Re: [Msi-workgroups-board] minutes of the MSI teleconference Thursday, October 11, 7-9 a.m. Pacific (10-12 a.m. EST)

[Susanna-Assunta S. <sa...@eb...>]

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
>
>