psidev-ms-dev — Mass spectroscopy standard development

[Psidev-ms-dev] Announcement next PSI autumn workshop in Geneva, Sept 4-6

[Pierre-Alain B. <pie...@is...>]

Dear all PSI members and participants,

it's a pleasure for us to make a first announcement for the next PSI 
workshop in Geneva next September.

As already proposed in Siena, we will have an additional PSI autumn 
workshop this year, to tackle the plethora of tasks more efficiently. 
The workshop will be held in Geneva, at the Swiss Institute of 
Bioinformatics. The dates are September 4-6 (2.5 days, from Sunday noon 
to Tuesday pm). This is just after the annual HUPO congress in Munich, 
so that particularly our overseas members do not have to organise a 
second trip to Europe in a two weeks period.

This PSI autumn workshop will be locally organised by Christine Hoogland 
and myself.

A number of practical activities are planed or under planing for this 
summer. They will be essentially be reported at HUPO in Munich.
At the workshop, according to the PSI group coordinators, we tentatively 
plan to follow the implementations for PSI-MI, to finalise the 
management and maintainance of CVs for mzData and mzIdent, to launch the 
first version of mzIdent, to finalise some MIAPE documents, to make 
practical progresses on Gel-ML, to make clear decisions about GPS 
implementations and to progress on implementation of PTMs. The workshop 
will have clearly defined practical goals.

The programme and more detailed information will be available on the PSI 
sourceforge website soon (http://psidev.sourceforge.net)

We are currently looking for sponsors to cover some of the logistical 
and gastronomical costs. Any interested body to participate as sponsor 
of this event can contact us directly.

See you soon in Geneva,

Christine Hoogland and Pierre-Alain Binz
Swiss Institute of Bioinformatics
Proteome Informatics Group
1, Rue Michel Servet
CH-1211 Geneve 4
Switzerland
- - - - - - - - - - - - - - - - -
Tel: +41-22-379 50 50
Fax: +41-22-379 58 58

[Psidev-ms-dev] problems with using IEEE-754 in mzData

[Geer, L. (NIH/NLM/NCBI) <le...@nc...>]

Hi,

I've only recently read the mzData standard and don't know what state it is
in, so I hope you will excuse the following comments.  

From an implementation viewpoint, the use of the IEEE-754 floating point
representation to specify the spectra creates several issues:

1. Uneven implementation of IEEE-754 on various platforms:  For example,
IEEE-754 allows "denormalized" floating point values.  It is my
understanding that this subset of the standard is implemented on some
platforms/compilers (e.g. windows) and not on others (e.g. mac).  So unless
an extensive conversion API is written, a float point exception or other
problems could arise from files moved across platform.

2. The IEEE-754 encoded spectral data can not be validated by an XML parser
and is not directly accessible from XML parsing api's.  As far as an XML
parser knows, the spectral data is an opaque blob.  If the data were stored
as XML floats or doubles, the XML parser could validate the data and provide
quick access to the individual peaks.  Otherwise the validation and access
is pushed back into a custom API that may not be readily available and may
have to be written from scratch.

3. A human can't read the IEEE-754 blob.  This may seem a trivial issue, but
it *really* helps in debugging, particularly with end users, to be able to
read the file.

Obviously, putting the data in XML float or double format will address these
issues at the expense of file size.  Gzipping XML can be a practical way to
minimize the file size.

Regards,
Lewis

[Psidev-ms-dev] Siena meeting report and talks

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

Hi all. The Siena report (thanks Sandra [a lot], Phil, Randy, Frank) 
page is now accessible from the top of the main PSI site 
(psidev.sf.net). Talks are mostly available now, bar a few -- all from 
the MS session (or MI if there were any beyond Henning's).

I will soon bundle all the talks into DLable zips for your pleasure, but 
while I am short of a few I'll avoid that to steer clear of repeat DLs 
and versions and all that.

Cheers, Chris.

P.S. Sorry for multiple posts to those who suffer that monstrous 
inconvenience -- one day I will update PSI Announce for this stuff :\

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Chris Taylor (ch...@eb...)
  HUPO PSI: GPS -- psidev.sf.net
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

[Psidev-ms-dev] New mzData Example Files on SourceForge

[Randy J. <rkj...@in...>]

Three new mzData 1.05 example files using the 1.0 release of the PSI-MS 
controlled vocabulary terms (from http://psidev.sf.net) are now 
available in the file release section : 
(http://sourceforge.net/project/showfiles.php?group_id=65472)

RE: [Psidev-ms-dev] ABI contact ?

[frank g. <Fra...@ne...>]

Hello

I am in the same position, and tried going through their contact email
system with a couple of questions and got nothing but an automated
repsonse saying we have received your email.

Frank=20

>-----Original Message-----
>From: psi...@li...=20
>[mailto:psi...@li...] On Behalf=20
>Of Steffen Neumann
>Sent: 17 May 2005 15:34
>To: psi...@li...
>Subject: [Psidev-ms-dev] ABI contact ?
>
>Hi,
>
>On the mzData web pages http://psidev.sourceforge.net/ms/#mzdata
>it is mentioned that ABI is in an exploratory phase.
>
>I'd like to get in touch with a person from ABI working on that.
>Is there anyone listening or anyone who knows that person ?
>
>Thanks in advance,
>Steffen
>
>

[Psidev-ms-dev] ABI contact ?

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

Hi,

On the mzData web pages http://psidev.sourceforge.net/ms/#mzdata
it is mentioned that ABI is in an exploratory phase.

I'd like to get in touch with a person from ABI working on that.
Is there anyone listening or anyone who knows that person ?

Thanks in advance,
Steffen

[Psidev-ms-dev] [Fwd: Re: [Psidev-gps-dev] PepXML]

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

-------- Original Message --------
Subject: Re: [Psidev-gps-dev] PepXML
Date: Tue, 03 May 2005 10:12:17 +0100
From: Chris Taylor <ch...@eb...>
To: psi...@li...

Hiya.

PepXML is (when considered together with protXML) a functional
equivalent to what will be mzIdent, but currently it is not clear how
close they will be to each other. mzIdent may itself (as a result of
discussions in Siena, that included an ISB representative) be split into
two parts; 'first-level' inferences -- your direct conclusions about
'what flew down you mass spec', allowing us to consider
non-proteomics-specific applications also such as metabolomics or
lipidomics; and 'second-level' inferences -- what (in the world of
peptides and other protein-related thingies) you assert about the
content of your source material (which may have been trypsin-digested or
whatever). No current name for the second format afaik and as I say it
is not yet settled, just likely.

Iirc (and forgice me ISBers if this is waaay off) there is some
redundancy (in the normal form database sense) between pepXML and
protXML, so that they can best do the jobs they are intended for, which
is to sit comfortably in the 'Trans-Proteomic Pipeline' from ISB (an
inter-compatible suite of tools and formats).

Cheers, Chris.


Arn...@sa... wrote:
> Hello,
> 
> Any idea how PepXML fits into the PSI standards - is the predecessor of mzIdent?
> 
> Any clarification is welcome.
> 
> 	+kind regards,
> 
> 	Arne
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by: NEC IT Guy Games.
> Get your fingers limbered up and give it your best shot. 4 great events, 4
> opportunities to win big! Highest score wins.NEC IT Guy Games. Play to
> win an NEC 61 plasma display. Visit http://www.necitguy.com/?r 
> _______________________________________________
> Psidev-gps-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-gps-dev
> 
> 

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Chris Taylor (ch...@eb...)
  HUPO PSI: GPS -- psidev.sf.net
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Chris Taylor (ch...@eb...)
  HUPO PSI: GPS -- psidev.sf.net
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

[Psidev-ms-dev] Keeping the PSI-MS webpage up to date

[Potthast, F. <fra...@fg...>]

Dear all,
=20
During the next three days, the PSI spring workshop
http://psidev.sourceforge.net/meetings/2005-04/index.html=20
is happening in Siena.
=20
We would like to use this opportunity to ensure that the PSI-MS page
http://psidev.sourceforge.net/ms/index.html
is up to date.=20
=20
Please send change requests / criticism / suggestions / comments to
fr...@fg...
=20
Thanks for your help ... Frank
---------------------------------
Functional Genomics Center Zurich
Frank Potthast, PhD
Senior Research Scientist
Proteome Informatics
fr...@fg...
+41 79 46 180 72
---------------------------------

[Psidev-ms-dev] updates for psidev-ms homepage ?

[Potthast, F. <fra...@fg...>]

Dear all,

You might want to check if you see anything which needs to be =
updated/corrected on our psidev-ms homepage=20

http://psidev.sourceforge.net/ms/

Please send change requests / suggestions to fra...@fg...

Thanks for all help in advance ... Frank

[Psidev-ms-dev] PSI Spring Meeting

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

Hello to you all.

Details and a rough agenda are now available for the next PSI Spring 
Meeting to be held in Siena, Italy, from April 17th to the 20th.

Please browse to the following page (also linked from the PSI homepage):
http://psidev.sourceforge.net/meetings/2005-04/index.html

Any questions or comments, email me on ch...@eb...

Looking forward to seeing as many as can make it, should be great fun 
and Siena is truly a weird and wonderful place.

Cheers, Chris Taylor.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Chris Taylor (ch...@eb...)
  HUPO PSI: GPS -- psidev.sf.net
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

[Psidev-ms-dev] Re: [Psidev-gps-dev] Ontology development list

[Chris S. <sto...@pc...>]

Hi Chris,
Congratulations on moving this forward! On behalf of the MGED Ontology 
working group, I'd like to offer the use of our resources if they can 
be of help. I recognize that you might want proteomics-focused 
resources to start with but you are welcome to use our tracker 
(http://sourceforge.net/tracker/?atid=603031&group_id=16076) and mail 
list (http://lists.sourceforge.net/lists/listinfo/mged-ontologies) to 
perhaps bring in more input and help.
Also, I would encourage you to take the plunge and start building your 
ontology with Protege rather than a simple text format as it will help 
you lots in organizing your terms, avoiding syntatic no-nos, and of 
course generating OWL files.

Cheers,
Chris

On Feb 3, 2005, at 7:47 AM, Chris Taylor wrote:

> Hello all.
>
> On Monday 7th, I will make available v0.01 of the PSI ontology in the 
> CVS (I'll announce it when done, with a location).
>
> In the first instance, and for obvious reasons, this ontology will (1) 
> be limited in richness, and (2) initially reflect the scope of the 
> mzData format. The ontology will widen out to cover the scope of the 
> draft mzIdent, the as yet undrafted GelML, and ultimately of course 
> the whole of the PSI-OM; it will also become much richer as we go. 
> [One could equally consider the scope of the various MIAPE modules...]
>
> The v0.01 file will be in a simple text format (so 'ontology' is 
> perhaps inappropriate for now, but that will change as we move into 
> OWL-based development); the aim is to get the fundamental conventions 
> settled (e.g. 'this_style' versus 'ThisStlye' and so on) and to simply 
> get the ball rolling so that mzData implementers have something to use 
> in their own software...
>
> I have set up a discussion list at 
> http://lists.sourceforge.net/lists/listinfo/psidev-onto-dev to which 
> all interested parties should subscribe. I am not yet sure which 
> mechanisms will work best for adding to and revising the ontology; I'd 
> imagine that a tracker would be the best solution long-term. For now 
> can we just stick to commenting on the list, with me implementing 
> agreed changes?
>
> Cheers, Chris.
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>  Chris Taylor (ch...@eb...)
>  HUPO PSI: GPS -- psidev.sf.net
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting
> Tool for open source databases. Create drag-&-drop reports. Save time
> by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc.
> Download a FREE copy at http://www.intelliview.com/go/osdn_nl
> _______________________________________________
> Psidev-gps-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-gps-dev

[Psidev-ms-dev] Ontology development list

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

Hello all.

On Monday 7th, I will make available v0.01 of the PSI ontology in the 
CVS (I'll announce it when done, with a location).

In the first instance, and for obvious reasons, this ontology will (1) 
be limited in richness, and (2) initially reflect the scope of the 
mzData format. The ontology will widen out to cover the scope of the 
draft mzIdent, the as yet undrafted GelML, and ultimately of course the 
whole of the PSI-OM; it will also become much richer as we go. [One 
could equally consider the scope of the various MIAPE modules...]

The v0.01 file will be in a simple text format (so 'ontology' is perhaps 
inappropriate for now, but that will change as we move into OWL-based 
development); the aim is to get the fundamental conventions settled 
(e.g. 'this_style' versus 'ThisStlye' and so on) and to simply get the 
ball rolling so that mzData implementers have something to use in their 
own software...

I have set up a discussion list at 
http://lists.sourceforge.net/lists/listinfo/psidev-onto-dev to which all 
interested parties should subscribe. I am not yet sure which mechanisms 
will work best for adding to and revising the ontology; I'd imagine that 
a tracker would be the best solution long-term. For now can we just 
stick to commenting on the list, with me implementing agreed changes?

Cheers, Chris.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Chris Taylor (ch...@eb...)
  HUPO PSI: GPS -- psidev.sf.net
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

[Psidev-ms-dev] the inclusion of other experimental data in mzIdent

[<sg...@pr...>]

Hi all,

=20

I have some questions regarding mzIdent format and data that would be =
nice to incorporate

=20

From the downstream (bioinformatics) analysis of MS identifications, I =
like to see mzIdent as being designed for the capture of the results of =
an analysis.

(It would be nice to enable references to the mzData file(s))

=20

An important component of such functionality would be the inclusion of =
other experimental data that the identification (e.g. quantification =
results besides the information about the peptides and proteins).

=20

Is this supposed to go into the controlled vocabularium?

Does anyone have some examples of the controlled vocabularium for =
mzIdent?

=20

To enable operability between MS identication software and downstream =
bioinformatics analysis tools - the controlled vocabularium should be a =
common format, right?

Else it is hard to know which associated data to import into software =
that uses mzIdent as input.

=20

Cheers - and thanks for some important initiatives

Soeren Schandorff

=20

_____________________

Soeren Schandorff, Ph.D.
Gade-Jorgensen
Principal Scientist
Proxeon Bioinformatics A/S <http://www.proxeon.com/> =20
Phone: +45 26332017
Sch...@Pr... <mailto:Sch...@Pr...>  =20

=20

[Psidev-ms-dev] Release schedule for mzData

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

Dear all.

It has been recognized that a stable version of mzData, and a stable 
release cycle, are both vitally important for developers implementing 
this format. After our first stable release (1.05) of the mzData XML 
Schema, we are now in a position to formalize the future release plan.

We plan to release annually (assuming there is cause to) just prior to
each year's HUPO Jamboree (i.e. in the Fall). Each release will
incorporate revisions made on the basis of three sources of feedback on
the current mzData version:

(1) Issues raised at the annual PSI Spring Meeting.

(2) Issues submitted to the tracker, which can be found by browsing to
http://sourceforge.net/tracker/?group_id=65472 and then looking for
"mzData Requests". Note that you will need to register with SourceForge
to be able to post to the tracker...

(3) Exceptionally, issues may be submitted to the list, where the
SourceForge tracker presents problems; issues submitted this way should
be clearly flagged as potential tracker items, so that a member of the
admin team can post them on your behalf.

Note that we plan to make each Fall's release available to developers
over the preceding Summer, to allow implementation prior to the pending
release becoming 'official'.

We consider this annual (when required) update schedule for mzData to
provide adequate version stability for implementers. If anyone has
comments to make on this planned release schedule, please forward them
to the ms-dev list (i.e. this list...).

Cheers, Chris Taylor.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Chris Taylor (ch...@eb...)
  HUPO PSI: GPS -- psidev.sf.net
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

[Psidev-ms-dev] mzData 1.05

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

Announcing the delivery of mzData 1.05 to the web page, linked from 
http://psidev.sourceforge.net/ms/#mzdata

In addition to some minor code tweaks and name changes, this version 
features significantly enhanced annotation of almost all schema 
elements, hopefully removing as many ambiguities as could be found. If 
there are any that still exist, please forward details to me and I will 
add them to the issues tracker (soon to be established), to be dealt 
with at the April PSI meeting in Siena, with a view to producing 1.06 
there -- a version that should remain stable for a long time. We can 
discuss submitting that version to an OMG-like process to guarantee 
version stability to implementers.

The ontology work is now getting going. Details and a first version of 
the ontology will be published to the web site within weeks. We are also 
now very close to delivering the MIAPE: MS reporting guidelines for mass 
spectrometry. Watch this space for updates.

FYI, MS informatics and gel electrophoresis (wet and in silico) are the 
next areas to receive 'the treatment' (XML, MIAPE, ontology). General 
modelling, and ontology development are also of course continuing.

Cheers, Chris Taylor.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Chris Taylor (ch...@eb...)
  HUPO PSI: GPS -- psidev.sf.net
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Re: [Psidev-ms-dev] Mass Spec file convertor

[Henning H. <hh...@eb...>]

Dear Frank,

I am not aware of such a converter, and we don't have it as an official 
contribution to the PSI-MS initiative. Ideally, this should be provided 
by Applied Biosystems themselves, because they know best about their 
data representation, and can also provide proper maintenance in case of 
internal format changes. It might help if you, as a customer, express 
your interest in the support of PSI-MS open standards to your AB 
representative. I BCC (for confidentiality reasons) this mail also to AB 
representatives which have participated in the Nice meeting, perhaps 
there are already concrete plans for mzData support, or they would be 
prepared to support development you would be doing.

In any case we would be very interested to document and link any 
suitable tool from the PSI web site.

--

Best regards,

Henning

-----------------------------------------------------------------------
Henning Hermjakob
Sequence Database Group Coordinator           Email:      hh...@eb...
European Bioinformatics Institute             Tel:    + 44 1223 49 4671
Wellcome Trust Genome Campus                  Fax:    + 44 1223 49 4468
Hinxton, Cambridge CB10 1SD
United Kingdom



frank gibson wrote:

>Hello
>
>At the risk of re-inventing the wheel does anybody have/know of a file
>convertor for the raw mass spec datafiles for Applied Biosystems,
>Voyager-DE STR to mzData. Or the process for finding out what the
>components in the datafile corresponds to?
>
>Cheers
>Frank
>
>
>-------------------------------------------------------
>SF email is sponsored by - The IT Product Guide
>Read honest & candid reviews on hundreds of IT Products from real users.
>Discover which products truly live up to the hype. Start reading now. 
>http://productguide.itmanagersjournal.com/
>_______________________________________________
>Psidev-ms-dev mailing list
>Psi...@li...
>https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>  
>

[Psidev-ms-dev] Mass Spec file convertor

[frank g. <Fra...@ne...>]

Hello

At the risk of re-inventing the wheel does anybody have/know of a file
convertor for the raw mass spec datafiles for Applied Biosystems,
Voyager-DE STR to mzData. Or the process for finding out what the
components in the datafile corresponds to?

Cheers
Frank

[Psidev-ms-dev] Is the mzData Viewer in CVS?

[Stephen G. <sgr...@bm...>]

Hello all,

=20

  As a database programmer for the Johns Hopkins NHLBI Proteomics =
Center, I
am in the process of writing a C# program to translate raw Mass =
Spectrometry
files of varying formats into the mzData format.  I am able to produce =
an
XML file that validates against the mzData schema, but I am unsure if =
the
method I am using to encode the mzArrayBinary and intenArrayBinary =
values
produces the correct output.  I read about the mzData converter and =
mzData
Viewer on the Mass Spectrometry Standards Working Group home page, but =
only
found the converter in CVS.  Does the mzData Viewer exist?  If so, where
exactly can it be found?  Thanks, in advance, for your help and
understanding.

=20

Sincerely yours,

=20

Stephen J. Granite, M.S.
Database Programmer
Center for Cardiovascular Bioinformatics and Modeling
Room 202 Clark Hall,=20
3400 North Charles Street=20
Baltimore, MD 21218-2686=20
e-mail:sgr...@bm...

=20

[Psidev-ms-dev] About mzIdent schema

[Sheng Q. <qh...@si...>]
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[Psidev-ms-dev] PSI-MS::our homepage::request for input

[Potthast, F. <fra...@fg...>]

Dear all,

The homepage of our group=20
http://psidev.sourceforge.net/ms/index.html
has been updated before the HUPO 2004 meeting (thanks to Chris Taylor!).

If you have any comments/ideas/requests, please let us know
so we can update. Especially, have a look at the list of
software supporting mzData - not really complete right now...

It is reasonable to expect a lot of traffic on our psi-ms page when
people return from the HUPO meeting, i.e. thursday/friday.

Thanks in advance ... Frank

-------------------------
Frank Potthast, PhD
Senior Research Scientist
Proteome Informatics
Functional Genomics Center Zurich
www.fgcz.ch
-------------------------

[Psidev-ms-dev] [Fwd: [Psidev-announce] HUPO Proteomics Standards Initiative workshops in Beijing]

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

Dear collegues,

this weekend, the PSI satellite meeting to the HUPO world congress will
take place in Beijing, October 23-24. This meeting will present the
current status of PSI in the different domains, and will be a forum to
present our work to a broader community and to get community feedback.

For the detailed agenda, please see the HPSI sections in
http://www.hupo2004.cn/HUPOworkshop.pdf

Discussion highlights are:
- Finalised PSI MI level 2 format
- Finalised mzData schema
- First draft of GPS object model
- PSI coordination with HUPO tissue projects

To facilitate planning, I would appreciate a brief mail if you plan to
attend the PSI meeting, ideally stating which of the workgroups you plan
to attend.

For HUPO congress information, please see
http://www.hupo2004.cn/

And for more information on PSI:
http://psidev.sourceforge.net

-- 

Looking forward to seeing you in Beijing,

Henning

-----------------------------------------------------------------------
Henning Hermjakob
Sequence Database Group Coordinator           Email:      hh...@eb...
European Bioinformatics Institute             Tel:    + 44 1223 49 4671
Wellcome Trust Genome Campus                  Fax:    + 44 1223 49 4468
Hinxton, Cambridge CB10 1SD
United Kingdom





-------------------------------------------------------
This SF.net email is sponsored by: IT Product Guide on ITManagersJournal
Use IT products in your business? Tell us what you think of them. Give us
Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out more
http://productguide.itmanagersjournal.com/guidepromo.tmpl
_______________________________________________
Psidev-announce mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-announce



-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Chris Taylor (ch...@eb...)
  HUPO PSI: GPS -- psidev.sf.net
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Re: [Psidev-ms-dev] base64binary issues...

[Kai R. <kr...@ce...>]

Dear Linus,

the data element in the current version of mzData (1.04) contains two=20
attributes: precision and endian. The documentation to <mzArrayBinary>=20
and <intenArrayBinary> in the XML Schema says:
"The array is stored as a base64 encoded binary. The only type allowed=20
is IEEE-754 floating point; the precision must be specified as either=20
32- or 64-bit; endianess must also be specified."
This documentation can be browsed in the generated documentation at:
http://psidev.sourceforge.net/ms/xml/mzdata/mzdata.html
Behind, for example, the element mzArrayBinary is a small questionmark=20
on a yellow background. A click on this questionmark opens a little=20
window that contains additional documentation to this element. These=20
popups are generated from the xs:annotation/xs:documentation elements in=20
the XML schema.
But no worries, I also missed these questionmarks the first couple of=20
times looking the documentation...

Cheers
  Kai

Linus G=F6ransson wrote:
> Hi all,
> I am working on coverting mass spectrum data into the mzData format, an=
d
> have some problems understanding the way intensity and mass values are
> stored. According to the mzData schema, these two arrays should be stor=
ed
> as base64binary elements. Correct me if I am wrong here, but wouldn't t=
hat
> make the data incompatible between different systems? I am working in
> Java, and if I encode my arrays into base64binary format they will make
> sense only to me. To conlude: Is there some definition in mzData on how=
 an
> array of floats should be transformed into base64binary format?
>=20
> cheers,
> Linus G=F6ransson
>=20
>=20
>=20
> -------------------------------------------------------
> This SF.net email is sponsored by: IT Product Guide on ITManagersJourna=
l
> Use IT products in your business? Tell us what you think of them. Give =
us
> Your Opinions, Get Free ThinkGeek Gift Certificates! Click to find out =
more
> http://productguide.itmanagersjournal.com/guidepromo.tmpl
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>=20

--=20
Real cats don't need names.
But they often get called them.
"Yaargeroffoutofityarbastard" does nicely.
         Terry Pratchett - The Unadulterated Cat

*********************************************************************
* email: kr...@ce...
*
* Universit=E4t Bielefeld
* CeBiTec
* 33594 Bielefeld
* Germany
*********************************************************************

[Psidev-ms-dev] base64binary issues...

[Linus <li...@th...>]

Hi all,
I am working on coverting mass spectrum data into the mzData format, and
have some problems understanding the way intensity and mass values are
stored. According to the mzData schema, these two arrays should be stored
as base64binary elements. Correct me if I am wrong here, but wouldn't that
make the data incompatible between different systems? I am working in
Java, and if I encode my arrays into base64binary format they will make
sense only to me. To conlude: Is there some definition in mzData on how an
array of floats should be transformed into base64binary format?

cheers,
Linus Göransson

[Psidev-ms-dev] Spectrum id's

[Chris A. <ch...@ma...>]

Hi,

Looking at the latest mzData schema, if my understanding is correct,
each peak list is represented by a "spectrum" element.  I note that
these now require an "id" attribute.  It appears that this ID is then
referred to in the "precursorList" element by the attribute 
"spectrumRef", correct?

If you are processing scan data from an LC-MSMS run, normally
peak lists are only produced for MS2 scans (and potentially groups of
them).  Therefore, the MS1 scans aren't output and so have no assigned
ID.  But that means that the precursor reference in the schema is 
invalid.  Does this mean we are required to output bogus MS1 peak lists?

I'm also a little unclear on the official intended purpose of the 
"precursorList" element, is it for:

(a) Where you have say an MS3 scan and you want to list the MS2 and MS1
precursor m/z values; or

(b) Where you have merged two or more grouped MS2 scans to produce a 
single peak list and you need to list each of the original MS1 precursor 
m/z values; or

(c) All of the above.

Thanks,
Chris

Re: [Psidev-ms-dev] Using mzData in Software Applications

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

Hi Per.

> as the project manager of, Proteios (http://www.proteios.org/) - a 
> bioinformatics software project in proteomics, I strongly greet the 
> standardization work for mzData. We are currently working on integrating 
> mzData in our (Proteios) data model.

Bravo! Please continue to forward your collective experiences to the 
list (or at least me). Jari Hakkinen and Frank Potthast gave an 
excellent presentation of Proteios at our Nice meeting last April -- I'm 
enormously glad that you and your team are still actively participating 
in this project.

> Has anyone done this before - actually used mzData in a software application 
> (apart from validation and the like with standard XML tools)? Putting mzData 
> into practical use should be very much in the interest of PSI. Unfortunately 
> there are, in my opinion, a few things which cause (uneccessary?) 
> difficulties in an implementation.

Some converters were written (by Kai) to go from .pkl, .dta and I think 
maybe some others (.mgf maybe) to mzData. They are out of data now as 
the format has evolved, but you can still get the source if you dig on 
the CVS a bit: 
http://cvs.sourceforge.net/viewcvs.py/psidev/psi/psi-ms/xml/mzData/converter/ 


There is also a guy at Leeds Uni doing an implementation [web submission 
-> XML-import -> DB -> XSLT rendering to HTML]. That is the extent of 
software implementations of the format to date afaik.

> First I would suggest not using common programming language keywords (e.g 
> "float") as element/attribute names. This is a possible source of confusion 
> and makes simple mapping onto source code data structures more difficult.

Hmm. Fair point (a reserved/key words thing yeah?). Something to 
consider for a future revision perhaps.

> Secondly, I wonder whether there is any pressing need for keeping two separate 
> arrays in cases where the apparent meaning is rather one single array of 
> pairs (e.g. "intenArray", "mzArray"). 

Base64-encoded arrays of IEEE-754 floats (endian and precision given) 
were chosen to capture the data to allow (1) some compression, and 
importantly, (2) maximal portability for the (compressed) data captured 
in the format without having to parse it all out locally. Moving to 
two-membered arrays would (I think) mess up this portability because 
complex arrays are likely to be handled differently on different 
systems. Also, were someone interested solely in m/z values, they would 
have a simpler job to grab them in isolation without decompresssing and 
then parsing them out. Hopefully, as far as implementing the XML goes, 
there will be little difference between two single-membered arrays and 
one two-membered one.

> The schema does not enforce the same 
> length on these two arrays.

Pardon my ignorance (which is significant) but is that possible in XML 
(although see below)? Or did you mean in the guidance notes perhaps? I 
appreciate that if we had a single array of pairs this wouldn't be an 
issue...

> I also wonder what the purpose of the attribute 
> length is. Can't it be removed, since the length is implicitely given by the 
> number of subelements? Consider the following excerpt from a valid(!) mzData 
> XML-file:
> 
>         <mzArray length="15">
>           <float>100</float>
>           <float>500</float>
>         </mzArray>
>         <intenArray length="7">
>           <float>10</float>
>           <float>100</float>
>           <float>20</float>
>         </intenArray>

Well there's valid and there's valid...  :)

We only rely to a minimal extent on XML to do any constraining -- we see 
that other tools will have to do a significant amount of validation 
anyway (CV is a biggie) and so went for simple things like putting in 
lengths/counts as attributes on some parents to allow some integrity 
checking; i.e. I say there are three analyser stages in my mass spec, 
you find two, something is clearly wrong (incidentally these sort of 
attributes could support the functionality to check equality of array 
length as discussed above, but of course only _stated_ array length, not 
actual).

Again do please let us/me know how the implementation goes -- this 
information is absolutely invaluable to us. And of course feel free to 
reply to these attempts to answer the points you raise.

Cheers, Chris.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Chris Taylor (ch...@eb...)
  HUPO PSI: GPS -- psidev.sf.net
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~