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

[Chris T. <chr...@eb...>]

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
> 
> 
> ------------------------------------------------------------------------
> 
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