MetaboMeeting 1.0 July 18th-19th, 2005 — Cambridge, UK

Contents

Original meeting announcement page is here

1. Introduction and organisers
2. Summary meeting report
3. Talk and poster downloads
4. Sponsors

Introduction and Organizers

On the 18-19th of July we held a meeting in Cambridge (UK) at which we:

1. Established a coordinated effort to generate appropriate data format and reporting standards for a range of experiment types and technologies appropriate to both metabolomics and metabonomics ('systems metabolomics')
    
2. Discussed general organisational matters (status of the SMRS group, relationship to the Metabolomics Society and NIH)
    
3. Considered the wider functional genomics context and discussed the coordination of development with the transcriptomics and proteomics standards communities (for example, the description of biological source material is seldom omics-specific)

The ‘omics’ suffix is rather overused these days, but clearly several major technological and biological domains do merit its application; amongst these are transcriptomics, proteomics and of course metabol/nomics. For the generation of public standards (data formats, controlled terminology and reporting guidelines) there are clear focal points for the first two of these communities (MGED and HUPO PSI respectively); the standards developed under the umbrellas of these organisations are continually increasing both the quality of data and its annotation, and the ease with which data can be exchanged, disseminated and analysed.

The fields concerned with the study of metabolites, whether on a cellular or systems scale, are now also moving towards a unified standards development process. We can now conceive of a body that is in principle representative of the field in the UK and Europe; both as a forum for interested parties and as a voice on the global stage. This new organisation will consist of an expansion of the Standard Metabolic Reporting Structures (SMRS) Group to become a truly representative body for UK and European metabolomics (both public and private); MetaboMeeting 1.0 will be the venue for the discussion and ratification of this initiative, and for discussion of the wider context (for example, the opportunity to operate under the Metabolomics Society's banner).

Having laid the groundwork for a community process of standards development, both for the study of metabolism in isolation and importantly for integration into an ongoing grand collaboration aimed at producing standards for functional genomics (simply defined as the combination of the three omics already described), the time is now right for a large scale meeting of UK and European academics, industrialists (both ‘pharma’ and technology vendors), government and publishers, to ratify what has been done to date and to consolidate effort, partly through a public project management system (as symbolically important as it is practical).

We organised a two day meeting at the University of Cambridge on the 18-19th of July. To this meeting we invited academic and industrial researchers, technology vendors, funders, other 'governmental types' and journal representatives from across Europe. This meeting immediately preceded one at the National Institutes of Health (Bethesda MD), at which the US metabolomics community (inter alia) considered similar issues of standardisation [LINK]; several of our confirmed attendees also travelled to this US meeting, affording an opportunity to present a unified UK/European voice in that forum.

The minutes from the exploratory MetaboMeeting 0.1 (which established that this meeting would be useful) can be found here.

We addressed all these issues and more at MetaboMeeting 1.0. Participation in the meeting was free, thanks to generous sponsorship.
Travel and accomodation are the responsibility of the attendee, but logistical help is available.

Organising Committee:

University of Cambridge, UK
      Jules Griffin

European Bioinformatics Institute, Hinxton, UK
      Chris Taylor
      Susanna-Assunta Sansone

Information and Correspondence: Chris Taylor [christ@ebi.ac.uk]

Summary meeting report (interim draft version)

• All thought the meeting timely and worthwhile; final attendee list is below. Lots of interesting talks and posters (all will appear here soon), but the main activity happened in the discussion/breakouts, and over breaks/lunch/wine/dinner. We came in under budget; all attendees thought that the meeting being free to attend was extremely useful (thanks to BBSRC, Springer-Verlag [Metabolomics], Genologics and the EBI's Industry Program).
  
• Metabolomics Society seen as something of real value to give a HUPO/MGED-like stamp of authority to sanctioned standards efforts in various areas; reporting [SMRS paper seen as high value]; data formats for various technologies and controlled vocabularies; promoting collaborative efforts and representing the community at the higher ('inter-omics') level, such as with the functional genomics ontology (FuGO) and the generic biological project description stuff from MGED SMRS (i.e. what is the biology I am doing, independent of the omics tech I will use); even to some extent the choice of conditions for 'standard' experimental techniques (acting more as an ABRF-like forum in that regard though).
• SMRS Nature Biotech paper seen as something to be followed up on with a view to generating full-blown community reporting requirements, geared to several levels (repository submission, publication, FDA).
  
• Much discussion of many 'political' issues; one stands out... While the SMRS group is very pharma-heavy; Met.Soc. is currently much less so, which was seen as a real issue (although a couple of people said they thought this was already firmly on the society's 'to do list'). Strong desire expressed to radically increase pharma membership and participation in Met.Soc. and to expand generally as rapidly as possible. This obviously should include instrument and software vendors, funders, government and publishers to that list of desirable communities to increase representation from (PSI and MGED can help with this). Amongst other political stuff discussed was the need for funders to strongly support both open data repositories, and the development of useful tools to assist in reporting and data sharing (that implement reporting guidelines and ontology support), with proactive assistance from securely funded core data centers.
  
• Major strides made towards a common NMR data format; Jules Griffin's group's white paper really drove discussion along in conjunction with input from Bruker (BioSpin), Varian, and the producers of an academic LIMS/repository package called ArMet. Agreement to coordinate on one schema/format for NMR at the earliest opportunity and to move forward as a group (using the sourceforge dev site and [ideally] sanctioned by Met.Soc.)
  [Update: first coordination meeting of the two groups of developers has now actually happened -- more anon -- watch this space]
  
• mzData format (originally from the HUPO Proteomics Standards Initiative) seen as entirely appropriate to capture data and params from metabo use of MS (no use cases 'broke' it); interest expressed in partner data analysis format mzIdent (in draft); need made clear for a simple 'upstream' partner format for G/LC to catch (inter alia) retention times measured at the column (as opposed to scan times from the mass spec). Bruker (Daltonic) and ABI had representation in the breakout meeting, sadly the Thermo person could only attend the Monday and Agilent could not mobilise given the short notice but are very eager to join in (I never got chance to approach Waters, although we can definitely count on them); and of course through PSI we already have the mzData format implemented by all major MS vendors and many of the appropriate software companies -- they just need to tweak their documentation essentially (well almost)...
  
• Great interest in the existing project (mostly MGED RSBI with input from PSI, at the moment) to cater to the needs of diverse _biological_ communities in describing their work, and to ensure that the product of that activity is applicable to all omics; the obvious example of something proteomics and transcriptomics would not consider without input from the metabo people is the idea of a 'footprint' or 'exometabolome' -- they just don't do that sort of stuff much!
  
• Ontology for describing the experimental process: We discussed this too. Funds have been obtained to develop an ontology for metabolic studies as part of a functional genomics ontology. There is a tight integration between MGED groups and the Proteomics Standard Initiative (PSI). Similarly, those two groups hope to achieve a tight integration with the Standard Metabolic Reporting Structure (SMRS) group, the Metabolomics Society and others in the metabol/nomics arena keen to work on semantics.
  
• Proposal from Mark Viant (Birmingham) to set up a library of reference NMR spectra; heavy discussion of techniques and conditions to be employed; some progress made in establishing the most useful / appropriate way forward for his group.
  
• Proposal from European Bioinformatics Institute to set up a repository for experimental MS data (building on the apparent acceptability of the mzData format, which we have already built a repository around for proteomics MS data). No discussion of an equivalent for NMR, but we could step in there also if that was seen to be desirable, or could support Cambridge in establishing such as thing based on their current schema work (cf. above). The meeting's attendees seemed to have a positive view of the EBI as both solid in the technical department (we do databases really well...) and politically neutral, with no institutional agenda beyond fulfilling our role in supporting and disseminating good science. Note that the repositories we propose would not be the same as the reference libraries proposed by Mark Viant for NMR and NIST/MPI for MS; these would be free, open submission repositories for data collected from a wide variety of experiments, as long as the annotation is reasonable (else the data are worthless...).

  Thanks again to all those listed below (along with many other people) who had a hand in making this a roaring success.
  

Companies

AstraZeneca
GlaxoSmithKline (Ware)
Novo Nordisk A/S
Pfizer
Scynexis Europe Ltd
Syngenta
TNO Quality of Life (Netherlands)

Applied Biosystems (Warrington)
Bruker BioSpin GmbH
Bruker Daltonic GmbH
Thermo Corporation
Varian Ltd.

Advanced Technologies (Cambridge) Ltd
BioWisdom
GenoLogics Life Sciences Software Inc.
Umetrics

Institutions

Biotechnology and Biological Sciences Research Council
National Measurement System Directorate, DTI
Natural Environment Research Council

Central Science Laboratory, York
Chemistry Dept. "La Sapienza" University of Rome
European Bioinformatics Institute
Imperial College, London
Institute of Food Research, Norwich
John Innes Centre, Norwich
Rothamsted Research
School of Pharmacy, University of London
Scottish Crop Research Institute
Technical University of Munich
University of Birmingham
University of Cambridge
University of Manchester
University of Nottingham
University of Sheffield
University of Southampton
University of Wales, Aberystwyth

Downloads

To appear here shortly...

Sponsors

Chris Taylor (christ@ebi.ac.uk), August 2nd, 2005