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

[Sue R. <rh...@ac...>]

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/
> ~~~~~~~~~~~~~~~~~~~~~~~~