MSI project. There are other points that >> contribute to these issues (e.g. accessibility and knowledge about >> databases, ontologies and else). However, at the current point, I tend not >> to believe that more workshops will foster or accelerate the MSI in a >> dramatic way, although of course we will continue to discuss MSI topics in >> meetings or dedicated workshops to keep the discussions going. >> >> >> >> I am not familiar enough with the FDA to make reasonable suggestions how >> you >> could help fostering and speeding up discussions. We can discuss this >> further if you call me, if you like (see number below)? >> >> >> >> >> >> With best regards, >> >> Oliver Fiehn >> >> >> >> >> >> >> >> 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... >> >> URL http://fiehnlab.ucdavis.edu/ >> >> tel +1-530-754-8258 >> >> fax +1-530-754-9658 >> >> >> >> _____ >> >> From: Goodsaid, Federico [mailto:Fed...@fd...] >> Sent: Montag, 15. Oktober 2007 08:05 >> To: Oliver Fiehn; Susanna; msi...@li...; >> rim...@du... >> Cc: Sue Rhee >> Subject: RE: minutes of the MSI teleconference Thursday, October 11, 7-9 >> a.m. Pacific (10-12 a.m. EST) >> >> >> >> Oliver, >> >> >> >> I listened in on part of this teleconference. Why do you think there >> continues to be hesitation in this area to commit to a systematic >> definition >> for data standards or to a broader set of recommendations for data >> generation, analysis, interpretation and reporting? Please let us know how >> we can help encourage a discussion leading to a consensus around data >> standards in this area. >> >> >> >> 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 4524 >> >> Silver Spring, MD 20903-0002 >> >> phone: 301-796-1535 >> >> email: <mailto:Fed...@fd...> >> Fed...@fd... >> >> >> >> >> >> _____ >> >> From: Oliver Fiehn [mailto:of...@uc...] >> Sent: Thursday, October 11, 2007 3:24 PM >> To: 'Oliver Fiehn'; 'Susanna'; msi...@li...; >> rim...@du... >> Cc: Goodsaid, Federico; 'Sue Rhee' >> Subject: minutes of the MSI teleconference Thursday, October 11, 7-9 a.m. >> Pacific (10-12 a.m. EST) >> >> >> >> Dear all, >> >> >> >> For those of you who could make the TC meeting today, thanks for your >> input. >> And I apologize to Susanna because we were unable to provide a toll-free >> dial in number - as it turned out, it was toll-free, but just within the >> U.S. >> >> Rima is trying to follow up for potential next meetings and see if we >> could >> get a provider for international toll-free dial ins. >> >> >> >> So, here are the >> >> >> >> Minutes of today's MSI TC >> >> >> >> Attendants: >> Norman Morrison, Oliver Fiehn, Rima Kaddurah-Daouk, Roy Goodacre, Bruce >> Kristal, Nigel Hardy, Don Robertson, Lloyd W Sumner. >> >> >> >> Teresa Fan, Mariet vd Werf, Susanna Assunta-Sansone, Basil Nikolau and >> Jules >> Griffin sent their apologies for being unavailable to join the TC for a >> variety reasons. Sue Rhee from Stanford expressed interest in being >> informed >> on the outcome of the TC, that's why I cc' her here. >> >> >> >> Single topic of discussion was 'next steps for the MSI' >> >> >> >> * MSI documents are published freely online accessible in the >> Metabolomics journal, thanks to Susanna and Roy for pushing that! It was >> recognized that the content published in these documents have variable >> degree of details of information. >> >> * Three options of going forward were initially put into the >> discussion: >> (a) efforts to persuade journals and agencies to endorse the 'minimal' >> standards >> (b) efforts to continue group activities towards 'best practice' documents >> (c) efforts to draft instances of units and data exchange formats >> originating from the 'minimal' standards >> >> * (a) efforts to persuade journals and agencies to endorse the >> 'minimal' standards >> The participants agreed that it was too early to actively enforce journals >> to use these 'minimal' standards in their editorial guidelines. Based on >> the >> example of our own 'Metabolomics' journal, it was instead suggested that >> the >> editor and reviewers will be asked to check submissions if papers are >> MSI-compliant 'with exceptions'. The list of such exceptions might then >> inform us on pitfalls or where researchers actually failed to accumulate >> data. In addition, the idea is to lead by example by submitting own papers >> and stating these papers to be MSI-compliant. Lloyd Sumner (for Plant >> Phys) >> and Oliver Fiehn (for Plant J) have submitted manuscripts that detail >> instances of MSI-compliant reports. In order to spread the idea of MSI >> standards, it would be important that (all) contributors of the MSI >> documents would submit their research manuscripts along with MSI-compliant >> data sheets. The idea here would be (right now) to compile all relevant >> MSI >> metadata in a single document (e.g. a data table) and submit such >> information as supplemental data in conjunction with scientific reports. >> Otherwise, method sections would become too verbose. >> In addition, Rima Kaddurah-Daouk will send out a letter to the >> Metabolomics >> Society members (which will be drafted by Oliver Fiehn) that calls for >> community feedback based on the current MSI documents. This period of >> feedback should extend to 6 months to gather a certain amount of >> experience. >> >> * (b) efforts to continue group activities towards 'best practice' >> documents >> Currently, MSI groups are mostly dormant. Writing initial MSI papers >> helped >> fostering group activities but groups have not been active since. The idea >> was revitalized to unify the 'biological context' documents into a single >> 'umbrella' document that would have further details for the different >> research areas; however, TC participants did not actively agree on that. >> A disagreement was stated on the usefulness of working towards 'best >> practice' documents, especially for the 'data processing' working group. >> One >> argument raised was that any official MSI 'best practice' document would >> be >> counterproductive because such an official stamp would be easily violating >> the idea of a continuation of improving practices and methods. Instead, a >> group of individuals might publish their view of 'current best practice' >> in >> order to lead by example which could be improved by other authors using >> the >> regular way of scientific discussion. Nevertheless, the point was raised >> that for 'data processing' it would be really hard to distinguish between >> 'minimal standards' and 'best practice' and that it would be MSI-compliant >> to report a wrong way to do a certain piece of research (the same would of >> course be true for all MSI-areas). So, in a way, right now MSI-compliant >> would give papers or projects a touch of validation, even if the study >> design or the way of data acquisition and processing would be very bad. >> This discussion was consolidated in the general agreement that >> 'lead-by-example' papers will also serve as best practice documents. One >> of >> such instances is a current submission to the journal Metabolomics on use >> and misuse of PLS in statistics. >> >> * (c) efforts to draft instances of units and data exchange formats >> originating from the 'minimal' standards >> In practical terms, currently there are a variety of efforts underway to >> accumulate data and distribute these via websites. However, none of the >> current efforts really embrace the need of data exchange formats in order >> to >> standardize and compile different data sets or data sets of different >> origins. Some cyberinfrastructure projects (e.g. NSF funded in plant >> science) will be carried out that might yield standardized repositories, >> e.g. for biological context data. It is unclear, if other fields of >> research >> (e.g. clinical, biomedical) have similar efforts, but it is clear that >> currently, there are no efforts for (U.S.) national repositories for >> metabolomics data although in Europe, there are consortia (e.g. Metafor) >> that might be working into that direction. So, for now this topic is an >> unsolved problem that would require active research and funding to go >> forward. >> >> * other points >> Before an email can be sent to the Metabolomics Soc members, it is >> important >> to ensure that the msi-sourceforge pages are up to date. Nigel will >> contact >> Susanna on that behalf to find out. The pages might need to be revisited >> with respect to easiness of communication and use - if we want to obtain >> feedback from members (or other researchers), there must be low-entry ways >> to do so. A wiki attached to the sourceforge pages was discussed or >> branching out to the Metabolomics Society pages. >> With respect to contacts to other efforts, especially the MIBBI efforts >> led >> by Chris Taylor, Nigel will serve as contact point (in addition to >> Susanna's >> continuing efforts). It is anticipated that there potentially might be >> significant synergies that could be gathered from such unifying >> biology-focused reporting efforts. Susanna has acquired funding for >> workshop(s) that will foster efforts in this direction. >> >> >> >> >> >> Best regards to all, >> >> >> >> 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... >> >> URL http://fiehnlab.ucdavis.edu/ >> >> tel +1-530-754-8258 >> >> fax +1-530-754-9658 >> >> >> > > |
|
From: Susanna-Assunta S. <sa...@eb...> - 2007-10-16 10:15:15
|
Hi Oliver, > The Society or the MSI is not a body .... > Almost every participant in the MSI process does this voluntarily... > No journal insists on (metabolomic) data sharing plans.... > So, there is simply neither a 'push' (by money [big consortia projects], > reputation or else) nor a 'pull' (by journals, vendors, pharmaceutical > industries or agencies).... It is also true for microarray and proteomics, and despite this but MGED and PSI have found reasons to go ahead. I reckon the main issue here is the lack of public repositories, willing to exchange datasets, the real strenght behind MGED and PSI efforts. Susanna Oliver Fiehn wrote: > Dear Federico, > > > > Thanks for your email. It is always very helpful to get questions that > seem > to be easy but are nevertheless difficult to be answered. There are > several > answers to your question, some more fundamental and some more practical > ones. > > > > * I think, discussions around standards are a little bit like > democracy: in order to have developing standards adopted, we cannot move > very fast but always have to try to get feedback from researchers who were > less actively involved. > > * The Society or the MSI is not a body that can or wants to declare > rules and regulations. > > * Almost every participant in the MSI process does this voluntarily > is > his/her spare time. That means, our salary and our reputation is depending > on other efforts, most of all scientific work and reporting (and for > academic PIs, grant writing and teaching). Basically, MSI is an unfunded > effort that just cannot gain very high priority on the agenda of most > people > who are involved. > > * Most grants we write (e.g. for NIH) have somewhere a section that > demands we share data. However, this section is rarely critically > reviewed, > in comparison to the experimental design sections. The MSI was > co-initiated > by the NIH/NIDDK, but when the next two 'requests for applications' came > out > from the NIH, these had nothing to do with data sharing but focused on > small > biochemical networks or on translational medicine. > > * No journal insists on (metabolomic) data sharing plans, neither is > this requested by reviewers of scientific publications. > > > So, there is simply neither a 'push' (by money [big consortia projects], > reputation or else) nor a 'pull' (by journals, vendors, pharmaceutical > industries or agencies). > > > In addition, there are of course also quite a few substantial scientific > arguments. > > > > * The field is still fairly new and researchers want to explore (and > publish) a wide variety of approaches. That means, any guideline or > document > that is too specific might hamper research, something we surely do not > want > to happen. > > * Researchers may simply disagree on topics, e.g. what are the > 'required' metadata compared to 'optional' metadata. > > * Metabolomics as an approach lends itself to an array of different > biological fields and studies, each of these having its own pace of > discussions. > > * We lack certified reference materials. It would be beneficial if > there were trusted resources of standard matrices (tissue, bodyfluids) > that > have certified contents of metabolites and that could be used to validate > novel approaches. > > * There is a lack of funding for comparison of existing techniques, > but > agencies (and researchers) have the tendency to push for 'novel > innovations' > instead of solidifying and validating methods that are already > implemented. > Ring trials would be beneficial to prove that certain techniques are > complementary or overlapping, or even that data can be compared across > laboratories. > > * Metabolism is more flexible than many researchers (outside the > metabolomic community) tend to believe. The sheer complexity of compounds > found in specimen makes it very difficult to chemically identify even the > most part of the detected signals. Hence, reporting 'quantifications of > unknown signals' between studies in a single laboratory is scientifically > very difficult, let alone comparisons and standardizations between > different > labs. > > * Metabolic signals cannot be 'sequenced', unlike peptides or RNA. > Libraries (NMR or MS) either do not comprise thousands of compounds or > technical differences (e.g. pH, solvent, instrument, other metadata) make > it > difficult to use spectra beyond the exact conditions under which these > spectra were acquired. > > > > So, there we are, at least from my point of view. I truly believe we need > metabolomic standards and databases to mature the field, and I am > convinced, > so do most participants of the MSI project. There are other points that > contribute to these issues (e.g. accessibility and knowledge about > databases, ontologies and else). However, at the current point, I tend not > to believe that more workshops will foster or accelerate the MSI in a > dramatic way, although of course we will continue to discuss MSI topics in > meetings or dedicated workshops to keep the discussions going. > > > > I am not familiar enough with the FDA to make reasonable suggestions how > you > could help fostering and speeding up discussions. We can discuss this > further if you call me, if you like (see number below)? > > > > > > With best regards, > > Oliver Fiehn > > > > > > > > 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... > > URL http://fiehnlab.ucdavis.edu/ > > tel +1-530-754-8258 > > fax +1-530-754-9658 > > > > _____ > > From: Goodsaid, Federico [mailto:Fed...@fd...] > Sent: Montag, 15. Oktober 2007 08:05 > To: Oliver Fiehn; Susanna; msi...@li...; > rim...@du... > Cc: Sue Rhee > Subject: RE: minutes of the MSI teleconference Thursday, October 11, 7-9 > a.m. Pacific (10-12 a.m. EST) > > > > Oliver, > > > > I listened in on part of this teleconference. Why do you think there > continues to be hesitation in this area to commit to a systematic > definition > for data standards or to a broader set of recommendations for data > generation, analysis, interpretation and reporting? Please let us know how > we can help encourage a discussion leading to a consensus around data > standards in this area. > > > > 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 4524 > > Silver Spring, MD 20903-0002 > > phone: 301-796-1535 > > email: <mailto:Fed...@fd...> > Fed...@fd... > > > > > > _____ > > From: Oliver Fiehn [mailto:of...@uc...] > Sent: Thursday, October 11, 2007 3:24 PM > To: 'Oliver Fiehn'; 'Susanna'; msi...@li...; > rim...@du... > Cc: Goodsaid, Federico; 'Sue Rhee' > Subject: minutes of the MSI teleconference Thursday, October 11, 7-9 a.m. > Pacific (10-12 a.m. EST) > > > > Dear all, > > > > For those of you who could make the TC meeting today, thanks for your > input. > And I apologize to Susanna because we were unable to provide a toll-free > dial in number - as it turned out, it was toll-free, but just within the > U.S. > > Rima is trying to follow up for potential next meetings and see if we > could > get a provider for international toll-free dial ins. > > > > So, here are the > > > > Minutes of today's MSI TC > > > > Attendants: > Norman Morrison, Oliver Fiehn, Rima Kaddurah-Daouk, Roy Goodacre, Bruce > Kristal, Nigel Hardy, Don Robertson, Lloyd W Sumner. > > > > Teresa Fan, Mariet vd Werf, Susanna Assunta-Sansone, Basil Nikolau and > Jules > Griffin sent their apologies for being unavailable to join the TC for a > variety reasons. Sue Rhee from Stanford expressed interest in being > informed > on the outcome of the TC, that's why I cc' her here. > > > > Single topic of discussion was 'next steps for the MSI' > > > > * MSI documents are published freely online accessible in the > Metabolomics journal, thanks to Susanna and Roy for pushing that! It was > recognized that the content published in these documents have variable > degree of details of information. > > * Three options of going forward were initially put into the > discussion: > (a) efforts to persuade journals and agencies to endorse the 'minimal' > standards > (b) efforts to continue group activities towards 'best practice' documents > (c) efforts to draft instances of units and data exchange formats > originating from the 'minimal' standards > > * (a) efforts to persuade journals and agencies to endorse the > 'minimal' standards > The participants agreed that it was too early to actively enforce journals > to use these 'minimal' standards in their editorial guidelines. Based on > the > example of our own 'Metabolomics' journal, it was instead suggested that > the > editor and reviewers will be asked to check submissions if papers are > MSI-compliant 'with exceptions'. The list of such exceptions might then > inform us on pitfalls or where researchers actually failed to accumulate > data. In addition, the idea is to lead by example by submitting own papers > and stating these papers to be MSI-compliant. Lloyd Sumner (for Plant > Phys) > and Oliver Fiehn (for Plant J) have submitted manuscripts that detail > instances of MSI-compliant reports. In order to spread the idea of MSI > standards, it would be important that (all) contributors of the MSI > documents would submit their research manuscripts along with MSI-compliant > data sheets. The idea here would be (right now) to compile all relevant > MSI > metadata in a single document (e.g. a data table) and submit such > information as supplemental data in conjunction with scientific reports. > Otherwise, method sections would become too verbose. > In addition, Rima Kaddurah-Daouk will send out a letter to the > Metabolomics > Society members (which will be drafted by Oliver Fiehn) that calls for > community feedback based on the current MSI documents. This period of > feedback should extend to 6 months to gather a certain amount of > experience. > > * (b) efforts to continue group activities towards 'best practice' > documents > Currently, MSI groups are mostly dormant. Writing initial MSI papers > helped > fostering group activities but groups have not been active since. The idea > was revitalized to unify the 'biological context' documents into a single > 'umbrella' document that would have further details for the different > research areas; however, TC participants did not actively agree on that. > A disagreement was stated on the usefulness of working towards 'best > practice' documents, especially for the 'data processing' working group. > One > argument raised was that any official MSI 'best practice' document would > be > counterproductive because such an official stamp would be easily violating > the idea of a continuation of improving practices and methods. Instead, a > group of individuals might publish their view of 'current best practice' > in > order to lead by example which could be improved by other authors using > the > regular way of scientific discussion. Nevertheless, the point was raised > that for 'data processing' it would be really hard to distinguish between > 'minimal standards' and 'best practice' and that it would be MSI-compliant > to report a wrong way to do a certain piece of research (the same would of > course be true for all MSI-areas). So, in a way, right now MSI-compliant > would give papers or projects a touch of validation, even if the study > design or the way of data acquisition and processing would be very bad. > This discussion was consolidated in the general agreement that > 'lead-by-example' papers will also serve as best practice documents. One > of > such instances is a current submission to the journal Metabolomics on use > and misuse of PLS in statistics. > > * (c) efforts to draft instances of units and data exchange formats > originating from the 'minimal' standards > In practical terms, currently there are a variety of efforts underway to > accumulate data and distribute these via websites. However, none of the > current efforts really embrace the need of data exchange formats in order > to > standardize and compile different data sets or data sets of different > origins. Some cyberinfrastructure projects (e.g. NSF funded in plant > science) will be carried out that might yield standardized repositories, > e.g. for biological context data. It is unclear, if other fields of > research > (e.g. clinical, biomedical) have similar efforts, but it is clear that > currently, there are no efforts for (U.S.) national repositories for > metabolomics data although in Europe, there are consortia (e.g. Metafor) > that might be working into that direction. So, for now this topic is an > unsolved problem that would require active research and funding to go > forward. > > * other points > Before an email can be sent to the Metabolomics Soc members, it is > important > to ensure that the msi-sourceforge pages are up to date. Nigel will > contact > Susanna on that behalf to find out. The pages might need to be revisited > with respect to easiness of communication and use - if we want to obtain > feedback from members (or other researchers), there must be low-entry ways > to do so. A wiki attached to the sourceforge pages was discussed or > branching out to the Metabolomics Society pages. > With respect to contacts to other efforts, especially the MIBBI efforts > led > by Chris Taylor, Nigel will serve as contact point (in addition to > Susanna's > continuing efforts). It is anticipated that there potentially might be > significant synergies that could be gathered from such unifying > biology-focused reporting efforts. Susanna has acquired funding for > workshop(s) that will foster efforts in this direction. > > > > > > Best regards to all, > > > > 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... > > URL http://fiehnlab.ucdavis.edu/ > > tel +1-530-754-8258 > > fax +1-530-754-9658 > > |
|
From: Sue R. <rh...@ac...> - 2007-10-12 17:03:06
|
Hi: If you want the letter and the MSI doc that you want comments from the plant community, I can have them on the breaking news on TAIR, and ask MaizeGDB and Gramene to do the same. Thanks, Sue Chris Taylor wrote: > Hi all. > > My sincere apologies for missing the call yesterday -- like an idiot I > messed up the time by an hour and was dutifully on the phone at 4pm uk > time (instead of 3). > > Anyway some comments on the minutes, for what it is worth: > >> In addition, Rima Kaddurah-Daouk will send out a letter to the >> Metabolomics Society members (which will be drafted by Oliver >> Fiehn) that calls for community feedback based on the current MSI >> documents. This period of feedback should extend to 6 months to >> gather a certain amount of experience. > > It is crucial that this be promoted more widely than just the society > (whether any extra responses are generated from that or not) if the > guidelines are intended to apply to that wider community (think about > the general science journals -- for example Nature Group would not > have taken the 'word' of PSI/HUPO that we got things right and even > after running their own consultation exercise they will not implement > immediately -- not till there are good tools). > > So at the very least we need another letter to as many big journals as > will take it promoting again the location of the documents and the > feedback mechanism. Probably there should be prior agreement from each > journal that takes such a letter that they will start to encourage > voluntary compliance for a probationary period (no-one will enforce > straight away); a sweetener Could be to have submitters who provide > compliant data sets benefit from a form of 'fast tracking' to print. > > Crucially, we need clear mechanisms in place though (in the form of a > formal _process_ document) if these standards are to thrive -- without > a visibly-responsive channel for comment and a robust, explicit > process for revision I don't think they'll do as well as they could > (i.e. to succeed in journals outside the sphere of influence of senior > MSI participants), as they will be perceived as a static entity > generated by a subset of the community they apply to, with no way for > the balance of that community to 'come on board'. > > Incdentally, NBT now expect that the MIAPE authors who are > experimentalists will provide MIAPE compliant material :) I'm not > sure they all knew that when they signed on but it is now the case -- > I think that reinforces your commendable idea that MSI participants > should lead by example, i.e. from the front. > >> /__/ >> * /_(b) efforts to continue group activities towards ‘best practice’ >> documents_/ >> Currently, MSI groups are mostly dormant. Writing initial MSI >> papers helped fostering group activities but groups have not been >> active since. The idea was revitalized to unify the ‘biological >> context’ documents into a single ‘umbrella’ document that would >> have further details for the different research areas; however, TC >> participants did not actively agree on that. > > A reasonable course of action here is to pursue that goal through > MIBBI, thereby involving other relevant groups such as the genomic > sequencing people and others concerned with the description of the > origin of a sample. This is also an issue further along the workflow > as it were -- chemical analysis, PSI and a couple of other groups need > to chat for one; then there's the likely leading role in the stats > activity within MIBBI to be taken by the data analysis group of MSI. > Again we desperately need clear documented processes so that come the > time that integrated reporting standards are available from MIBBI, the > different contributing communities can credibly sign off on them. > >> A disagreement was stated on the usefulness of working towards >> ‘best practice’ documents, especially for the ‘data processing’ >> working group. One argument raised was that any official MSI ‘best >> practice’ document would be counterproductive because such an >> official stamp would be easily violating the idea of a >> continuation of improving practices and methods. Instead, a group >> of individuals might publish their view of ‘current best practice’ >> in order to lead by example which could be improved by other >> authors using the regular way of scientific discussion. > > This is a minefield and I would counsel extreme caution. I know > everyone knows that it's a potentially controversial area, but my > specific point is that to link the relatively uncontroversial (by > comparison) activity of guidelines/formats/CV development to arguing > about best practice threatens to bog down our current products in the > unending scrap about whose favourite method is best (whatever the > objective merits of each). These things are best kept completely > separate. If there is a real will to do it then perhaps the approach > taken by HUPO, of instituting an entirely separate body to do it, > would be best. > >> Nevertheless, the point was raised that for ‘data processing’ it >> would be really hard to distinguish between ‘minimal standards’ >> and ‘best practice’ and that it would be MSI-compliant to report a >> wrong way to do a certain piece of research (the same would of >> course be true for all MSI-areas). So, in a way, right now >> MSI-compliant would give papers or projects a touch of validation, >> even if the study design or the way of data acquisition and >> processing would be very bad. > > Such quality judgements are (even where most think it clear cut) a > nightmare for all sorts of reasons and even for the DA group (as we > discussed on Boston) this is not a good idea. It is _always_ possible > to provide guidance on how to report _without_ straying into value > judgements. Really such judgements are best made by referees, guided > by journal policy (reference Molecular and Cellular Proteomics' > approach to this wrt mass spectrometry -- they are very clear about > their view of certain methods). If the wider Society wants to have an > input to that and try to help build consensus amongst journals (itself > an almost impossible goal anyway tbh) then fine, but I implore you, > keep it separate from the other standards stuff. We don't need to > argue about the pipes _and_ what should flow through them at the same > time. > >> This discussion was consolidated in the general agreement that >> ‘lead-by-example’ papers will also serve as best practice >> documents. One of such instances is a current submission to the >> journal Metabolomics on use and misuse of PLS in statistics. > > This is a good approach, because the leverage comes through the > journal and the community, rather than an 'authority'; really though > this is just a recasting of how things happen anyway no? > >> * /_(c) efforts to draft instances of units and data exchange >> formats originating from the ‘minimal’ standards_// >> /In practical terms, currently there are a variety of efforts >> underway to accumulate data and distribute these via websites. >> However, none of the current efforts really embrace the need of >> data exchange formats in order to standardize and compile >> different data sets or data sets of different origins. Some >> cyberinfrastructure projects (e.g. NSF funded in plant science) >> will be carried out that might yield standardized repositories, >> e.g. for biological context data. It is unclear, if other fields >> of research (e.g. clinical, biomedical) have similar efforts, but >> it is clear that currently, there are no efforts for (U.S.) >> national repositories for metabolomics data although in Europe, >> there are consortia (e.g. Metafor) that might be working into that >> direction. So, for now this topic is an unsolved problem that >> would require active research and funding to go forward. > > Well, there is some stuff coming; funding is always tricky but we're > nearly there at EBI for one (probably two years maximum to a working > three-omics system). > > A different approach is to build something that is just > 'FuGE-friendly' (FuGE was in NBT this month btw) like CPAS -- that way > the domain specificity is sacrificed but nothing is lost per se. In > the interim such an approach can fairly straightforwardly provide the > repository needed, while we wait for more sophisticated resources; > that said I'm not aware of many doing that at the moment apart from > the Fred Hutch (CPAS) and a couple of universities in the UK (not for > general use though). There is a strong argument that if the job is > done unimpeachably with the MI documents and they achieve decent > market penetration then you create a market for databases and tools > from both the public and private sectors and thus (with a little > encouragement) tools and DBs will 'appear'. Honest. > >> * /_other points >> _/Before an email can be sent to the Metabolomics Soc members, it >> is important to ensure that the *msi-sourceforge* pages are up to >> date. Nigel will contact Susanna on that behalf to find out. The >> pages might need to be revisited with respect to easiness of >> communication and use – if we want to obtain feedback from members >> (or other researchers), there must be low-entry ways to do so. A >> wiki attached to the sourceforge pages was discussed or branching >> out to the Metabolomics Society pages. >> With respect to contacts to other efforts, especially the *MIBBI* >> efforts led by Chris Taylor, Nigel will serve as contact point (in >> addition to Susanna’s continuing efforts). It is anticipated that >> there potentially might be significant synergies that could be >> gathered from such unifying biology-focused reporting efforts. >> Susanna has acquired funding for workshop(s) that will foster >> efforts in this direction. // > > Great to see that -- thanks. I'll of course have my brain engaged > though and will be able to make future calls myself to represent > MIBBI. I do think there's more to do for the MI groups though than > ensure that the email address(es) work okay and such -- we need stated > (in documents) mechanisms and structures -- we have to be a grown up > body now in the manner of any of the large standards bodies. > Confidence will be inspired in others by our having a visible process > that works and that we cannot lightly alter. If there is even the > chance that we could arbitrarily alter the 'release' version of these > things, confidence (especially in commercial settings) will evaporate > quicker than liquid helium at RTP. > > Sorry for the length... > > Cheers, Chris. > > ~~~~~~~~~~~~~~~~~~~~~~~~ > chr...@eb... > http://mibbi.sf.net/ > ~~~~~~~~~~~~~~~~~~~~~~~~ |
|
From: Chris T. <chr...@eb...> - 2007-10-12 10:17:56
|
Hi all. My sincere apologies for missing the call yesterday -- like an idiot I messed up the time by an hour and was dutifully on the phone at 4pm uk time (instead of 3). Anyway some comments on the minutes, for what it is worth: > In addition, Rima Kaddurah-Daouk will send out a letter to the > Metabolomics Society members (which will be drafted by Oliver > Fiehn) that calls for community feedback based on the current MSI > documents. This period of feedback should extend to 6 months to > gather a certain amount of experience. It is crucial that this be promoted more widely than just the society (whether any extra responses are generated from that or not) if the guidelines are intended to apply to that wider community (think about the general science journals -- for example Nature Group would not have taken the 'word' of PSI/HUPO that we got things right and even after running their own consultation exercise they will not implement immediately -- not till there are good tools). So at the very least we need another letter to as many big journals as will take it promoting again the location of the documents and the feedback mechanism. Probably there should be prior agreement from each journal that takes such a letter that they will start to encourage voluntary compliance for a probationary period (no-one will enforce straight away); a sweetener Could be to have submitters who provide compliant data sets benefit from a form of 'fast tracking' to print. Crucially, we need clear mechanisms in place though (in the form of a formal _process_ document) if these standards are to thrive -- without a visibly-responsive channel for comment and a robust, explicit process for revision I don't think they'll do as well as they could (i.e. to succeed in journals outside the sphere of influence of senior MSI participants), as they will be perceived as a static entity generated by a subset of the community they apply to, with no way for the balance of that community to 'come on board'. Incdentally, NBT now expect that the MIAPE authors who are experimentalists will provide MIAPE compliant material :) I'm not sure they all knew that when they signed on but it is now the case -- I think that reinforces your commendable idea that MSI participants should lead by example, i.e. from the front. > /__/ > * /_(b) efforts to continue group activities towards ‘best practice’ > documents_/ > Currently, MSI groups are mostly dormant. Writing initial MSI > papers helped fostering group activities but groups have not been > active since. The idea was revitalized to unify the ‘biological > context’ documents into a single ‘umbrella’ document that would > have further details for the different research areas; however, TC > participants did not actively agree on that. A reasonable course of action here is to pursue that goal through MIBBI, thereby involving other relevant groups such as the genomic sequencing people and others concerned with the description of the origin of a sample. This is also an issue further along the workflow as it were -- chemical analysis, PSI and a couple of other groups need to chat for one; then there's the likely leading role in the stats activity within MIBBI to be taken by the data analysis group of MSI. Again we desperately need clear documented processes so that come the time that integrated reporting standards are available from MIBBI, the different contributing communities can credibly sign off on them. > A disagreement was stated on the usefulness of working towards > ‘best practice’ documents, especially for the ‘data processing’ > working group. One argument raised was that any official MSI ‘best > practice’ document would be counterproductive because such an > official stamp would be easily violating the idea of a > continuation of improving practices and methods. Instead, a group > of individuals might publish their view of ‘current best practice’ > in order to lead by example which could be improved by other > authors using the regular way of scientific discussion. This is a minefield and I would counsel extreme caution. I know everyone knows that it's a potentially controversial area, but my specific point is that to link the relatively uncontroversial (by comparison) activity of guidelines/formats/CV development to arguing about best practice threatens to bog down our current products in the unending scrap about whose favourite method is best (whatever the objective merits of each). These things are best kept completely separate. If there is a real will to do it then perhaps the approach taken by HUPO, of instituting an entirely separate body to do it, would be best. > Nevertheless, the point was raised that for ‘data processing’ it > would be really hard to distinguish between ‘minimal standards’ > and ‘best practice’ and that it would be MSI-compliant to report a > wrong way to do a certain piece of research (the same would of > course be true for all MSI-areas). So, in a way, right now > MSI-compliant would give papers or projects a touch of validation, > even if the study design or the way of data acquisition and > processing would be very bad. Such quality judgements are (even where most think it clear cut) a nightmare for all sorts of reasons and even for the DA group (as we discussed on Boston) this is not a good idea. It is _always_ possible to provide guidance on how to report _without_ straying into value judgements. Really such judgements are best made by referees, guided by journal policy (reference Molecular and Cellular Proteomics' approach to this wrt mass spectrometry -- they are very clear about their view of certain methods). If the wider Society wants to have an input to that and try to help build consensus amongst journals (itself an almost impossible goal anyway tbh) then fine, but I implore you, keep it separate from the other standards stuff. We don't need to argue about the pipes _and_ what should flow through them at the same time. > This discussion was consolidated in the general agreement that > ‘lead-by-example’ papers will also serve as best practice > documents. One of such instances is a current submission to the > journal Metabolomics on use and misuse of PLS in statistics. This is a good approach, because the leverage comes through the journal and the community, rather than an 'authority'; really though this is just a recasting of how things happen anyway no? > * /_(c) efforts to draft instances of units and data exchange > formats originating from the ‘minimal’ standards_// > /In practical terms, currently there are a variety of efforts > underway to accumulate data and distribute these via websites. > However, none of the current efforts really embrace the need of > data exchange formats in order to standardize and compile > different data sets or data sets of different origins. Some > cyberinfrastructure projects (e.g. NSF funded in plant science) > will be carried out that might yield standardized repositories, > e.g. for biological context data. It is unclear, if other fields > of research (e.g. clinical, biomedical) have similar efforts, but > it is clear that currently, there are no efforts for (U.S.) > national repositories for metabolomics data although in Europe, > there are consortia (e.g. Metafor) that might be working into that > direction. So, for now this topic is an unsolved problem that > would require active research and funding to go forward. Well, there is some stuff coming; funding is always tricky but we're nearly there at EBI for one (probably two years maximum to a working three-omics system). A different approach is to build something that is just 'FuGE-friendly' (FuGE was in NBT this month btw) like CPAS -- that way the domain specificity is sacrificed but nothing is lost per se. In the interim such an approach can fairly straightforwardly provide the repository needed, while we wait for more sophisticated resources; that said I'm not aware of many doing that at the moment apart from the Fred Hutch (CPAS) and a couple of universities in the UK (not for general use though). There is a strong argument that if the job is done unimpeachably with the MI documents and they achieve decent market penetration then you create a market for databases and tools from both the public and private sectors and thus (with a little encouragement) tools and DBs will 'appear'. Honest. > * /_other points > _/Before an email can be sent to the Metabolomics Soc members, it > is important to ensure that the *msi-sourceforge* pages are up to > date. Nigel will contact Susanna on that behalf to find out. The > pages might need to be revisited with respect to easiness of > communication and use – if we want to obtain feedback from members > (or other researchers), there must be low-entry ways to do so. A > wiki attached to the sourceforge pages was discussed or branching > out to the Metabolomics Society pages. > With respect to contacts to other efforts, especially the *MIBBI* > efforts led by Chris Taylor, Nigel will serve as contact point (in > addition to Susanna’s continuing efforts). It is anticipated that > there potentially might be significant synergies that could be > gathered from such unifying biology-focused reporting efforts. > Susanna has acquired funding for workshop(s) that will foster > efforts in this direction. // Great to see that -- thanks. I'll of course have my brain engaged though and will be able to make future calls myself to represent MIBBI. I do think there's more to do for the MI groups though than ensure that the email address(es) work okay and such -- we need stated (in documents) mechanisms and structures -- we have to be a grown up body now in the manner of any of the large standards bodies. Confidence will be inspired in others by our having a visible process that works and that we cannot lightly alter. If there is even the chance that we could arbitrarily alter the 'release' version of these things, confidence (especially in commercial settings) will evaporate quicker than liquid helium at RTP. Sorry for the length... Cheers, Chris. ~~~~~~~~~~~~~~~~~~~~~~~~ chr...@eb... http://mibbi.sf.net/ ~~~~~~~~~~~~~~~~~~~~~~~~ |
|
From: Oliver F. <of...@uc...> - 2007-10-11 19:23:48
|
Dear all, For those of you who could make the TC meeting today, thanks for your input. And I apologize to Susanna because we were unable to provide a toll-free dial in number - as it turned out, it was toll-free, but just within the U.S. Rima is trying to follow up for potential next meetings and see if we could get a provider for international toll-free dial ins. So, here are the Minutes of today's MSI TC Attendants: Norman Morrison, Oliver Fiehn, Rima Kaddurah-Daouk, Roy Goodacre, Bruce Kristal, Nigel Hardy, Don Robertson, Lloyd W Sumner. Teresa Fan, Mariet vd Werf, Susanna Assunta-Sansone, Basil Nikolau and Jules Griffin sent their apologies for being unavailable to join the TC for a variety reasons. Sue Rhee from Stanford expressed interest in being informed on the outcome of the TC, that's why I cc' her here. Single topic of discussion was 'next steps for the MSI' * MSI documents are published freely online accessible in the Metabolomics journal, thanks to Susanna and Roy for pushing that! It was recognized that the content published in these documents have variable degree of details of information. * Three options of going forward were initially put into the discussion: (a) efforts to persuade journals and agencies to endorse the 'minimal' standards (b) efforts to continue group activities towards 'best practice' documents (c) efforts to draft instances of units and data exchange formats originating from the 'minimal' standards * (a) efforts to persuade journals and agencies to endorse the 'minimal' standards The participants agreed that it was too early to actively enforce journals to use these 'minimal' standards in their editorial guidelines. Based on the example of our own 'Metabolomics' journal, it was instead suggested that the editor and reviewers will be asked to check submissions if papers are MSI-compliant 'with exceptions'. The list of such exceptions might then inform us on pitfalls or where researchers actually failed to accumulate data. In addition, the idea is to lead by example by submitting own papers and stating these papers to be MSI-compliant. Lloyd Sumner (for Plant Phys) and Oliver Fiehn (for Plant J) have submitted manuscripts that detail instances of MSI-compliant reports. In order to spread the idea of MSI standards, it would be important that (all) contributors of the MSI documents would submit their research manuscripts along with MSI-compliant data sheets. The idea here would be (right now) to compile all relevant MSI metadata in a single document (e.g. a data table) and submit such information as supplemental data in conjunction with scientific reports. Otherwise, method sections would become too verbose. In addition, Rima Kaddurah-Daouk will send out a letter to the Metabolomics Society members (which will be drafted by Oliver Fiehn) that calls for community feedback based on the current MSI documents. This period of feedback should extend to 6 months to gather a certain amount of experience. * (b) efforts to continue group activities towards 'best practice' documents Currently, MSI groups are mostly dormant. Writing initial MSI papers helped fostering group activities but groups have not been active since. The idea was revitalized to unify the 'biological context' documents into a single 'umbrella' document that would have further details for the different research areas; however, TC participants did not actively agree on that. A disagreement was stated on the usefulness of working towards 'best practice' documents, especially for the 'data processing' working group. One argument raised was that any official MSI 'best practice' document would be counterproductive because such an official stamp would be easily violating the idea of a continuation of improving practices and methods. Instead, a group of individuals might publish their view of 'current best practice' in order to lead by example which could be improved by other authors using the regular way of scientific discussion. Nevertheless, the point was raised that for 'data processing' it would be really hard to distinguish between 'minimal standards' and 'best practice' and that it would be MSI-compliant to report a wrong way to do a certain piece of research (the same would of course be true for all MSI-areas). So, in a way, right now MSI-compliant would give papers or projects a touch of validation, even if the study design or the way of data acquisition and processing would be very bad. This discussion was consolidated in the general agreement that 'lead-by-example' papers will also serve as best practice documents. One of such instances is a current submission to the journal Metabolomics on use and misuse of PLS in statistics. * (c) efforts to draft instances of units and data exchange formats originating from the 'minimal' standards In practical terms, currently there are a variety of efforts underway to accumulate data and distribute these via websites. However, none of the current efforts really embrace the need of data exchange formats in order to standardize and compile different data sets or data sets of different origins. Some cyberinfrastructure projects (e.g. NSF funded in plant science) will be carried out that might yield standardized repositories, e.g. for biological context data. It is unclear, if other fields of research (e.g. clinical, biomedical) have similar efforts, but it is clear that currently, there are no efforts for (U.S.) national repositories for metabolomics data although in Europe, there are consortia (e.g. Metafor) that might be working into that direction. So, for now this topic is an unsolved problem that would require active research and funding to go forward. * other points Before an email can be sent to the Metabolomics Soc members, it is important to ensure that the msi-sourceforge pages are up to date. Nigel will contact Susanna on that behalf to find out. The pages might need to be revisited with respect to easiness of communication and use - if we want to obtain feedback from members (or other researchers), there must be low-entry ways to do so. A wiki attached to the sourceforge pages was discussed or branching out to the Metabolomics Society pages. With respect to contacts to other efforts, especially the MIBBI efforts led by Chris Taylor, Nigel will serve as contact point (in addition to Susanna's continuing efforts). It is anticipated that there potentially might be significant synergies that could be gathered from such unifying biology-focused reporting efforts. Susanna has acquired funding for workshop(s) that will foster efforts in this direction. Best regards to all, 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... URL http://fiehnlab.ucdavis.edu/ tel +1-530-754-8258 fax +1-530-754-9658 |
|
From: <t....@in...> - 2007-10-11 15:53:05
|
Hi Oliver=2C I=27m in Taiwan for a meeting at the moment and won=27t be able to join = in=2E Hope to learn about the discussion later=2E Cheeers=2C Teresa ----- Original Message ----- From=3A Oliver Fiehn =3Cofiehn=40ucdavis=2Eedu=3E Date=3A Wednesday=2C October 10=2C 2007 12=3A01 Subject=3A Re=3A =5BMsi-workgroups-board=5D MSI teleconference Thursday=2C= October 11=2C 7-9 a=2Em=2E Pacific (10-12 a=2Em=2E EST) To=3A rima=2Ekaddurahdaouk=40duke=2Eedu=2C =27Susanna=27 =3Csansone=40eb= i=2Eac=2Euk=3E=2C t=2Efan=40insightbb=2Ecom=2C msi-workgroups-board=40li= sts=2Esourceforge=2Enet=2C =27Oliver Fiehn=27 =3Cofiehn=40ucdavis=2Eedu=3E= Cc=3A Federico=27 =27Goodsaid =3CFederico=2EGoodsaid=40fda=2Ehhs=2Egov=3E= =3E Dear all=2C =3E = =3E =A0 =3E = =3E Below please find the contact information for tomorrow=27s telephone= =3E conference on progress of the Metabolomics Standards Initiative=2E =3E = =3E =A0 =3E = =3E I am looking forward to the TC=2C =3E = =3E Best regards=2C =3E = =3E Oliver Fiehn =3E = =3E =A0 =3E = =3E Top of Form =3E = =3E =A0 =3E = =3E = =3E =A0The following conference call has been reserved=3A = =3E = =3E = =3E = =3E = =3E = =3E = =3E Date=3A = =3E = =3E Thursday=2C October 11=2C 2007 = =3E = =3E = =3E Time=3A = =3E = =3E 10=3A00 AM Eastern = =3E = =3E = =3E =A0 = =3E = =3E 9=3A00 AM Central=2C 8=3A00 AM Mountain=2C 7=3A00 AM Pacific = =3E = =3E = =3E Duration=3A = =3E = =3E 2 Hours = =3E = =3E = =3E Participants=3A = =3E = =3E 15 = =3E = =3E = =3E Title=3A = =3E = =3E MSI = =3E = =3E = =3E Options=3A = =3E = =3E Start recording call using control pad =3E = =3E = =3E = =3E = =3E = =3E = =3E = =3E =A0To join this conference=3A = =3E = =3E = =3E = =3E = =3E For quick access=2C go to=A0 = =3E =3Chttps=3A//www=2Espiderphone=2Ecom/63704111=3Ehttps=3A//www=2Espid= erphone=2Ecom/63704111 =3E (This link will help connect both your browser and telephone to = =3E the call) =3E = =3E OR dial 1 (888) 550-5602 or +1 212-812-2800 and enter 6370 4111 =3E = =3E You may want to copy this page into your email invitations=2E = =3E =A0 =3E =A0=A0=A0=A0=A0 = =3E =3Cjavascript=3Adocument=2EEmail=2Esubmit()=3B=3E Email others an = =3E invitation to =3E this conference = =3E =A0=A0=A0=A0=A0 = =3E =3Cjavascript=3Adocument=2EShare=2Esubmit()=3B=3E Share files with t= his = =3E conference =3E = =3E Bottom of Form =3E = =3E =A0 =3E = =3E Top of Form =3E = =3E = =3E = =3E Bottom of Form =3E = =3E =A0 =3E = =3E =A0 =3E = =3E Oliver Fiehn=2C Assoc=2E Prof=2E MCB =3E = =3E - Metabolomics - =3E = =3E UC Davis Genome Center =3E = =3E GBSF Building room 1315 = =3E = =3E 451 East Health Sciences Drive =3E = =3E Davis (CA) 95616-8816 =3E = =3E =A0 =3E = =3E email=A0=A0=A0 ofiehn=40ucdavis=2Eedu =3E = =3E URL=A0=A0=A0=A0 http=3A//fiehnlab=2Eucdavis=2Eedu/ =3E = =3E tel=A0=A0=A0=A0=A0=A0=A0=A0 +1-530-754-8258 =3E = =3E fax=A0=A0=A0=A0=A0=A0=A0 +1-530-754-9658 =3E = =3E |
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From:
<mar...@tn...> - 2007-10-11 12:05:28
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Dear=20Oliver, =20 I=20am=20sorry=20that=20also=20I=20am=20not=20able=20to=20attent=20this=20= telecon,=20as=20I=20have=20a=20meeting=20at=20the=20same=20time=20that=20I= =20have=20to=20attent.=20I=20hope=20to=20join=20in=20to=20later=20conversa= tions. =20 Kind=20regards, Mari=EBt =20 =20 =20 ________________________________ From:=20m...@li...=20[mailto:msi-w= ork...@li...]=20On=20Behalf=20Of=20Oliver= =20Fiehn Sent:=2010=20October=202007=2018:01 To:=20'Oliver=20Fiehn';=20'Susanna';=20m...@li...= rge.net;=20r...@du... Cc:=20'Goodsaid,=20Federico' Subject:=20Re:=20[Msi-workgroups-board]=20MSI=20teleconference=20Thursday,= =20October=2011,7-9=20a.m.=20Pacific=20(10-12=20a.m.=20EST) =20 Dear=20all, =20 Below=20please=20find=20the=20contact=20information=20for=20tomorrow's=20t= elephone=20conference=20on=20progress=20of=20the=20Metabolomics=20Standard= s=20Initiative. =20 I=20am=20looking=20forward=20to=20the=20TC, Best=20regards, Oliver=20Fiehn =20 Top=20of=20Form =20 =20The=20following=20conference=20call=20has=20been=20reserved:=20 =20 Date:=20 Thursday,=20October=2011,=202007=20 Time:=20 10:00=20AM=20Eastern=20 =20=20 9:00=20AM=20Central,=208:00=20AM=20Mountain,=207:00=20AM=20Pacific=20 Duration:=20 2=20Hours=20 Participants:=20 15=20 Title:=20 MSI=20 Options:=20 Start=20recording=20call=20using=20control=20pad =20To=20join=20this=20conference:=20 For=20quick=20access,=20go=20to=20https://www.spiderphone.com/63704111=20<= https://www.spiderphone.com/63704111>=20 (This=20link=20will=20help=20connect=20both=20your=20browser=20and=20telep= hone=20to=20the=20call) OR=20dial=201=20(888)=20550-5602=20or=20+1=20212-812-2800=20and=20enter=20= 6370=204111 You=20may=20want=20to=20copy=20this=20page=20into=20your=20email=20invitat= ions.=20 =20 =20=20=20=20=20Email=20others=20an=20invitation=20to=20this=20conference=20= <javascript:document.Email.submit();>=20 =20=20=20=20=20Share=20files=20with=20this=20conference=20<javascript:docu= ment.Share.submit();>=20 Bottom=20of=20Form =20 Top=20of=20Form =20=20 =20=20 Bottom=20of=20Form =20 =20 Oliver=20Fiehn,=20Assoc.=20Prof.=20MCB -=20Metabolomics=20- UC=20Davis=20Genome=20Center GBSF=20Building=20room=201315=20 451=20East=20Health=20Sciences=20Drive Davis=20(CA)=2095616-8816 =20 ema...@uc... URL=20=20=20=20=20http://fiehnlab.ucdavis.edu/ tel=20=20=20=20=20=20=20=20=20+1-530-754-8258 fax=20=20=20=20=20=20=20=20+1-530-754-9658 This=20e-mail=20and=20its=20contents=20are=20subject=20to=20the=20DISCLAIM= ER=20at=20http://www.tno.nl/disclaimer/email.html |
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From: Susanna-Assunta S. <sa...@eb...> - 2007-10-10 18:19:44
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Dear Oliver, I am at my parent place in Italy and unless there is a toll free number I will not be able to call in, sorry. If this is the case then I look forward to hearing the outcome of the discussion. Best regards, Susanna Oliver Fiehn wrote: > Dear all, > > > > Below please find the contact information for tomorrow's telephone > conference on progress of the Metabolomics Standards Initiative. > > > > I am looking forward to the TC, > > Best regards, > > Oliver Fiehn > > > > Top of Form > > > > > The following conference call has been reserved: > > > > > > > Date: > > Thursday, October 11, 2007 > > > Time: > > 10:00 AM Eastern > > > > > 9:00 AM Central, 8:00 AM Mountain, 7:00 AM Pacific > > > Duration: > > 2 Hours > > > Participants: > > 15 > > > Title: > > MSI > > > Options: > > Start recording call using control pad > > > > > > > > To join this conference: > > > > > For quick access, go to <https://www.spiderphone.com/63704111> > https://www.spiderphone.com/63704111 > (This link will help connect both your browser and telephone to the call) > > OR dial 1 (888) 550-5602 or +1 212-812-2800 and enter 6370 4111 > > You may want to copy this page into your email invitations. > > <javascript:document.Email.submit();> Email others an invitation to > this conference > <javascript:document.Share.submit();> Share files with this > conference > > > Bottom of Form > > > > Top of Form > > > > Bottom of Form > > > > > > 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... > > URL http://fiehnlab.ucdavis.edu/ > > tel +1-530-754-8258 > > fax +1-530-754-9658 > > |
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From: Oliver F. <of...@uc...> - 2007-10-10 16:00:30
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Dear all, Below please find the contact information for tomorrow's telephone conference on progress of the Metabolomics Standards Initiative. I am looking forward to the TC, Best regards, Oliver Fiehn Top of Form The following conference call has been reserved: Date: Thursday, October 11, 2007 Time: 10:00 AM Eastern 9:00 AM Central, 8:00 AM Mountain, 7:00 AM Pacific Duration: 2 Hours Participants: 15 Title: MSI Options: Start recording call using control pad To join this conference: For quick access, go to <https://www.spiderphone.com/63704111> https://www.spiderphone.com/63704111 (This link will help connect both your browser and telephone to the call) OR dial 1 (888) 550-5602 or +1 212-812-2800 and enter 6370 4111 You may want to copy this page into your email invitations. <javascript:document.Email.submit();> Email others an invitation to this conference <javascript:document.Share.submit();> Share files with this conference Bottom of Form Top of Form Bottom of Form 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... URL http://fiehnlab.ucdavis.edu/ tel +1-530-754-8258 fax +1-530-754-9658 |
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From: Basil N. <di...@ia...> - 2007-10-09 20:45:27
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Dear everyone, Due to travels in Europe, I will not be able to join this initial conversation - this is not due to lack of interest but rather to prior arrangements - I hope to join in to later conversations Basil Nikolau At 6:48 PM -0700 10/8/07, Oliver Fiehn wrote: >Dear all, > > > >I have received responses from most of you, thanks for that. Anybody who is >on that list is invited to join _ 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. > > > >The best time for a TC on _how to proceed with the MSI_ is on > >Thursday, October 11, 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). > >I will try to get a free dial-in number, so you_ll receive another email >tomorrow or latest on Wednesday. > > > >WARNING: The remainder of this 76K message has not been transferred. >Turn on the "Fetch" button in the icon bar and check mail again to >get the whole thing. -- Basil J. Nikolau Professor of Biochemistry, Director, Center for Metabolic Biology, Director, W.M. Keck Metabolomics Research Laboratory Iowa State University Phone: 515-294-9423 Fax: 515-294-0453 |
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From: Oliver F. <of...@uc...> - 2007-10-09 01:48:06
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Dear all, =20 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. =20 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. =20 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. =20 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 =20 Thanks so far,=20 =20 Please bookmark your calendars! =20 Oliver =20 =20 =20 =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: 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 =20 Dear Susanna, dear all, =20 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 =20 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 -------- 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 =20 =20 Susanna, =20 Go ahead. Let me know of possible dates and times to do this. =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: > <mailto:Fed...@fd...> 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 =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, =20 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... =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 =20 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) =20 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. =20 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. =20 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. =20 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. =20 =20 --=20 Susanna-Assunta Sansone, PhD =20 Project - Coordinator www.ebi.ac.uk/net-project =20 =20 =20 =20 =20 =20 --=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 =20 =20 =20 =20 --=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 |
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From: Susanna-A S. <sa...@eb...> - 2007-10-02 22:16:16
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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 > > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2005. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > > ------------------------------------------------------------------------ > > _______________________________________________ > Msi-workgroups-board mailing list > Msi...@li... > <mailto:Msi...@li...> > https://lists.sourceforge.net/lists/listinfo/msi-workgroups-board > [attachment "don.robertson.vcf" deleted by Rima > Kaddurah-Daouk/Psych/mc/Duke] |
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From: Sumner, L. <lws...@no...> - 2007-10-02 18:24:08
|
I am only available Wednesday & Thursday (Oct 10-11). Several next = steps could include =20 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 =20 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 =20 Dear Susanna, dear all, =20 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 =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 ________________________________ 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 =20 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 =20 -------- 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 =20 =20 Susanna, =20 Go ahead. Let me know of possible dates and times to do this. =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> 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 =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, =20 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> 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 =20 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) =20 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. =20 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. =20 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. =20 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. =20 =20 --=20 Susanna-Assunta Sansone, PhD =20 Project - Coordinator www.ebi.ac.uk/net-project =20 =20 =20 =20 =20 =20 --=20 Susanna-Assunta Sansone, PhD =20 NET Project - Coordinator =20 www.ebi.ac.uk/net-project =20 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 =20 =20 =20 =20 --=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 |
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From: Rima Kaddurah-D. <rim...@du...> - 2007-10-02 17:56:20
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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=20 with regulatory agencies a must. best rima Don Robertson <don...@bm...>=20 Sent by: don...@bm... 10/02/2007 01:47 PM To Oliver Fiehn <of...@uc...> cc "'Susanna'" <sa...@eb...>,=20 msi...@li..., rim...@du...,=20 "'Goodsaid, Federico'" <Fed...@fd...> Subject Re: [Msi-workgroups-board] Availability October 08-12 for TC with MSI=20 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=20 impression is that such feedback has been minimal so far (though as I've=20 been out of touch for a few months - maybe I've missed a groundswell of=20 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=20 already??? If not, our telecon with Federico may be a good first step so=20 we can see how consumer friendly the standards are in their present form=20 and where we need to expand or clarify things. I think we should also=20 think about contacting editors and/or editorial boards of relevant=20 journals to solicit feedback. I'm not sure how best to do that , but I=20 hope you or some of your academic colleagues might have suggestions for a=20 mechanism to accomplish that.=20 My thoughts for what they are worth... BTW - from 10 -12 USEDT next week works for me Tuesday through Thursday=20 with no problem. Monday is doable but not ideal and Friday is not very=20 good at all.=20 Don Oliver Fiehn wrote:=20 Dear Susanna, dear all, =20 Now that all MSI documents are available online at the Metabolomics=20 journal site ( http://www.springerlink.com/content/j85g85483103/?p=3D69c352ecf23641afa10a3= 72c251b9cf7&pi=3D0=20 ), we should discuss how to move forward. The view may be different for=20 different groups, so I would like to see opinions expressed from each=20 group chair. We will set up a date and time for a telephone conference,=20 but by experience, it may happen that not every WG chair can join the=20 discussion. In this case I would like to get input by email from those=20 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=20 U.S. pacific coast and central Europe. So, the time seems to be fixed=20 somewhere around=20 7-9 a.m. Pacific (10-12 a.m. US east coast, 15:00-17:00 UK time,=20 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=20 08 to Friday October 12. =20 A one hour TC should be fine. Please respond to me, no need to respond to=20 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 From: Susanna [mailto:sa...@eb...]=20 Sent: Mittwoch, 26. September 2007 12:17 To: msi...@li...;=20 rim...@du...; of...@uc... Cc: Goodsaid, Federico Subject: FDA's request for teleconference with MSI chairs Importance: High =20 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=20 inviting the working groups' chairs (or alternative leading people), a=20 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.=20 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=20 (Federico, please, you too). Please, let me know if you cannot make any of the proposed dates (approx=20 last 2 weeks of October and early Nov). Best regards, Susanna * Federico is also responsible for the "Guidance for Industry -=20 Pharmacogenomic Data Submissions" just released by FDA:=20 http://www.fda.gov/CBER/gdlns/pharmdtasubcomp.pdf =20 -------- Original Message --------=20 Subject:=20 RE: Metabolomics standards' papers- Nature Biotechnology and Metabolomics=20 journal Date:=20 Wed, 26 Sep 2007 13:08:31 -0400 From:=20 "Goodsaid, Federico" <Fed...@fd...> To:=20 "Susanna" <sa...@eb...> References:=20 =20 =20 Susanna, =20 Go ahead. Let me know of possible dates and times to do this. =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: Fed...@fd... =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=20 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=20 proteomics standard groups. To provide you with a summary overview of the=20 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=20 know. Thanks, Susanna Goodsaid, Federico wrote: Susanna, =20 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: Fed...@fd... =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,=20 Ikram; Fuscoe, James; Jean-Charles. Gautier (E-mail); Jennifer Fostel=20 (E-mail); Jim Stevens (E-mail); Leighton, John K; John. N. Haselden=20 (E-mail); Jonathan. Tugwood (E-mail); Joseph F. Sina (E-mail); KDaniels=20 (E-mail); Laura Suter-Dick {PRBN~Basel} (E-mail); Freed, Lois M;=20 McCarroll. Nancy (E-mail); Michael Lawton (E-mail); Orr, Michael; Mike=20 Waters (E-mail); Nie, Alex [PRDUS]; Pine, P Scott; Roger Ulrich (E-mail);=20 Ronald Snyder (E-mail); Francke, Sabine; Thurmond, Scott; Spanhaak, Steven = [PRDBE]; Choudhuri, Supratim; Syril Pettit; Papoian, Thomas; Tong, Weida;=20 William Mattes (E-mail); Ying Jiang (E-mail) Subject: Metabolomics standards' papers- Nature Biotechnology and=20 Metabolomics journal =20 Dear All, several open access papers from the Metabolomics Standards Initiative=20 (MSI) are now available. We look forward to your comments and participation in the future=20 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,=20 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=20 Metabolomics Standards Initiative. Nat Biotechnol. 2007 Aug;25(8):846-8. Special issue papers in Metabolomics Journal ( http://springerlink.metapress.com/content/j85g85483103/?p=3Dc2b8952a7cdb443= 98c0c4f2f7291c0c6&pi=3D0 ) =20 Fiehn, O., Robertson, D., Griffin, J., van der Werf, M., Nikolau, B.,=20 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,=20 J.C. & Sansone, S.-A. (2007) The metabolomics standards initiative (MSI).=20 Metabolomics 3, 175-178. =20 Griffin, J.L., Nicholls, A.W., Daykin, C., Heald, S., Keun, H.,=20 Schuppe-Koistinen, I., Griffiths, J.R., Cheng, L., Rocca-Serra, P.,=20 Rubtsov, D.V. & Robertson, D. (2007) Standard reporting requirements for=20 biological samples in metabolomics experiments: mammalian/in vivo=20 experiments. Metabolomics 3, 179-188. =20 van der Werf, M.J., Takors, R., Smedsgaard, J., Nielsen, J., Ferenci, T.,=20 Portais. J.C., Wittmann, C., Hooks, M., Tomassini, A., Oldiges, M.,=20 Fostel, J. & Sauer, U. (2007) Standard reporting requirements for=20 biological samples in metabolomics experiments: microbial and in vitro=20 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=20 standards for plant biology context information in metabolomic studies.=20 Metabolomics 3, 195-201. =20 Morrison, N., Bearden, D., Bundy, J.G., Collette, T., Currie, F., Davey,=20 M.P., Haigh, N.S., Hancock, D., Jones, O.A.H., Rochfort, S., Sansone,=20 S.-A., =A9tys, D., Teng, Q., Field, D. & Viant, M.R. (2007) Standard=20 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,=20 R., Kopka, J., Lindon, J.C., Lane, A.N., Marriott, P., Nicholls, A.W.,=20 Reily, M.D. & Viant, M. (2007) Proposed minimum reporting standards for=20 chemical analysis. Metabolomics 3, 211-221. =20 Rubtsov, D.V., Jenkins, H., Ludwig, C., Easton, J., Viant, M.R., G=FCnther,= =20 U., Griffin, J.L. & Hardy, N. (2007) Proposed reporting requirements for=20 the description of NMR-based metabolomics experiments. Metabolomics 3,=20 223-229. =20 Goodacre, R., Broadhurst, D., Smilde, A., Kristal, B.S., Baker, J.D.,=20 Beger, R., Bessant, C., Connor, S., Capuani, G., Craig, A., Ebbels, T.,=20 Kell, D.B., Manetti, C., Newton, J., Paternostro, G., Somorjai, R.,=20 Sj=F6str=F6m, M., Trygg, J. & Wulfert, F. (2007) Proposed minimum reporting= =20 standards for data analysis in metabolomics. Metabolomics 3, 231-241. =20 Hardy, N.W. & Taylor, C.F. (2007) A roadmap for the establishment of=20 standard data exchange structures for metabolomics. Metabolomics 3,=20 243-248. =20 Sansone, S.-A., Schober, D., Atherton, H.J., Fiehn, O., Jenkins, H.,=20 Rocca-Serra, P., Rubtsov, D.V., Spasic, I., Soldatova, L., Taylor, C.,=20 Tseng, A., Viant, M.R. & The Ontology Working Group Members (2007)=20 Metabolomics standards initiative - ontology working group - work in=20 progress. Metabolomics 3, 249-256. =20 =20 --=20 Susanna-Assunta Sansone, PhD =20 Project - Coordinator www.ebi.ac.uk/net-project =20 =20 =20 =20 =20 =20 --=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 =20 --=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 ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2005. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F Msi-workgroups-board mailing list Msi...@li... https://lists.sourceforge.net/lists/listinfo/msi-workgroups-board [attachment "don.robertson.vcf" deleted by Rima=20 Kaddurah-Daouk/Psych/mc/Duke]=20 |
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From: Oliver F. <of...@uc...> - 2007-10-02 16:52:06
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Dear Susanna, dear all, =20 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 =20 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 -------- 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 =20 =20 Susanna, =20 Go ahead. Let me know of possible dates and times to do this. =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: > <mailto:Fed...@fd...> 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 =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, =20 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... =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 =20 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) =20 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. =20 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. =20 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. =20 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. =20 =20 --=20 Susanna-Assunta Sansone, PhD =20 Project - Coordinator www.ebi.ac.uk/net-project =20 =20 =20 =20 =20 =20 --=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 =20 =20 =20 --=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 |
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From: Oliver F. <of...@uc...> - 2007-09-28 15:44:04
|
Hi all, I am out of office until Tuesday and will then ask all of you for a good date/time for a TC. Thanks so far; Oliver Thanks Susanna for incredible energy and great determination we need it. I > > think it is important that we connect as a group and discuss the next > phase of this project and before we share with others. Having a clear > vision forward is important. I spoke to Oliver and he promised to arrange > > for a conference call to get team together and where we can express our > collective thoughts about what should be done next. Then after that i > think it is a great opportunity to link with FDA and all others who are > interested in this important initiative. What do you think? Oliver do you > > want to arrange for the call early October? how can we help? Best Rima > > > > > > > > > Susanna <sa...@eb...> > 09/26/2007 03:17 PM > > To > msi...@li..., rim...@du..., > of...@uc... > cc > "Goodsaid, Federico" <Fed...@fd...> > Subject > FDA's request for teleconference with MSI chairs > > > > > > > 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...> > To: > "Susanna" <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: 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: 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 > ) > > 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 > > > > > > > > -- > Susanna-Assunta Sansone, PhD > > NET Project - Coordinator > > www.ebi.ac.uk/net-project > > 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 > > > > > -- > Susanna-Assunta Sansone, PhD > > NET Project - Coordinator > > www.ebi.ac.uk/net-project > > 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 > > > Dr. Oliver Fiehn, Assoc. Prof. UC Davis Genome Center 1315 GBSF Building 451 E. Health Sci. Drive Davis (CA) 95616 URL http://fiehnlab.ucdavis.edu/ email of...@uc... phone 530-754-8258 |
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From: <dgr...@ao...> - 2007-09-27 13:53:30
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Hi Susanna, Good to hear from you again.=C2=A0 Yes - please do change my e-mail to my BM= S adress. Don don...@bm... -----Original Message----- From: Susanna <sa...@eb...> To: dgr...@ao... Cc: Fed...@fd...; msi...@li...= t Sent: Thu, 27 Sep 2007 9:04 am Subject: Re: [Msi-workgroups-board] FDA's request for teleconference with MS= I chairs Hi Don, good to hear from you and congratulation for your new position. I do hope you are still keen on MSI activities.=20 Rima suggests we hold a internal call before talking to Federico, and Oliver= will follow up. For the Board mailing list, do you want me to replace your aol-temp address=20= with your new one? Best regards, Susanna=C2=A0=20 dgr...@ao... wrote: Susanna/all, I just started a new position at Bristol-Myers Squibb (Monday to be exact) s= o I am avaialbe to get back into the effort if you still need me.=C2=A0 I wo= uld be interested in particpating with the FDA telecon, but would understand= if you folks have moved on to other individuals.=C2=A0 Let me know if you a= re still interested in my invovlement.=C2=A0 By the way - my new business e-= mail adress is don...@bm.... Don Robertson Bristol-Myers Squibb Route 206 & Province Line Road Princeton, NJ=C2=A0 08543-4000 Phone: 609-252-5661=C2=A0 -----Original Message----- From: Susanna <sa...@eb...> To: msi...@li...; rim...@du...;= of...@uc... Cc: Goodsaid, Federico <Fed...@fd...> Sent: Wed, 26 Sep 2007 3:17 pm Subject: [Msi-workgroups-board] FDA's request for teleconference with MSI ch= airs Dear Rima, Oliver and WGs' chairs, In the light of our latest papers, Federico Goodsaid* (FDA's CDER and here c= c-e) suggests having a Webex meeting to discuss the MSI activities. As you can see from our communication -copied below- I have suggested inviti= ng the working groups' chairs (or alternative leading people), a total of 5=20= 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.=20= =C2=A0To start identifying possible date and time I have set up a doodle pag= e: Go to http://www.doodle.ch/xsv4ur7h43bxvune and enter your availability (Fed= erico, please, you too). Please, let me know if you cannot make any of the proposed dates (approx las= t 2 weeks of October and early Nov). Best regards, Susanna * Federico is also responsible for the "Guidance for Industry - Pharmacogeno= mic Data Submissions" just released by FDA: http://www.fda.gov/CBER/gdlns/ph= armdtasubcomp.pdf -------- Original Message --------=20 Subject:=20 RE: Metabolomics standards' papers- Nature Biotechnology and Metabolomics jo= urnal Date:=20 Wed, 26 Sep 2007 13:08:31 -0400 From:=20 "Goodsaid, Federico" <Fed...@fd...> To:=20 "Susanna" <sa...@eb...> References:=20 Susanna, =C2=A0 Go ahead. Let me know of possible dates and times to do this. =C2=A0 Thanks, =C2=A0 Federico =C2=A0 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:=C2=A0 301-796-1535 email:=C2=A0 Fed...@fd... =C2=A0 =C2=A0 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 Metabo= lomics journal =C2=A0 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 activiti= es, my suggestion would be to invite the other working groups' leaders or ot= her 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, =C2=A0 Would you be ale to give us a Webex presentation about these standards? We c= ould provide a Webex link from this end. =C2=A0 Thanks, =C2=A0 Federico =C2=A0 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:=C2=A0 301-796-1535 email:=C2=A0 Fed...@fd... =C2=A0 =C2=A0 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, F= ederico; Eshete, Feleke; Frueh, Felix; Frank Sistare; Friedlieb Pfannkuch (E= -mail); Gregory Akerman (E-mail); 'Haymes. Kenneth (E-mail); Elayan, Ikram;=20= Fuscoe, James; Jean-Charles. Gautier (E-mail); Jennifer Fostel (E-mail); Jim= Stevens (E-mail); Leighton, John K; John. N. Haselden (E-mail); Jonathan. T= ugwood (E-mail); Joseph F. Sina (E-mail); KDaniels (E-mail); Laura Suter-Dic= k {PRBN~Basel} (E-mail); Freed, Lois M; McCarroll. Nancy (E-mail); Michael L= awton (E-mail); Orr, Michael; Mike Waters (E-mail); Nie, Alex [PRDUS]; Pine,= P Scott; Roger Ulrich (E-mail); Ronald Snyder (E-mail); Francke, Sabine; Th= urmond, Scott; Spanhaak, Steven [PRDBE]; Choudhuri, Supratim; Syril Pettit;=20= Papoian, Thomas; Tong, Weida; William Mattes (E-mail); Ying Jiang (E-mail) Subject: Metabolomics standards' papers- Nature Biotechnology and Metabolomi= cs journal =C2=A0 Dear All, several open access papers from the Metabolomics Standards Initiative (MSI)=20= 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, Krist= al BS, Lindon J, Mendes P, Morrison N, Nikolau B, Robertson D, Sumner LW, Ta= ylor C, van der Werf M, van Ommen B, Fiehn O. (2007) The Metabolomics Standa= rds Initiative. Nat Biotechnol. 2007 Aug;25(8):846-8. Special issue papers in Metabolomics Journal (http://springerlink.metapress.com/content/j85g85483103/?p=3Dc2b8952a7cdb443= 98c0c4f2f7291c0c6&pi=3D0) =C2=A0 Fiehn, O., Robertson, D., Griffin, J., van der Werf, M., Nikolau, B., Morris= on, N., Sumner, L.W., Goodacre, R., Hardy, N.W., Taylor, C., Fostel, J., Kri= stal, B. Kaddurah-Daouk, R., Mendes, P., van Ommen, B., Lindon, J.C. & Sanso= ne, S.-A. (2007) The metabolomics standards initiative (MSI). Metabolomics 3= , 175-178. =C2=A0 Griffin, J.L., Nicholls, A.W., Daykin, C., Heald, S., Keun, H., Schuppe-Kois= tinen, I., Griffiths, J.R., Cheng, L., Rocca-Serra, P., Rubtsov, D.V. & Robe= rtson, D. (2007) Standard reporting requirements for biological samples in m= etabolomics experiments: mammalian/in vivo experiments. Metabolomics 3, 179-= 188. =C2=A0 van der Werf, M.J., Takors, R., Smedsgaard, J., Nielsen, J., Ferenci, T., Po= rtais. J.C., Wittmann, C., Hooks, M., Tomassini, A., Oldiges, M., Fostel, J.= & Sauer, U. (2007) Standard reporting requirements for biological samples i= n metabolomics experiments: microbial and in vitro biology experiments. Meta= bolomics 3, 189-194. =C2=A0 Fiehn, O., Sumner, L.W., Rhee, S.Y., Ward, J., Dickerson, J., Lange, B.M., L= ane, G., Roessner, U., Last, R. & Nikolau1, B. (2007) Minimum reporting stan= dards for plant biology context information in metabolomic studies. Metabolo= mics 3, 195-201. =C2=A0 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.,=20= =C2=A9tys, D., Teng, Q., Field, D. & Viant, M.R. (2007) Standard reporting r= equirements for biological samples in metabolomics experiments: environmenta= l context. Metabolomics 3, 203-210. =C2=A0 Sumner, L.W., Amberg, A., Barrett, D., Beger, R., Beale, M.H., Daykin, C., F= an, 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 ana= lysis. Metabolomics 3, 211-221. =C2=A0 Rubtsov, D.V., Jenkins, H., Ludwig, C., Easton, J., Viant, M.R., G=C3=BCnthe= r, U., Griffin, J.L. & Hardy, N. (2007) Proposed reporting requirements for=20= the description of NMR-based metabolomics experiments. Metabolomics 3, 223-2= 29. =C2=A0 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=C3=B6str=C3=B6m= , M., Trygg, J. & Wulfert, F. (2007) Proposed minimum reporting standards fo= r data analysis in metabolomics. Metabolomics 3, 231-241. =C2=A0 Hardy, N.W. & Taylor, C.F. (2007) A roadmap for the establishment of standar= d data exchange structures for metabolomics. Metabolomics 3, 243-248. =C2=A0 Sansone, S.-A., Schober, D., Atherton, H.J., Fiehn, O., Jenkins, H., Rocca-S= erra, P., Rubtsov, D.V., Spasic, I., Soldatova, L., Taylor, C., Tseng, A., V= iant, M.R. & The Ontology Working Group Members (2007) Metabolomics standard= s initiative - ontology working group - work in progress. Metabolomics 3, 24= 9-256. =C2=A0 =C2=A0 --=20 Susanna-Assunta Sansone, PhD =C2=A0 Project - Coordinator www.ebi.ac.uk/net-project =C2=A0 =C2=A0=20 =C2=A0 =C2=A0=20 =C2=A0 --=20 Susanna-Assunta Sansone, PhD =C2=A0 NET Project - Coordinator =C2=A0 www.ebi.ac.uk/net-project =C2=A0=20 The European Bioinformatics Institute=C2=A0=C2=A0 email:=C2=A0 sansone@ebi.a= c.uk EMBL Outstation - Hinxton=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 direct: +44 (0)1223 494 691 Wellcome Trust Genome Campus=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0 fax: +44 (0)1223 494 468 Cambridge CB10 1SD, UK=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 room: A229=C2=A0=C2=A0= =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=20 =C2=A0 =C2=A0=20 =C2=A0 --=20 usanna-Assunta Sansone, PhD NET Project - Coordinator www.ebi.ac.uk/net-project =20 he European Bioinformatics Institute email: sa...@eb... MBL Outstation - Hinxton direct: +44 (0)1223 494 691 ellcome Trust Genome Campus fax: +44 (0)1223 494 468 ambridge CB10 1SD, UK room: A229 =20 =20 ------------------------------------------------------------------------- his SF.net email is sponsored by: Microsoft efy all challenges. Microsoft(R) Visual Studio 2005. ttp://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ si-workgroups-board mailing list si-...@li... ttps://lists.sourceforge.net/lists/listinfo/msi-workgroups-board Email and AIM finally together. You've gotta check out free AOL Mail! --=20 usanna-Assunta Sansone, PhD NET Project - Coordinator www.ebi.ac.uk/net-project =20 he European Bioinformatics Institute email: sa...@eb... MBL Outstation - Hinxton direct: +44 (0)1223 494 691 ellcome Trust Genome Campus fax: +44 (0)1223 494 468 ambridge CB10 1SD, UK room: A229 =20 =20 ------------------------------------------------------------------------- his SF.net email is sponsored by: Microsoft efy all challenges. Microsoft(R) Visual Studio 2005. ttp://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ si-workgroups-board mailing list si-...@li... ttps://lists.sourceforge.net/lists/listinfo/msi-workgroups-board ________________________________________________________________________ Email and AIM finally together. You've gotta check out free AOL Mail! - http= ://mail.aol.com |
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