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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: Sue R. <rh...@ac...> - 2007-10-16 16:34:44
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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 >> >> >> > > |
