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Re: [Msi-workgroups-board] minutes of the MSI teleconference Thursday, October 11, 7-9 a.m. Pacific (10-12 a.m. EST)
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From: Chris T. <chr...@eb...> - 2007-10-17 09:35:45
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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? 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