Re: [Psidev-pi-dev] storing intermediate results in mzML

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

This reminds me that I noticed we have a problem with the PSI website. If you
follow the links from Groups to Proteomics Informatics on the PSI site, you get
this page: http://psidev.info/index.php?q=node/70 which is unclear what it
contains.

I don't know how you can actually browse to the main page
(http://psidev.info/index.php?q=node/319).

And even worse... if you browse via Workgroups, you get to this page:
http://psidev.info/index.php?q=node/40 

Would someone be able to fix these please? All links to Proteomics Informatics
should go here: http://psidev.info/index.php?q=node/319

thanks
Andy





> -----Original Message-----
> From: David Creasy [mailto:dc...@ma...]
> Sent: 15 December 2008 16:13
> To: Richard Scheltema
> Cc: psi...@li...
> Subject: Re: [Psidev-pi-dev] storing intermediate results in mzML
> 
> Hi Richard,
> 
> You've posted this to the analysisXML list.
> I think you should post it to:
>    psi...@li...
> Sorry for any confusion between the two lists.
> 
>  > Another thing, I
>  > once heard somebody mention AnalysisML to be something along these
>  > lines, however this project seems to have suffered a fatal end as I
>  > cannot find anything?
> 
> We're still alive (I think!), but I don't think we have what you want:
> 
> http://psidev.info/index.php?q=node/319
> 
> David
> 
> 
> Richard Scheltema wrote:
> > Dear all,
> >
> > I'm writing a metabolomics Java library for my processing software
> > targeted towards high resolution LC/MS data (components like: peak
> > picking, noise detection, etc). The basic element for this library is a
> > mass chromatogram (x-axis time, y-axis intensity). In order to deal with
> > the size of the datasets, enable other people to easily write
> > components, etc. an intermediate file format is required. I've already
> > defined one myself to see what would be required for a really dynamic
> > pipeline and created a library on top of it. In order to hop on the
> > international standards bandwagon I would off course like to move to a
> > recognized standard like mzML. However, this _seems_ to fall short of my
> > requirements. I've been browsing through this list and the standards
> > document and tried to implement something, but I can't seem to figure
> > out how to approach this.
> >
> > What I would like to be able to do is store the following pieces of
> > information:
> >
> > - Multiple runs in a single file
> >  From the specification document: "A run in mzML should correspond to a
> > single, consecutive and coherent set of scans on an instrument". This
> > means that I essentially can only store data from a single raw file? I
> > would like to do mix-models (see sets).
> >
> > - MassChromatograms (single mass)
> > I would like to ubiquitously store mass chromatograms picked from the
> > raw data. This means that both mass chromatograms made from centroid as
> > well as profile data need to be stored. There is the option to store
> > chromatogram data, but this seems limited to '2D' data where mass
> > chromatogram data build with profile data needs '3D' data. In order to
> > solve this the accession="MS:1000627" name="selected ion current
> > chromatogram" needs sub-children? Or can it be set globally in the
> > header or run, but then I would like to be able to mix models (see sets).
> >
> > - BackgroundIons
> > The use of background ions are part of the pipeline. To store this an
> > addition to the CV needs to be made.
> >  name: backgroundion chromatogram
> >  is_a: chromatogram type (MS:1000626)
> >  definition: chromatogram created by creating an array of a ubiquitously
> > present mass.
> >
> > - sets
> > The goal of the pipeline is to combine information from lots of
> > measurements (biological, technical replicates, different machines, etc)
> > and do perform various analysis methods. This means for example that
> > background ions or mass chromatograms from various measurements need to
> > be combined into sets. Different operations and visualizations are then
> > possible on the data stored in the files. The same as the different runs
> > applies here. Another option would be to make sets of sets, which means
> > that the relation needs to be recursive. I can probably solve some of
> > the issues with id-fields, but that would make it hard to parse for
> > other people and sort of rule out the recursive relation.
> >
> >
> > I can off course solve a lot with the use of userParam tags, but then
> > other people will have a hard time reading the data. Another thing, I
> > once heard somebody mention AnalysisML to be something along these
> > lines, however this project seems to have suffered a fatal end as I
> > cannot find anything? Am I trying to use mzML outside of its boundries?
> > If so, is a viable alternative available which I have so far been unable
> > to find?
> >
> >
> > Cheers,
> > Richard
> >
> 
> --
> David Creasy
> Matrix Science
> 64 Baker Street
> London W1U 7GB, UK
> Tel: +44 (0)20 7486 1050
> Fax: +44 (0)20 7224 1344
> 
> dc...@ma...
> http://www.matrixscience.com
> 
> Matrix Science Ltd. is registered in England and Wales
> Company number 3533898
> 
> ------------------------------------------------------------------------------
> SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada.
> The future of the web can't happen without you.  Join us at MIX09 to help
> pave the way to the Next Web now. Learn more and register at
> http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/
> _______________________________________________
> Psidev-pi-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev