msi-workgroups-exchange-format — This is the list for the msi exchange format WG

[Msi-workgroups-exchange-format] Can mzIdentML encode a spectral library?

[Steffen N. <sne...@ip...>]

On Tue, 2009-06-30 at 08:32 -0700, Eric Deutsch wrote:
> +Can mzIdentML encode a spectral library?

I am unsure whether this was discussed during the conference call, 
or is left as an open point to the list.

Anyway, I am inclined to say "no" about this,
for two reasons: 

1) I don't know enough about analys^H^H^H^H^mzIdentML,
   because my very brief looks made it look like proteomics-only.
   (Or are you actually referring to a proteomics-spectral library?!
    in that case I'll shut up and you can skip the rest of this mail.)

2) A spectral library will (at least in the future)
   contain sets of spectra (different eV, MS1-MS^n, ...) 
   and associated annotations, which might be as complicated 
   as a molecule and its fragmentation brake-down products.
   This requires a rich set of links between individual peaks 
   and their (molecular) annotation.

So for small molecules (read: metabolomics stuff) we have started
to create mzAnnotate under the umbrella of the Metabolomics Standards
Initiative (MSI). http://msi-workgroups.sourceforge.net/exchange-format/

We have drafted some use cases, shown on
http://sourceforge.net/apps/mediawiki/metware/index.php?title=MzAnnotate
and prepared a converter for both the spectral library www.massbank.jp 
and our own MassFrontier clone MetFrag, and will present these
on the MSI mailing list soon.

Yours,
Steffen

Re: [Msi-workgroups-exchange-format] Invitation to draft a standard for annotated mass spectra

[Steffen N. <sne...@ip...>]

On Fri, 2009-02-13 at 16:45 +0000, Jones, Andy wrote:
..
> Is there a relevant part of a reporting requirements document for what
> you would like to capture?
I think there will be a mix:

1) The MSI Chemical Analysis Workgroup has a document
   http://www.springerlink.com/content/k8v0632383j8111u/fulltext.html

   which covers 

	2.1   Proposed minimum metadata for sample preparation
	2.2   Proposed minimum metadata relative to chromatography 
	2.3   Proposed minimum metadata relative to mass spectrometry
and 	2.8   Proposed minimum metadata relative to data pre-processing

which are probably covered pretty well in mzML as you suggested. 
Not yet included, and definitely a target for this standard is 

	2.9   Proposed minimum metadata relative to metabolite identification

which covers how one came to the conclusion that the molecule and spectrum
correspond to each other.

> separate into two formats, one for representing just the spectra
> collected and instrument parameters (mzML) and the other for
> representing the peptides / proteins that spectra correspond with
> (AnalysisXML).
For which the documentation is available at 
http://www.psidev.info/index.php?q=node/319 and [1]

I think that the fundamental difference in philosphy is to split 
the information about query/input/reference spectra 
and the analysis results into separate files. 

> my guess is that mzML should fit your requirements pretty well, and
> might require no modification at all. Do you have any example data
> sets in native format so I can understand the requirements a bit
> better.

In metabolomics it is not (yet?) very common to run automated LC-MS/MS,
which would afterwards be piped to the equivalent of Sequest or Mascot.

Usually people will run profiling experiments, looking for 
differential/interesting peaks, and only afterwards conduct 
a separate MS/MS experiment to obtain some identification.

Second I'd like to have the format be self-contained such that 
there is only a single answer from a spectrum database, which contains 
the stored spectrum plus the structure of the identified molecule.

Finally, as Oliver Kohlbacher also pointed out, there is 
the requirement to store multiple peak lists / spectra 
e.g. at various MS Levels (spectral trees) and manually 
assign the annotation between peaks and (parts of) the molecule.
You can find one such rawfile at [2], which results from 
a direct-infusion Orbitrap measurement of the pure compound.

Yours,
Steffen


[1] http://psi-pi.googlecode.com/svn/trunk/specification_document/AnalysisXML_releaseCandidate1.doc
[2] http://metware.svn.sourceforge.net/viewvc/metware/playground/malick-library/i486-pc-linux-gnu-library/2.6/msdata/src_MassFrontier_Readw/threonine_i2_e35_pH_tree_mzxml3.mzXML?revision=442&view=markup


-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

Re: [Msi-workgroups-exchange-format] Invitation to draft astandard for annotated mass spectra

[Neumann, S. <sne...@ip...>]

Hi Miguel, 

thanks for your example.

On Mon, 2009-02-16 at 09:47 +0100, Miguel Rojas Cherto wrote:
> read and write it. The only dirty think still is that the metadata is
> added as a properties in the molecule and not a CMLSpect (see example
>
http://cdk.svn.sourceforge.net/viewvc/cdk/cdk/branches/cdk-1.2.x/src/test/dat
a/cml/reactionSchemeMoleculeSet.cml?view=markup). 
> The reasons of that is CDK can not handle spectrum concepts yet :(.

For this discussion it is sufficient to have mockups,
even if current software is not yet able to read/write it.

But while you mention it, Metadata will have to be discussed, 
and that will be the major part of the work. I'd suggest to recycle 
as much from the mzML standard http://psidev.info/index.php?q=node/257
as possible, for the machine description, acquisition settings, 
and possibly even for the software parameters used to extract 
the spectrum.

We'll have to find out how we can import or adapt the <cvParm/>
logic into CMLSpect. I think CML was/is using something similar, 
and encodes them in XSD dictionaries.

> I think CML could be the best format to store MS information because the
> flexibility that it can provide. One of the important issues to define
> is how to linke between CMLSpect-CMLReact-CMLMol and what library to

I have the feeling that the flexibility of CML is one of its 
weak points, because it allows to express things in quite many ways. 

So it might be a good idea to also recycle the concept of a 
semantic validator. Here CML is already using some schematron, 
which defines an XSLT that has assertions to catch invalid documents,
or the somewhat equivalent solution by mzML (and analysisXM), 
which takes a separate ontology mapping file. The latter has the 
enourmous benefit that there are several OBO ontologies to use,
and secondly that the hierarchical concept allows to specify 
"this term or any of its children".

Yours,
Steffen










-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

Re: [Msi-workgroups-exchange-format] Invitation to draft a standard for annotated mass spectra

[Egon W. <ego...@gm...>]

Miguel,

On Mon, Feb 16, 2009 at 9:47 AM, Miguel Rojas Cherto
<m....@la...> wrote:
> At the moment I am using CMLReact to store MS^n which works very fine
> for this issue.

Can you contribute a document on this? So that everyone can see what
it looks like?

Egon

-- 
----
Post-doc @ Uppsala University
http://chem-bla-ics.blogspot.com/

Re: [Msi-workgroups-exchange-format] Invitation to draft a standard for annotated mass spectra

[Miguel R. C. <m....@la...>]

Dear all

On Sat, 2009-02-14 at 08:34 +0100, Oliver Kohlbacher wrote:
> > but also the "full blown" annotation where you assign
> > a peak from the spectrum to a molecular structure.
> > Because the molecule might undergo rearrangements
> > upon fragmentation, real mass spectrometrists sometimes
> > draw the fragmentation reaction(s) similar to
> > a chemical reaction. CMLReact http://pubs.acs.org/doi/abs/10.1021/ci0502698
> > can represent such reactions,
At the moment I am using CMLReact to store MS^n which works very fine
for this issue. I am implemented all code in CDK with the capability to
read and write it. The only dirty think still is that the metadata is
added as a properties in the molecule and not a CMLSpect (see example
http://cdk.svn.sourceforge.net/viewvc/cdk/cdk/branches/cdk-1.2.x/src/test/data/cml/reactionSchemeMoleculeSet.cml?view=markup). The reasons of that is CDK can not handle spectrum concepts yet :(.
I think CML could be the best format to store MS information because the
flexibility that it can provide. One of the important issues to define
is how to linke between CMLSpect-CMLReact-CMLMol and what library to
use.

Best regards,
 Miquel

Re: [Msi-workgroups-exchange-format] Invitation to draft a standard for annotated mass spectra

[Steffen N. <sne...@ip...>]

On Sat, 2009-02-14 at 08:34 +0100, Oliver Kohlbacher wrote:
> good idea this, we will try to get involved to the extent possible.
Great to hear!

> What I consider a fully annotated MS^n experiment would basically be a
> tree of spectra (MS, some peaks of MS related to MS^2 spectra, some
> peaks of those related to the corresponding MS^3 spectra etc.)

That seems to be what I meant with "Spectral Trees" on
https://apps.sourceforge.net/mediawiki/metware/index.php?title=MzAnnot_UseCases

> and a matching structural tree containing the fragment structures  
> corresponding
> to the parent molecule/fragment. The format should provision for that
> level of annotation.
That's what I meant with "Spectral Trees with assigned 
Fragmentation Pattern", but you're right, the example picture
so far shows only a two-step process. I think CMLReact would 
also cater for nested reactions, which is what you suggested.

Do you have any examples / mockups / links for a fully annotated 
MS^n experiment ?

Yours,
Steffen
 

Re: [Msi-workgroups-exchange-format] Invitation to draft a standard for annotated mass spectra

[Oliver K. <oli...@un...>]

> Dear all,


good idea this, we will try to get involved to the extent possible.

> but also the "full blown" annotation where you assign
> a peak from the spectrum to a molecular structure.
> Because the molecule might undergo rearrangements
> upon fragmentation, real mass spectrometrists sometimes
> draw the fragmentation reaction(s) similar to
> a chemical reaction. CMLReact http://pubs.acs.org/doi/abs/10.1021/ci0502698
> can represent such reactions,
I would also like to see included the hierarchical representation
of MS^n spectra. What Steffen suggested here -- unless I am mistaken --
is basically a two-step hierarchy of the structures. Parent structure
and then fragment structures. In a similar way, one shoudl also be able
to store the spectra arising from a series of MS^n experiments.
What I consider a fully annotated MS^n experiment would basically be a
tree of spectra (MS, some peaks of MS related to MS^2 spectra, some
peaks of those related to the corresponding MS^3 spectra etc.)
and a matching structural tree containing the fragment structures  
corresponding
to the parent molecule/fragment. The format should provision for that
level of annotation.

Cheers,
   Oliver

Re: [Msi-workgroups-exchange-format] Invitation to draft a standard for annotated mass spectra

[Steffen N. <sne...@ip...>]

On Fri, 2009-02-13 at 17:48 +0900, Takaaki Nishioka wrote:
> I am also interested in the drafting and would like to contribute something 
> to your activity.
Great to hear that!

> Before my contribution, I would like to know the definition of "annotated" 
> mass spectra.
I don't have a fixed definition of annotated spectra,
this has yet to be discussed. I started to collect use cases
on the wiki https://apps.sourceforge.net/mediawiki/metware/index.php?title=MzAnnot_UseCases

I think the format should be able to represent 
simple cases where you simply bundle a molfile 
with the corresponding single spectrum (or multiple spectra,
e.g. collision energies or polarities),

but also the "full blown" annotation where you assign 
a peak from the spectrum to a molecular structure.
Because the molecule might undergo rearrangements 
upon fragmentation, real mass spectrometrists sometimes
draw the fragmentation reaction(s) similar to 
a chemical reaction. CMLReact http://pubs.acs.org/doi/abs/10.1021/ci0502698
can represent such reactions, 

> Do you know any WEB sites where show an example of annotated mass spectra?
Actually, the only web site / database I am aware of 
which has annotations of fragment peaks is MassBank,
with an example on p.14 of http://www.massbank.jp/pub/MSSJ2007.pdf
So capturing the (automatically created and/or manually curated) 
sum formula for a fragment should definitely be covered by the format,
and I think it readily does. I just have to make up an example.

The idea of the format is to be able to capture all different levels 
of annotations, from simple to complex, so you can have a single file
which accumulates better and better annotations passing through several
annotation programs and human curators.

Yours,
Steffen

Re: [Msi-workgroups-exchange-format] Invitation to draft a standard for annotated mass spectra

[Peter Murray-R. <pm...@ca...>]

Christoph Steinbeck wrote:
> Hi all,
> 
> I just joined the MSI exchange mailing list. As one of the organizers of
> this metabolomics workshop at EBI, I would very much like see this
> exchange format for annotated mass spectra developed.
> 
> As one of the authors of [4], metioned below, I would like to point out
> that CMLSpect was by no means designed for NMR only.
> In fact, we focused on a general solution for coding spectra, with the
> particular goal of facilitating annotations of spectra with structure
> and other features, not so much for holding the raw data.
>
Agreed. It would certainly manage GC-MS, etc.

P.

Re: [Msi-workgroups-exchange-format] Invitation to draft a standard for annotated mass spectra

[Jones, A. <And...@li...>]

Hi all,

I work on the PSI's data formats and have looked at MSI format requirements in the past, so I'm happy to advise as to how the two might overlap.

Is there a relevant part of a reporting requirements document for what you would like to capture? As you probably know, the PSI's approach to this problem has been to separate into two formats, one for representing just the spectra collected and instrument parameters (mzML) and the other for representing the peptides / proteins that spectra correspond with (AnalysisXML).

I doubt that much of AnalysisXML will help metabolomics, since it is built around common peptide/protein identification software. However, my guess is that mzML should fit your requirements pretty well, and might require no modification at all. Do you have any example data sets in native format so I can understand the requirements a bit better.

Cheers
Andy


> -----Original Message-----
> From: Steffen Neumann [mailto:sne...@ip...]
> Sent: 12 February 2009 22:11
> To: msi...@li...
> Subject: [Msi-workgroups-exchange-format] Invitation to draft a standard for
> annotated mass spectra
> 
> Dear all,
> 
> You are receiving this email because you are an active member
> of the mass spectrometry metabolomics community, or have experience
> in designing and drafting (XML based) standards
> for data exchange (or both :-)
> 
> Last month there was a workshop on Metabolomics
> at the EBI in Cambridge[1] and among the participants
> there was great interest in the creation of an exchange format
> for annotated mass spectra.
> 
> Now seems to be a good point in time to do so,
> because we can build on experience from drafting various
> data exchange standards by the Proteome Standards Initiative PSI,
> including their mzML[2] and analysisXML[3] standards,
> and the CML format for annotated NMR spectra[4,5,6].
> 
> We decided to continue the discussion under the umbrella
> of the Exchange format working group[7] of the Metabolomics Standards
> Initiative (MSI). You are invited to join the mailing list[8]
> and help forming a common standard for annotated mass spectra.
> 
> Yours sincerely,
> Steffen Neumann
> 
> [1] http://www.elixir-europe.org/page.php?page=metabolomics_workshop
> [2] http://psidev.info/index.php?q=node/257
> [3] http://www.psidev.info/index.php?q=node/403
> [4] http://pubs.acs.org/doi/abs/10.1021/ci600531a
> [5] http://nmrshiftdb.ice.mpg.de/portal/js_pane/P-
> Results?nmrshiftdbaction=showDetailsFromHome&molNumber=20154202&tab=1
> [6]
> http://nmrshiftdb.ice.mpg.de/download/NmrshiftdbServlet/nmrshiftdb.chemie.uni-
> mainz.de_Kolshorn_2008-12-
> 05_02:38:58_0603.cml?spectrumid=20173793&nmrshiftdbaction=exportspec
> [7] http://msi-workgroups.sourceforge.net/exchange-format/
> [8] http://msi-workgroups.sourceforge.net/index.html#joinmail
> 
> 
> ------------------------------------------------------------------------------
> Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco,
> CA
> -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
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> -Receive a $600 discount off the registration fee with the source code: SFAD
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[Msi-workgroups-exchange-format] Very basic proposal for annotated mass spectra format

[Florian R. <flo...@un...>]

Hi everybody!

I'm working together with Steffen Neumann on the automated analysis of
Tandem MS spectra.
Since our group (The one of Sebastian Boecker, Jena University) had to
find a way to store fragmentation trees, we have tried to combine
CMLSpect and CMLReact to do so. I attach an example of our format
(containing only one edge for clarity).

Spectra (MS1, MS2 or MSn) can be added as SpectrumList as defined by
CMLSpect. Peaks can have a referance to the corresponding ion in the ion
list. Another advantage is that the structure of the ions could be given
using the respective CML tags.
Atoms could receive the same ID in different ions to emphasize that it
is infact the same atom, again as CMLReact suggests.
Another possibility would be a global atom mapping, but that is
currently not conform with CML Specifications. We dropped the idea of an
per reaction atom mapping, because that would produce a lot of
redundancy in the annotation.

I'm far from an expert in designing formats, so this is just a bunch of
ideas. There's plenty of information we have not considered, e.g. adduct
type, isotopes and so on...

Happy about any comments and look forward to work with you on this
standard.

Regards
Florian

Here's the example:

<?xml version="1.0" encoding="UTF-8"?>
<cml xmlns="http://www.xml-cml.org/schema">
   <moleculeList title="ions">
      <molecule id="ion0_C9H7NO" formula="C 9 H 7 N 1 O 1">
         <name>C9H7NO</name>
      </molecule>
      <molecule id="ion1_C8H7N" formula="C 8 H 7 N 1">
         <name>C8H7N</name>
      </molecule>
   </moleculeList>
   <moleculeList title="Neutral loss list">
      <molecule id="nl0_CO" formula="C 1 O 1"/>
         <name>CO</name>
      </molecule>
   </moleculeList>
   <reactionList>
      <reaction>
         <reactantList>
            <reactant>
               <molecule ref="ion0_C9H7NO"/>
            </reactant>
         </reactantList>
         <productList>
            <product role="ion">
               <molecule ref="ion1_C8H7N"/>
            </product>
            <product role="neutral_loss">
               <molecule ref="nl0_CO"/>
            </product>
         </productList>
      </reaction>
   </reactionList>
</cml>
 
-- 
Florian Rasche, PhD Student
Lehrstuhl fuer Bioinformatik
Friedrich-Schiller-Universitaet Jena
Ernst-Abbe-Platz 2
D-07743 Jena, Germany
Phone +49 (0)3641 946456, Fax +49 (0)3641 9-46452
http://bio.informatik.uni-jena.de/

Re: [Msi-workgroups-exchange-format] Invitation to draft a standard for annotated mass spectra

[Christoph S. <ste...@eb...>]

Hi all,

I just joined the MSI exchange mailing list. As one of the organizers of
this metabolomics workshop at EBI, I would very much like see this
exchange format for annotated mass spectra developed.

As one of the authors of [4], metioned below, I would like to point out
that CMLSpect was by no means designed for NMR only.
In fact, we focused on a general solution for coding spectra, with the
particular goal of facilitating annotations of spectra with structure
and other features, not so much for holding the raw data.

Cheers,

Chris

Steffen Neumann wrote:
> Dear all,
> 
> You are receiving this email because you are an active member 
> of the mass spectrometry metabolomics community, or have experience 
> in designing and drafting (XML based) standards 
> for data exchange (or both :-)
> 
> Last month there was a workshop on Metabolomics 
> at the EBI in Cambridge[1] and among the participants 
> there was great interest in the creation of an exchange format 
> for annotated mass spectra. 
> 
> Now seems to be a good point in time to do so, 
> because we can build on experience from drafting various 
> data exchange standards by the Proteome Standards Initiative PSI,
> including their mzML[2] and analysisXML[3] standards, 
> and the CML format for annotated NMR spectra[4,5,6].
> 
> We decided to continue the discussion under the umbrella 
> of the Exchange format working group[7] of the Metabolomics Standards 
> Initiative (MSI). You are invited to join the mailing list[8] 
> and help forming a common standard for annotated mass spectra.
> 
> Yours sincerely, 
> Steffen Neumann
> 
> [1] http://www.elixir-europe.org/page.php?page=metabolomics_workshop
> [2] http://psidev.info/index.php?q=node/257
> [3] http://www.psidev.info/index.php?q=node/403
> [4] http://pubs.acs.org/doi/abs/10.1021/ci600531a 
> [5] http://nmrshiftdb.ice.mpg.de/portal/js_pane/P-Results?nmrshiftdbaction=showDetailsFromHome&molNumber=20154202&tab=1
> [6] http://nmrshiftdb.ice.mpg.de/download/NmrshiftdbServlet/nmrshiftdb.chemie.uni-mainz.de_Kolshorn_2008-12-05_02:38:58_0603.cml?spectrumid=20173793&nmrshiftdbaction=exportspec
> [7] http://msi-workgroups.sourceforge.net/exchange-format/
> [8] http://msi-workgroups.sourceforge.net/index.html#joinmail

-- 
Dr. Christoph Steinbeck
Head of Chemoinformatics and Metabolism
European Bioinformatics Institute (EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD UK
Phone +44 1223 49 2640

What is man but that lofty spirit - that sense of enterprise.
... Kirk, "I, Mudd," stardate 4513.3..

[Msi-workgroups-exchange-format] Invitation to draft a standard for annotated mass spectra

[Steffen N. <sne...@ip...>]

Dear all,

You are receiving this email because you are an active member 
of the mass spectrometry metabolomics community, or have experience 
in designing and drafting (XML based) standards 
for data exchange (or both :-)

Last month there was a workshop on Metabolomics 
at the EBI in Cambridge[1] and among the participants 
there was great interest in the creation of an exchange format 
for annotated mass spectra. 

Now seems to be a good point in time to do so, 
because we can build on experience from drafting various 
data exchange standards by the Proteome Standards Initiative PSI,
including their mzML[2] and analysisXML[3] standards, 
and the CML format for annotated NMR spectra[4,5,6].

We decided to continue the discussion under the umbrella 
of the Exchange format working group[7] of the Metabolomics Standards 
Initiative (MSI). You are invited to join the mailing list[8] 
and help forming a common standard for annotated mass spectra.

Yours sincerely, 
Steffen Neumann

[1] http://www.elixir-europe.org/page.php?page=metabolomics_workshop
[2] http://psidev.info/index.php?q=node/257
[3] http://www.psidev.info/index.php?q=node/403
[4] http://pubs.acs.org/doi/abs/10.1021/ci600531a 
[5] http://nmrshiftdb.ice.mpg.de/portal/js_pane/P-Results?nmrshiftdbaction=showDetailsFromHome&molNumber=20154202&tab=1
[6] http://nmrshiftdb.ice.mpg.de/download/NmrshiftdbServlet/nmrshiftdb.chemie.uni-mainz.de_Kolshorn_2008-12-05_02:38:58_0603.cml?spectrumid=20173793&nmrshiftdbaction=exportspec
[7] http://msi-workgroups.sourceforge.net/exchange-format/
[8] http://msi-workgroups.sourceforge.net/index.html#joinmail

[Msi-workgroups-exchange-format] MIBBI published in August's Nature Biotechnology

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

Dear colleagues,

We would like to inform you that the paper describing the Minimum
Information for Biological and Biomedical Investigations (MIBBI) project
-- http://www.mibbi.org/ -- has been published this month in Nature
Biotechnology. This represents a significant step towards a comprehensive
set complementary reporting guidelines for the biosciences; both by
describing our work to date, and by acting as a beacon for new
participants.

A PDF of the paper is freely-available for download:
http://www.nature.com/nbt/journal/v26/n8/pdf/nbt.1411.pdf

This paper:
1. Describes the foundational work performed by the ever-growing list of
participants in this project.
2. Provides analysis of the various MI specifications registered at the
site (scope, conflicts, etc.), including the MSI's CIMR
3. Addresses the view of funders and publishers on the enforcement of
consensual reporting guidelines.
4. Outlines our plans for future work, which all are strongly encouraged
to monitor, and in which all are invited to participate.

 Any questions can be directed to:
 Chris Taylor
 Susanna-Assunta Sansone
 Dawn Field

 Yours Sincerely,

 Susanna, Chris and Dawn, on behalf of all authors.

 --

[Msi-workgroups-exchange-format] Community consultation on FuGE manuscript

[Andy J. <aj...@cs...>]

Apologies if you receive multiple copies, for groups with an interest in
FuGE:

 

The manuscript describing FuGE has been posted on the Nature Biotech website
as part as the NBT community consultation process on standards. If you would
like to read the draft and post comments, go to
http://www.nature.com/nbt/consult/index.html. It should be noted that the
NBT paper describes the motivation for FuGE and gives a general introduction
to the main concepts. The official specification document on FuGE is
currently in the PSI document process and will be open for public comment
early in 2007. I'll send instructions in a few weeks describing how groups
can participate in the process of getting FuGE to a stable version 1. 

 

Please forward this on to any other groups who may be interested.

 

Best wishes,

Andy Jones

[Msi-workgroups-exchange-format] Data transformation terms - discussion

[Susanna <sa...@eb...>]

Dear Stys,

I am fw your reply to me to the lists - in particular the Ontology and 
Data Processing WGs- so they are e able to comment on this.

Thanks,
Susanna

Dalibor Stys wrote:

> Dear All,
>
> I believe that simple definitions of data transformation are 
> dangerous. These methods are developing, we, for example, in our 
> Expertomica software for chromatography-mass spectrometry use adaptive 
> noise filtration and subtraction of backgroun in each data point. That 
> means that we analyse the information content of the data and subtract 
> the random noise, spikes and the background contributions separately. 
> This is principially impossible to describe by simple terms but it is 
> quite similar to what a qualified operator is doing, i.e. considering 
> how good are the data surrounding each peak and assessing the baseline 
> and the precision by which data may be integrated. We have 
> algoritmised the operator knowledge, added mathematical description of 
> noise and do it automatically.
> Other programs, i.e. Hyperchem, ask you to introduce couple of 
> parameter defined precisely only as mathematical equations inside the 
> program, which are then used for data transformation.
> This is true for MS, NMR, but in principle for any dataset.
> I, actually, suggested some terms but the more I think about it, the 
> more I do not like it. The only absolutely correct way would be the 
> reference to place where the original data may be downloaded, the 
> reference to the software and to all parameters which were used in 
> data analysis.
>
> Best regards
>
> Dalibor Stys
>
> Susanna-A Sansone wrote:
>
>> Dear Ontology and Data WGs,
>>
>> We are collecting these terms for MSI and then feed these in 
>> FuGO/OBI,  here is more info for you:
>>
>> *Definition for Data Transformation* (up for discussion):  The 
>> process of redefining data based on some predefined rules. The values 
>> are redefined based on a specific formula or technique.  This 
>> includes mapping data elements from from a source data format into 
>> destination data.
>>
>> *An example:*
>> NAME:  low_intensity_filter DEF:  A transformation method that 
>> involves removal of low intensity values in a data set.  For 
>> microarrays and gels the threshold for exclusion is usually based on 
>> some estimation of local or global background intensity; for mass 
>> spectrometry and NMR, it is usually based on the signal-to-noise 
>> ratio in the spectrum.
>>
>> Can you please send Daniel your tems, as a tab-delimited file with 
>> the following information in the file:
>>
>> Person Submitting:
>> NAME: DEF:
>> NAME: DEF:
>> NAME: DEF:
>> etc.
>>
>> Thanks,
>> Susanna
>>
>>
>> Susanna-A Sansone wrote:
>>
>>> ***sorry for cross-posting***
>>>
>>> Dear Ontology and Data WGs,
>>> (cc to Exchange, Chemical, Biology WGs fyi)
>>>
>>> We are in the process of collecting terms for **data 
>>> transformation** terms.
>>>
>>> Please, send your list of terms and definitions (if you have these) 
>>> to Daniel Schober -here cc- in an excel sheet.
>>>
>>> Thanks,
>>> Susanna
>>> ------------------------------------------------------------------------ 
>>>
>>>
>>> ------------------------------------------------------------------------- 
>>>
>>> Take Surveys. Earn Cash. Influence the Future of IT
>>> Join SourceForge.net's Techsay panel and you'll get the chance to 
>>> share your
>>> opinions on IT & business topics through brief surveys - and earn cash
>>> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV 
>>>
>>> ------------------------------------------------------------------------ 
>>>
>>>
>>> _______________________________________________
>>> msi-ontology-devel mailing list
>>> msi...@li...
>>> https://lists.sourceforge.net/lists/listinfo/msi-ontology-devel
>>>   
>>
>> ------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------- 
>>
>> Take Surveys. Earn Cash. Influence the Future of IT
>> Join SourceForge.net's Techsay panel and you'll get the chance to 
>> share your
>> opinions on IT & business topics through brief surveys - and earn cash
>> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV 
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Msi-workgroups-data-processing mailing list
>> Msi...@li...
>> https://lists.sourceforge.net/lists/listinfo/msi-workgroups-data-processing 
>>
>>   
>

-- 
Susanna-Assunta Sansone, PhD

NET Project - Coordinator

www.ebi.ac.uk/net-project
	
The European Bioinformatics Institute   email:  sa...@eb...
EMBL Outstation - Hinxton               direct: +44 (0)1223 494 691
Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK                  room: A229            

  

[Msi-workgroups-exchange-format] Data transformation terms - needed

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

***sorry for cross-posting***

Dear Ontology and Data WGs,
(cc to Exchange, Chemical, Biology WGs fyi)

We are in the process of collecting terms for *data transformation* terms.

Please, send your list of terms and definitions (if you have these) to 
Daniel Schober -here cc- in an excel sheet.

Thanks,
Susanna

[Msi-workgroups-exchange-format] joining the exchange format workgroup

[Agnieszka L. <a.l...@uq...>]

I am a new member of the metabolomics society and I am very interested
in generation of metabolomics standards.
In view of my joined use of microarrays and metabonomics I am highly
interested in exchange formats, not only between instruments but also
across technology platforms, in order to combine the data into one
complete picture.
Currently we have data from arrays and NMR metabonomics and we realized
how important it would be to be able to combine the data. 

Regards,

Agnes
 
____________
Dr Agnieszka M. Lichanska (PhD)
Oral Biology and Pathology
School of Dentistry
5th Floor MacGregor Building, St. Lucia
University of Queensland
4072 Australia
Phone:+61 7 3365 3074
Fax: +61 7 3365 1109
e-mail: A.L...@uq...
website: http://www.uq.edu.au/~uqalicha/ 

[Msi-workgroups-exchange-format] special issue of OMICS journal on data standards - announcement

[Susanna <sa...@eb...>]

**** Sorry for the multiple postings *****

Dear All,

This is just a note to flag the *special issue of OMICS journal on data standards*. 

The online version is *free* and available at the following URL:
 http://www.liebertonline.com/toc/omi/10/2;jsessionid=nWAx67n0VoVdcUfY8Z

It containts 20 invited articles, including a piece on MSI, MGED and PSI.

 Best regards,
 Susanna

 --
 Susanna-Assunta Sansone, PhD

 Project Coordinator

 The European Bioinformatics Institute (EBI)
 EMBL Outstation - Hinxton
 Wellcome Trust Genome Campus
 Cambridge CB10 1SD, UK

[Msi-workgroups-exchange-format] PSI sample processing and MSI

[Susanna <sa...@eb...>]

Hi Nigel and Chris,

As agreed in our last joint meeting in Manchster, we are planning our 
work in the chromatography domain as a joint activity with PSI.

We aim to delived a first draft of the CV for the spML format for the 
next PSI meeting in Sept.

I gather that currently http://psidev.sourceforge.net/gps/ is the PSI 
website for spML stuff.
We have the (first) draft of the MIAPE Column Chromatography document 
and now also a excel sheet with all the named associations to 
OntologyTerm in spML and in FuGE (kindly provided by Andy Jones).

Please, let us know waht are your plans/steps for 'reviewing' this model 
for metabolomics applications.

Thanks,
Susanna


-- 
Susanna-Assunta Sansone, PhD

Project Coordinator
	
The European Bioinformatics Institute   email:  sa...@eb...
EMBL Outstation - Hinxton               direct: +44 (0)1223 494 691
Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK                  

Project page: www.ebi.ac.uk/microarray/Projects/tox-nutri/index.html                  

  

Re: [Msi-workgroups-exchange-format] reporting requirements and o ther efforts

[Beger, R. <ric...@fd...>]

Oliver,

Thanks for your input and I agree there are many issues in regard to QC =
that
need to be resolved or at least tested further.  I agree that =
development of
QC standards is not suited for MSI but they are something the =
Metabolomics
Society and other key players need to discuss in the future in regard =
to
best practices for metabolomics. =20

Rick=20

Richard Beger
Ric...@fd...
(work) 870-543-7080
(FAX) 870-543-7686


-----Original Message-----
From: Oliver Fiehn [mailto:of...@uc...]=20
Sent: Friday, July 21, 2006 11:49 AM
To: Beger, Richard; 'Sumner, Lloyd'; 'Susanna'; tw...@uc...;
msi...@li...;
ter...@lo...; 'Robertson, Donald'
Cc: msi...@li...
Subject: Re: [Msi-workgroups-exchange-format] reporting requirements =
and o
ther efforts

Dear Rick,

thanks for that input.=20
Often, I have used a mixed aliquot of samples in a 'reference design', =
which
was quite cumbersome. It would be great to have certified reference
material, say for the 10 most important tissues or body fluids that =
would be
sent off by demand. An interesting question would be how to ensure that =
that
certified reference material doesn't change over time, i.e. during =
storage,
but that's something to explore for those who'd be responsible for =
handling
and maintaining the tissue. By the way, the same idea would rightly =
apply
for proteomics and transcript studies.

Now, to my opinion this is a rational strategy to follow, but several
problems are associated with that: (a) which vectors are you looking =
at? If
you use those vectors with dominant explanatory power (be it PCA or PLS =
or
else), then smaller changes in the QC reference design samples will =
remain
hidden. Curse of dimensionality. (b) Often, there are some compounds =
just
being far more biologically relevant than others. In any multivariate
method, these would receive too little attention. (c) For small studies
with, say, 100 samples, this will almost certainly work. For larger =
studies,
say 20,000 samples, there is inevitably some machine drift, especially =
for
MS approaches..=20

Surely, we should follow this up. As for the 'Standards' initiative, my =
take
is that this cannot be a 'reporting standard' right now, other than =
that
people should report what kind of QC they have taken. It might be added =
to
'best practice' documents, though, once somebody publishes his/her =
long-time
studies with such reference design QCs.=20

I would love to see a discussion around this topic. To my personal =
opinion,
we need public metabolome databases that are based on and validated by =
QC.
Otherwise, we'll continue seeing papers stating that groups A,B,C are
different without being able to compare these differences to 'former
experiments' and 'similar lines / experimental designs' that would =
comprise
groups D-Z. Thanks for starting this, Rick!

Oliver


.=20

Oliver Fiehn, Assoc. Prof. MCB
- Metabolomics -
UC Davis Genome Center
GBSF Building room 1315=A0
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

-----Original Message-----
From: Beger, Richard [mailto:ric...@fd...]=20
Sent: Freitag, 21. Juli 2006 09:16
To: 'Sumner, Lloyd'; Susanna; tw...@uc...;
msi...@li...;
ter...@lo...; 'Robertson, Donald'
Cc: of...@uc...; =
msi...@li...
Subject: RE: [Msi-workgroups-exchange-format] reporting requirements =
and o
ther efforts

Hi All,

It has been suggested to me that QC during GCMS and LCMS Metabolomics
experiments can be achieved by mixing contributions from all samples =
used in
a Metabolomics study and evaluating this sample every 10 or so samples. =
 If
the QC samples cluster together in the center of the PCA of all the =
samples
analyzed, it is reasonable to assume that QC is OK.  When one of the QC
samples starts to wonder away from the QC cluster, it would a sign that =
the
GCMS or LCMS system isn't functioning the same way as it was when they =
all
clustered together.  I think this is something that has a reasonable =
chance
of working.  My question is whether we want or could to have a mixed QC
sample that every body could use in all Metabolomics experiments, along =
the
lines of what is happening in
MACQ,.(http://www.fda.gov/nctr/science/centers/toxicoinformatics/maqc/in=
dex.
htm ), instead of making QC samples that each scientist would have to
produce before their experiment for genomics experiments.  It might be =
that
we need QC samples for each type of sample (urine, serum, plant, =
tissue).
What does everybody think?  Is QC something that MSI wants to even =
think
about?

Best,
Rick

Richard Beger
Branch Chief, Center for Metabolomics
Division of Systems Toxicology
National Center for Toxicological Research
3900 NCTR Road
Jefferson, AR 72079
Ric...@fd...
(work) 870-543-7080
(FAX) 870-543-7686

-----Original Message-----
From: Sumner, Lloyd [mailto:lws...@no...]=20
Sent: Thursday, July 20, 2006 12:24 PM
To: Susanna; tw...@uc...;
msi...@li...;
ter...@lo...
Cc: of...@uc...; =
msi...@li...
Subject: Re: [Msi-workgroups-exchange-format] reporting requirements =
and
other efforts

Hello Susanna et al,

The PSI chromatography info is very consistent with what we have for =
the
MSI; however the PSI doc is better structured and appears to have a few
more details than the MSI.  My plan was to further trim down the MSI
document towards a more minimum concept, but we may reconsider this
based on the details associated with PSI doc.

Thanks for the input.

Lloyd

-----Original Message-----
From: Susanna [mailto:sa...@eb...]=20
Sent: Thursday, July 20, 2006 7:47 AM
To: Sumner, Lloyd; tw...@uc...;
msi...@li...
Cc: of...@uc...;
msi...@li...
Subject: reporting requirements and other efforts

Dear Lloyd and Teresa,

I have not heard from you on this matter, so I fw the message again=20
(please see below).

There are few reporting requirements, being developed by related=20
communities, for example HUPO-PSI for chromatography and MS. But I am=20
not sure I understand how these are evaluated and/or referred to from=20
your reporting document.

The Ontology WG is working closely with the Format WG, here cc, to=20
evaluate existing standards such as HUPO-PSI. It would be nice to know=20
that we are working in the same directions.

Look forward to hearing from you,
Susanna

Susanna-Assunta Sansone wrote:

>Dear Lloyd and Teresa,
>
>would like to bring to your attention the MIAPE Column Chromatography
>document by the HUPO-PSI group.
>
>I guess it does overlap with the "Proposed Minimum Metadata Relative =
to
>Chromatography" section in your document.
>
>See email and link below.
>
>Best regards,
>Susanna
>
>
>---------------------------- Original Message
----------------------------
>Subject: [Psidev-gps-dev] MIAPE Column Chromatography
>From:    "Norman Paton" <no...@cs...>
>Date:    Tue, June 27, 2006 12:07 pm
>To:      psi...@li...
>-----------------------------------------------------------------------=

---
>
>
>An initial draft of a MIAPE Column Chromatography document has been=20
>produced, which is available from:
>
>http://www.cs.man.ac.uk/~norm/MIAPE/
>
>The next step in the development of the proposal is validation by=20
>capturing example data sets, to try to establish whether or not the=20
>proposal is appropriate in terms of scope, level of detail, etc.  The=20
>above URL also provides a template that can be used to describe data
sets
>using the MIAPE Column Chromatography draft, and some example data
sets
>that have already been captured.  As such:
>
>1. If you would be willing to help validate the proposal by describing
an
>experiment using the template, this would be valuable input to the=20
>process. Please either just go ahead and do so, and/or discuss the=20
>process with Andy Jones or me. We will try to provide
>guidance/clarification where this is required.
>
>2. If you aren't in a position to help with validation, we would still
be
>interested to receive your comments on the draft MIAPE document or  =
the
>utility of the examples provided.
>
>Regards, Norman
>
>
>
>Using Tomcat but need to do more? Need to support web services,
security?
>Get stuff done quickly with pre-integrated technology to make your job
>easier Download IBM WebSphere Application Server v.1.0.1 based on
Apache
>Geronimo
>http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=
=3D12164
2
>_______________________________________________
>Psidev-gps-dev mailing list
>Psi...@li...
>https://lists.sourceforge.net/lists/listinfo/psidev-gps-dev
>
>
> =20
>

--=20
Susanna-Assunta Sansone, PhD

Nutri/Toxicogenomics Project Coordinator, EBI
=09
The European Bioinformatics Institute   email:  sa...@eb...
EMBL Outstation - Hinxton               direct: +44 (0)1223 494 691
Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK                 =20

Project page: www.ebi.ac.uk/microarray/Projects/tox-nutri/index.html


 =20




------------------------------------------------------------------------=
-
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share =
your
opinions on IT & business topics through brief surveys -- and earn cash
http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D=
DEVDEV
_______________________________________________
Msi-workgroups-exchange-format mailing list
Msi...@li...
https://lists.sourceforge.net/lists/listinfo/msi-workgroups-exchange-for=
mat



------------------------------------------------------------------------=
-
Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share =
your
opinions on IT & business topics through brief surveys -- and earn cash
http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D=
DEVDEV
_______________________________________________
Msi-workgroups-exchange-format mailing list
Msi...@li...
https://lists.sourceforge.net/lists/listinfo/msi-workgroups-exchange-for=
mat

Re: [Msi-workgroups-exchange-format] reporting requirements and o ther efforts

[Oliver F. <of...@uc...>]

Dear Rick,

thanks for that input.=20
Often, I have used a mixed aliquot of samples in a 'reference design', =
which
was quite cumbersome. It would be great to have certified reference
material, say for the 10 most important tissues or body fluids that =
would be
sent off by demand. An interesting question would be how to ensure that =
that
certified reference material doesn't change over time, i.e. during =
storage,
but that's something to explore for those who'd be responsible for =
handling
and maintaining the tissue. By the way, the same idea would rightly =
apply
for proteomics and transcript studies.

Now, to my opinion this is a rational strategy to follow, but several
problems are associated with that: (a) which vectors are you looking at? =
If
you use those vectors with dominant explanatory power (be it PCA or PLS =
or
else), then smaller changes in the QC reference design samples will =
remain
hidden. Curse of dimensionality. (b) Often, there are some compounds =
just
being far more biologically relevant than others. In any multivariate
method, these would receive too little attention. (c) For small studies
with, say, 100 samples, this will almost certainly work. For larger =
studies,
say 20,000 samples, there is inevitably some machine drift, especially =
for
MS approaches..=20

Surely, we should follow this up. As for the 'Standards' initiative, my =
take
is that this cannot be a 'reporting standard' right now, other than that
people should report what kind of QC they have taken. It might be added =
to
'best practice' documents, though, once somebody publishes his/her =
long-time
studies with such reference design QCs.=20

I would love to see a discussion around this topic. To my personal =
opinion,
we need public metabolome databases that are based on and validated by =
QC.
Otherwise, we'll continue seeing papers stating that groups A,B,C are
different without being able to compare these differences to 'former
experiments' and 'similar lines / experimental designs' that would =
comprise
groups D-Z. Thanks for starting this, Rick!

Oliver


.=20

Oliver Fiehn, Assoc. Prof. MCB
- Metabolomics -
UC Davis Genome Center
GBSF Building room 1315=A0
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

-----Original Message-----
From: Beger, Richard [mailto:ric...@fd...]=20
Sent: Freitag, 21. Juli 2006 09:16
To: 'Sumner, Lloyd'; Susanna; tw...@uc...;
msi...@li...;
ter...@lo...; 'Robertson, Donald'
Cc: of...@uc...; =
msi...@li...
Subject: RE: [Msi-workgroups-exchange-format] reporting requirements and =
o
ther efforts

Hi All,

It has been suggested to me that QC during GCMS and LCMS Metabolomics
experiments can be achieved by mixing contributions from all samples =
used in
a Metabolomics study and evaluating this sample every 10 or so samples.  =
If
the QC samples cluster together in the center of the PCA of all the =
samples
analyzed, it is reasonable to assume that QC is OK.  When one of the QC
samples starts to wonder away from the QC cluster, it would a sign that =
the
GCMS or LCMS system isn't functioning the same way as it was when they =
all
clustered together.  I think this is something that has a reasonable =
chance
of working.  My question is whether we want or could to have a mixed QC
sample that every body could use in all Metabolomics experiments, along =
the
lines of what is happening in
MACQ,.(http://www.fda.gov/nctr/science/centers/toxicoinformatics/maqc/ind=
ex.
htm ), instead of making QC samples that each scientist would have to
produce before their experiment for genomics experiments.  It might be =
that
we need QC samples for each type of sample (urine, serum, plant, =
tissue).
What does everybody think?  Is QC something that MSI wants to even think
about?

Best,
Rick

Richard Beger
Branch Chief, Center for Metabolomics
Division of Systems Toxicology
National Center for Toxicological Research
3900 NCTR Road
Jefferson, AR 72079
Ric...@fd...
(work) 870-543-7080
(FAX) 870-543-7686

-----Original Message-----
From: Sumner, Lloyd [mailto:lws...@no...]=20
Sent: Thursday, July 20, 2006 12:24 PM
To: Susanna; tw...@uc...;
msi...@li...;
ter...@lo...
Cc: of...@uc...; =
msi...@li...
Subject: Re: [Msi-workgroups-exchange-format] reporting requirements and
other efforts

Hello Susanna et al,

The PSI chromatography info is very consistent with what we have for the
MSI; however the PSI doc is better structured and appears to have a few
more details than the MSI.  My plan was to further trim down the MSI
document towards a more minimum concept, but we may reconsider this
based on the details associated with PSI doc.

Thanks for the input.

Lloyd

-----Original Message-----
From: Susanna [mailto:sa...@eb...]=20
Sent: Thursday, July 20, 2006 7:47 AM
To: Sumner, Lloyd; tw...@uc...;
msi...@li...
Cc: of...@uc...;
msi...@li...
Subject: reporting requirements and other efforts

Dear Lloyd and Teresa,

I have not heard from you on this matter, so I fw the message again=20
(please see below).

There are few reporting requirements, being developed by related=20
communities, for example HUPO-PSI for chromatography and MS. But I am=20
not sure I understand how these are evaluated and/or referred to from=20
your reporting document.

The Ontology WG is working closely with the Format WG, here cc, to=20
evaluate existing standards such as HUPO-PSI. It would be nice to know=20
that we are working in the same directions.

Look forward to hearing from you,
Susanna

Susanna-Assunta Sansone wrote:

>Dear Lloyd and Teresa,
>
>would like to bring to your attention the MIAPE Column Chromatography
>document by the HUPO-PSI group.
>
>I guess it does overlap with the "Proposed Minimum Metadata Relative to
>Chromatography" section in your document.
>
>See email and link below.
>
>Best regards,
>Susanna
>
>
>---------------------------- Original Message
----------------------------
>Subject: [Psidev-gps-dev] MIAPE Column Chromatography
>From:    "Norman Paton" <no...@cs...>
>Date:    Tue, June 27, 2006 12:07 pm
>To:      psi...@li...
>-----------------------------------------------------------------------
---
>
>
>An initial draft of a MIAPE Column Chromatography document has been=20
>produced, which is available from:
>
>http://www.cs.man.ac.uk/~norm/MIAPE/
>
>The next step in the development of the proposal is validation by=20
>capturing example data sets, to try to establish whether or not the=20
>proposal is appropriate in terms of scope, level of detail, etc.  The=20
>above URL also provides a template that can be used to describe data
sets
>using the MIAPE Column Chromatography draft, and some example data
sets
>that have already been captured.  As such:
>
>1. If you would be willing to help validate the proposal by describing
an
>experiment using the template, this would be valuable input to the=20
>process. Please either just go ahead and do so, and/or discuss the=20
>process with Andy Jones or me. We will try to provide
>guidance/clarification where this is required.
>
>2. If you aren't in a position to help with validation, we would still
be
>interested to receive your comments on the draft MIAPE document or  the
>utility of the examples provided.
>
>Regards, Norman
>
>
>
>Using Tomcat but need to do more? Need to support web services,
security?
>Get stuff done quickly with pre-integrated technology to make your job
>easier Download IBM WebSphere Application Server v.1.0.1 based on
Apache
>Geronimo
>http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D=
12164
2
>_______________________________________________
>Psidev-gps-dev mailing list
>Psi...@li...
>https://lists.sourceforge.net/lists/listinfo/psidev-gps-dev
>
>
> =20
>

--=20
Susanna-Assunta Sansone, PhD

Nutri/Toxicogenomics Project Coordinator, EBI
=09
The European Bioinformatics Institute   email:  sa...@eb...
EMBL Outstation - Hinxton               direct: +44 (0)1223 494 691
Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK                 =20

Project page: www.ebi.ac.uk/microarray/Projects/tox-nutri/index.html


 =20




-------------------------------------------------------------------------=

Take Surveys. Earn Cash. Influence the Future of IT
Join SourceForge.net's Techsay panel and you'll get the chance to share =
your
opinions on IT & business topics through brief surveys -- and earn cash
http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D=
DEVDEV
_______________________________________________
Msi-workgroups-exchange-format mailing list
Msi...@li...
https://lists.sourceforge.net/lists/listinfo/msi-workgroups-exchange-form=
at

Re: [Msi-workgroups-exchange-format] reporting requirements and o ther efforts

[Beger, R. <ric...@fd...>]

Hi All,

It has been suggested to me that QC during GCMS and LCMS Metabolomics
experiments can be achieved by mixing contributions from all samples used in
a Metabolomics study and evaluating this sample every 10 or so samples.  If
the QC samples cluster together in the center of the PCA of all the samples
analyzed, it is reasonable to assume that QC is OK.  When one of the QC
samples starts to wonder away from the QC cluster, it would a sign that the
GCMS or LCMS system isn't functioning the same way as it was when they all
clustered together.  I think this is something that has a reasonable chance
of working.  My question is whether we want or could to have a mixed QC
sample that every body could use in all Metabolomics experiments, along the
lines of what is happening in
MACQ,.(http://www.fda.gov/nctr/science/centers/toxicoinformatics/maqc/index.
htm ), instead of making QC samples that each scientist would have to
produce before their experiment for genomics experiments.  It might be that
we need QC samples for each type of sample (urine, serum, plant, tissue).
What does everybody think?  Is QC something that MSI wants to even think
about?

Best,
Rick

Richard Beger
Branch Chief, Center for Metabolomics
Division of Systems Toxicology
National Center for Toxicological Research
3900 NCTR Road
Jefferson, AR 72079
Ric...@fd...
(work) 870-543-7080
(FAX) 870-543-7686

-----Original Message-----
From: Sumner, Lloyd [mailto:lws...@no...] 
Sent: Thursday, July 20, 2006 12:24 PM
To: Susanna; tw...@uc...;
msi...@li...;
ter...@lo...
Cc: of...@uc...; msi...@li...
Subject: Re: [Msi-workgroups-exchange-format] reporting requirements and
other efforts

Hello Susanna et al,

The PSI chromatography info is very consistent with what we have for the
MSI; however the PSI doc is better structured and appears to have a few
more details than the MSI.  My plan was to further trim down the MSI
document towards a more minimum concept, but we may reconsider this
based on the details associated with PSI doc.

Thanks for the input.

Lloyd

-----Original Message-----
From: Susanna [mailto:sa...@eb...] 
Sent: Thursday, July 20, 2006 7:47 AM
To: Sumner, Lloyd; tw...@uc...;
msi...@li...
Cc: of...@uc...;
msi...@li...
Subject: reporting requirements and other efforts

Dear Lloyd and Teresa,

I have not heard from you on this matter, so I fw the message again 
(please see below).

There are few reporting requirements, being developed by related 
communities, for example HUPO-PSI for chromatography and MS. But I am 
not sure I understand how these are evaluated and/or referred to from 
your reporting document.

The Ontology WG is working closely with the Format WG, here cc, to 
evaluate existing standards such as HUPO-PSI. It would be nice to know 
that we are working in the same directions.

Look forward to hearing from you,
Susanna

Susanna-Assunta Sansone wrote:

>Dear Lloyd and Teresa,
>
>would like to bring to your attention the MIAPE Column Chromatography
>document by the HUPO-PSI group.
>
>I guess it does overlap with the "Proposed Minimum Metadata Relative to
>Chromatography" section in your document.
>
>See email and link below.
>
>Best regards,
>Susanna
>
>
>---------------------------- Original Message
----------------------------
>Subject: [Psidev-gps-dev] MIAPE Column Chromatography
>From:    "Norman Paton" <no...@cs...>
>Date:    Tue, June 27, 2006 12:07 pm
>To:      psi...@li...
>-----------------------------------------------------------------------
---
>
>
>An initial draft of a MIAPE Column Chromatography document has been 
>produced, which is available from:
>
>http://www.cs.man.ac.uk/~norm/MIAPE/
>
>The next step in the development of the proposal is validation by 
>capturing example data sets, to try to establish whether or not the 
>proposal is appropriate in terms of scope, level of detail, etc.  The 
>above URL also provides a template that can be used to describe data
sets
>using the MIAPE Column Chromatography draft, and some example data
sets
>that have already been captured.  As such:
>
>1. If you would be willing to help validate the proposal by describing
an
>experiment using the template, this would be valuable input to the 
>process. Please either just go ahead and do so, and/or discuss the 
>process with Andy Jones or me. We will try to provide
>guidance/clarification where this is required.
>
>2. If you aren't in a position to help with validation, we would still
be
>interested to receive your comments on the draft MIAPE document or  the
>utility of the examples provided.
>
>Regards, Norman
>
>
>
>Using Tomcat but need to do more? Need to support web services,
security?
>Get stuff done quickly with pre-integrated technology to make your job
>easier Download IBM WebSphere Application Server v.1.0.1 based on
Apache
>Geronimo
>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=12164
2
>_______________________________________________
>Psidev-gps-dev mailing list
>Psi...@li...
>https://lists.sourceforge.net/lists/listinfo/psidev-gps-dev
>
>
>  
>

-- 
Susanna-Assunta Sansone, PhD

Nutri/Toxicogenomics Project Coordinator, EBI
	
The European Bioinformatics Institute   email:  sa...@eb...
EMBL Outstation - Hinxton               direct: +44 (0)1223 494 691
Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK                  

Project page: www.ebi.ac.uk/microarray/Projects/tox-nutri/index.html


  




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_______________________________________________
Msi-workgroups-exchange-format mailing list
Msi...@li...
https://lists.sourceforge.net/lists/listinfo/msi-workgroups-exchange-format

Re: [Msi-workgroups-exchange-format] reporting requirements and other efforts

[Sumner, L. <lws...@no...>]

Hello Susanna et al,

The PSI chromatography info is very consistent with what we have for the
MSI; however the PSI doc is better structured and appears to have a few
more details than the MSI.  My plan was to further trim down the MSI
document towards a more minimum concept, but we may reconsider this
based on the details associated with PSI doc.

Thanks for the input.

Lloyd

-----Original Message-----
From: Susanna [mailto:sa...@eb...]=20
Sent: Thursday, July 20, 2006 7:47 AM
To: Sumner, Lloyd; tw...@uc...;
msi...@li...
Cc: of...@uc...;
msi...@li...
Subject: reporting requirements and other efforts

Dear Lloyd and Teresa,

I have not heard from you on this matter, so I fw the message again=20
(please see below).

There are few reporting requirements, being developed by related=20
communities, for example HUPO-PSI for chromatography and MS. But I am=20
not sure I understand how these are evaluated and/or referred to from=20
your reporting document.

The Ontology WG is working closely with the Format WG, here cc, to=20
evaluate existing standards such as HUPO-PSI. It would be nice to know=20
that we are working in the same directions.

Look forward to hearing from you,
Susanna

Susanna-Assunta Sansone wrote:

>Dear Lloyd and Teresa,
>
>would like to bring to your attention the MIAPE Column Chromatography
>document by the HUPO-PSI group.
>
>I guess it does overlap with the "Proposed Minimum Metadata Relative to
>Chromatography" section in your document.
>
>See email and link below.
>
>Best regards,
>Susanna
>
>
>---------------------------- Original Message
----------------------------
>Subject: [Psidev-gps-dev] MIAPE Column Chromatography
>From:    "Norman Paton" <no...@cs...>
>Date:    Tue, June 27, 2006 12:07 pm
>To:      psi...@li...
>-----------------------------------------------------------------------
---
>
>
>An initial draft of a MIAPE Column Chromatography document has been=20
>produced, which is available from:
>
>http://www.cs.man.ac.uk/~norm/MIAPE/
>
>The next step in the development of the proposal is validation by=20
>capturing example data sets, to try to establish whether or not the=20
>proposal is appropriate in terms of scope, level of detail, etc.  The=20
>above URL also provides a template that can be used to describe data
sets
>using the MIAPE Column Chromatography draft, and some example data
sets
>that have already been captured.  As such:
>
>1. If you would be willing to help validate the proposal by describing
an
>experiment using the template, this would be valuable input to the=20
>process. Please either just go ahead and do so, and/or discuss the=20
>process with Andy Jones or me. We will try to provide
>guidance/clarification where this is required.
>
>2. If you aren't in a position to help with validation, we would still
be
>interested to receive your comments on the draft MIAPE document or  the
>utility of the examples provided.
>
>Regards, Norman
>
>
>
>Using Tomcat but need to do more? Need to support web services,
security?
>Get stuff done quickly with pre-integrated technology to make your job
>easier Download IBM WebSphere Application Server v.1.0.1 based on
Apache
>Geronimo
>http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D=
12164
2
>_______________________________________________
>Psidev-gps-dev mailing list
>Psi...@li...
>https://lists.sourceforge.net/lists/listinfo/psidev-gps-dev
>
>
> =20
>

--=20
Susanna-Assunta Sansone, PhD

Nutri/Toxicogenomics Project Coordinator, EBI
=09
The European Bioinformatics Institute   email:  sa...@eb...
EMBL Outstation - Hinxton               direct: +44 (0)1223 494 691
Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK                 =20

Project page: www.ebi.ac.uk/microarray/Projects/tox-nutri/index.html


 =20

[Msi-workgroups-exchange-format] reporting requirements and other efforts

[Susanna <sa...@eb...>]

Dear Lloyd and Teresa,

I have not heard from you on this matter, so I fw the message again 
(please see below).

There are few reporting requirements, being developed by related 
communities, for example HUPO-PSI for chromatography and MS. But I am 
not sure I understand how these are evaluated and/or referred to from 
your reporting document.

The Ontology WG is working closely with the Format WG, here cc, to 
evaluate existing standards such as HUPO-PSI. It would be nice to know 
that we are working in the same directions.

Look forward to hearing from you,
Susanna

Susanna-Assunta Sansone wrote:

>Dear Lloyd and Teresa,
>
>would like to bring to your attention the MIAPE Column Chromatography
>document by the HUPO-PSI group.
>
>I guess it does overlap with the "Proposed Minimum Metadata Relative to
>Chromatography" section in your document.
>
>See email and link below.
>
>Best regards,
>Susanna
>
>
>---------------------------- Original Message ----------------------------
>Subject: [Psidev-gps-dev] MIAPE Column Chromatography
>From:    "Norman Paton" <no...@cs...>
>Date:    Tue, June 27, 2006 12:07 pm
>To:      psi...@li...
>--------------------------------------------------------------------------
>
>
>An initial draft of a MIAPE Column Chromatography document has been 
>produced, which is available from:
>
>http://www.cs.man.ac.uk/~norm/MIAPE/
>
>The next step in the development of the proposal is validation by 
>capturing example data sets, to try to establish whether or not the 
>proposal is appropriate in terms of scope, level of detail, etc.  The 
>above URL also provides a template that can be used to describe data  sets
>using the MIAPE Column Chromatography draft, and some example data  sets
>that have already been captured.  As such:
>
>1. If you would be willing to help validate the proposal by describing  an
>experiment using the template, this would be valuable input to the 
>process. Please either just go ahead and do so, and/or discuss the 
>process with Andy Jones or me. We will try to provide
>guidance/clarification where this is required.
>
>2. If you aren't in a position to help with validation, we would still  be
>interested to receive your comments on the draft MIAPE document or  the
>utility of the examples provided.
>
>Regards, Norman
>
>
>
>Using Tomcat but need to do more? Need to support web services, security?
>Get stuff done quickly with pre-integrated technology to make your job
>easier Download IBM WebSphere Application Server v.1.0.1 based on Apache
>Geronimo
>http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>_______________________________________________
>Psidev-gps-dev mailing list
>Psi...@li...
>https://lists.sourceforge.net/lists/listinfo/psidev-gps-dev
>
>
>  
>

-- 
Susanna-Assunta Sansone, PhD

Nutri/Toxicogenomics Project Coordinator, EBI
	
The European Bioinformatics Institute   email:  sa...@eb...
EMBL Outstation - Hinxton               direct: +44 (0)1223 494 691
Wellcome Trust Genome Campus            fax: +44 (0)1223 494 468
Cambridge CB10 1SD, UK                  

Project page: www.ebi.ac.uk/microarray/Projects/tox-nutri/index.html