psidev-ms-dev — Mass spectroscopy standard development

[Psidev-ms-dev] Minutes from 25 October Teleconference

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

The minutes from the 25 October teleconference have been posted:

http://psidev.sourceforge.net/docstore/browse.php?sess=0&parent=4&expand=1

Please let me know if there are any corrections or comments.

Thanks,
Randy

[Psidev-ms-dev] RE: [Psidev-gps-dev] MIAPE.GE

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

Hello all,
This is a reminder that we are planning to have a conference call to discuss
the draft MIAPE GE document next Monday (7th Nov) at 4pm GMT. The details of
how to access the document are given below.

If you would like to comment prior to the call, please send comments to the
GPS list or send edited documents back to Frank directly.

The access details for the call are the same as for gelML calls. If you need
the number and access code, please send me an email (aj...@cs...),
Best wishes,
Andy

> -----Original Message-----
> From: psi...@li... [mailto:psidev-gps-dev-
> ad...@li...] On Behalf Of frank gibson
> Sent: 25 October 2005 11:49
> To: psi...@li...
> Subject: [Psidev-gps-dev] MIAPE.GE
> 
> 
> Hi,
> 
> This is a cross posting on the PSI mailing lists regarding MIAPE.GE.
> *There are 11 days left to return comments*
> 
> Version 0.6 of the MIAPE.Gel Electrophoreis guidelines have now been
> published on the gps website at the following links (word and pdf).
> The document is open for review and comments on the gps list. If you
> wish to comment on the MIAPE.GE document please return your commented
> document to me (Fra...@nc...) on or before Friday 4th of
> November to allow us to have a MIAPE conference call to discuss the
> document on Monday 7th November 1600 BST.
> 
> http://psidev.sourceforge.net/gps/miape/MIAPE_GE_0.6.pdf
> http://psidev.sourceforge.net/gps/miape/MIAPE_GE_0.6.doc
> 
> Cheers
> Frank
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.
> Get Certified Today * Register for a JBoss Training Course
> Free Certification Exam for All Training Attendees Through End of 2005
> Visit http://www.jboss.com/services/certification for more information
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> Psi...@li...
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[Psidev-ms-dev] Time of Next Teleconference

[Ruth M. <mcn...@Ca...>]

Prior to the next teleconference,  a number of time zones, including EST, will
be adopting daylight saving time. So we need to clarify the time of the next
teleconference. Also, although a different opinion was expressed at the last
Teleconference, I still think that previous Teleconferences have taken place at
1000 EST. Perhaps Kent, you could tell us what time it will be for you & the
rest of us can work it out from there. 

Have a good weekend, Ruth

Dr Ruth McNally
Senior Research Associate
ESRC Centre for Economic and Social Aspects of Genomics (CESAGen)
Cardiff University
6 Museum Place
Cardiff CF10 3BG
Tel: +44 (0)1234 296057
Fax: +44 (0)1234 294157
Mobile: +44 (0)7834489770
Email: McN...@cf...
http://www.cesagen.lancs.ac.uk/staff/mcnally2.htm

Re: [Psidev-ms-dev] Agenda for 25 Oct 2005 PSI-MS Teleconference

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

Just for reference, here's the FuGO 'charter'.

Cheers, Chris.


Randy Julian wrote:
> The PSI-MS biweekly call is scheduled for 10:00 EST on 25 October 2005 
> at the usual call-in number. Please sent an e-mail to Kent Laursen 
> (Ken...@ge...) if you need dialing instructions for the 
> call.
> 
> The agenda for the PSI-MS teleconference will focus on launching:
> 
> 1. mzData
>    a. Specification team assignment
>    b. Charter
>    c. Deliverables
>    d. Schedule
> 
> 2. analysisXML
>    a. Specification team assignment
>    b. Charter
>    c. Deliverables
>    d. Schedule
> 
> 3. Protein Modifications
>    a. Specification team assignment
>    b. Charter
>    c. Deliverables
>    d. Schedule
> 
> 4. Discuss dependencies between WG's:
>    a. MIAPE/Reporting & MS/MSI/Separations
>    b. Extensions & mzData/analysisXML/...
> 
> 5. Comments/Feedback/Next Steps for MCP response
> 
> 6. New website & Document management system feedback
> 
> 
> Here is a proposed 'summary' charter for the work of the mzData 
> Specification team:
> 
> mzData Charter:
> 
> The group will focus on improvements to the mzData format and creation 
> of documentation.  Changes to the format should be backward compatible 
> with mzData 1.05 as much as possible with new features added as 
> extensions. Some desired extensions are:
> 
>    * Reduced redundancy of parameters through experiment descriptions
>    * Representation of mass chromatograms for direct support of 
> SIM/SRM/MRM experiments
>    * Improved ontology support
>    * Improved extension capability
> 
> Goals and Milestones:
> 
>   1. Publish mzData 1.05 format document as an official PSI document - 
> by PSI Spring 2006 Meeting (PSI6)
>   2. Collect and discuss list of improvements to mzData 1.05 - by Spring 
> 2006 Meeting (PSI6)
>   3. Produce mzData v1.1 format - Spring 2006 Meeting (PSI6)
>   4. Draft merger of mzData with mzXML - Fall 2006 Meeting (PSI7)
> 
> 
> Thanks,
> Randy Julian
> 
> 
> 
> -------------------------------------------------------
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> Get Certified Today * Register for a JBoss Training Course
> Free Certification Exam for All Training Attendees Through End of 2005
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> _______________________________________________
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> 

-- 
~~~~~~~~~~~~~~~~~~~~~~~~
  chr...@eb...
  http://psidev.sf.net/
~~~~~~~~~~~~~~~~~~~~~~~~

Re: [Psidev-ms-dev] Agenda for 25 Oct 2005 PSI-MS Teleconference

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

Is there anybody out there?

It's 10am on the eastern seaboard...

In limbo (with lift muzak), Chris.


Randy Julian wrote:
> The PSI-MS biweekly call is scheduled for 10:00 EST on 25 October 2005 
> at the usual call-in number. Please sent an e-mail to Kent Laursen 
> (Ken...@ge...) if you need dialing instructions for the 
> call.
> 
> The agenda for the PSI-MS teleconference will focus on launching:
> 
> 1. mzData
>    a. Specification team assignment
>    b. Charter
>    c. Deliverables
>    d. Schedule
> 
> 2. analysisXML
>    a. Specification team assignment
>    b. Charter
>    c. Deliverables
>    d. Schedule
> 
> 3. Protein Modifications
>    a. Specification team assignment
>    b. Charter
>    c. Deliverables
>    d. Schedule
> 
> 4. Discuss dependencies between WG's:
>    a. MIAPE/Reporting & MS/MSI/Separations
>    b. Extensions & mzData/analysisXML/...
> 
> 5. Comments/Feedback/Next Steps for MCP response
> 
> 6. New website & Document management system feedback
> 
> 
> Here is a proposed 'summary' charter for the work of the mzData 
> Specification team:
> 
> mzData Charter:
> 
> The group will focus on improvements to the mzData format and creation 
> of documentation.  Changes to the format should be backward compatible 
> with mzData 1.05 as much as possible with new features added as 
> extensions. Some desired extensions are:
> 
>    * Reduced redundancy of parameters through experiment descriptions
>    * Representation of mass chromatograms for direct support of 
> SIM/SRM/MRM experiments
>    * Improved ontology support
>    * Improved extension capability
> 
> Goals and Milestones:
> 
>   1. Publish mzData 1.05 format document as an official PSI document - 
> by PSI Spring 2006 Meeting (PSI6)
>   2. Collect and discuss list of improvements to mzData 1.05 - by Spring 
> 2006 Meeting (PSI6)
>   3. Produce mzData v1.1 format - Spring 2006 Meeting (PSI6)
>   4. Draft merger of mzData with mzXML - Fall 2006 Meeting (PSI7)
> 
> 
> Thanks,
> Randy Julian
> 
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by the JBoss Inc.
> Get Certified Today * Register for a JBoss Training Course
> Free Certification Exam for All Training Attendees Through End of 2005
> Visit http://www.jboss.com/services/certification for more information
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> 

-- 
~~~~~~~~~~~~~~~~~~~~~~~~
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  http://psidev.sf.net/
~~~~~~~~~~~~~~~~~~~~~~~~

[Psidev-ms-dev] MIAPE.GE

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

Hi,

This is a cross posting on the PSI mailing lists regarding MIAPE.GE.
*There are 11 days laeft to return comments*

Version 0.6 of the MIAPE.Gel Electrophoreis guidelines have now been
published on the gps website at the following links (word and pdf).=20
The document is open for review and comments on the gps list. If you
wish to comment on the MIAPE.GE document please return your commented
document to me (Fra...@nc...) on or before Friday 4th of
November to allow us to have a MIAPE conference call to discuss the
document on Monday 7th November 1600 BST.

http://psidev.sourceforge.net/gps/miape/MIAPE_GE_0.6.pdf
http://psidev.sourceforge.net/gps/miape/MIAPE_GE_0.6.doc

Cheers
Frank

[Psidev-ms-dev] Agenda for 25 Oct 2005 PSI-MS Teleconference

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

The PSI-MS biweekly call is scheduled for 10:00 EST on 25 October 2005 
at the usual call-in number. Please sent an e-mail to Kent Laursen 
(Ken...@ge...) if you need dialing instructions for the 
call.

The agenda for the PSI-MS teleconference will focus on launching:

1. mzData
    a. Specification team assignment
    b. Charter
    c. Deliverables
    d. Schedule

2. analysisXML
    a. Specification team assignment
    b. Charter
    c. Deliverables
    d. Schedule

3. Protein Modifications
    a. Specification team assignment
    b. Charter
    c. Deliverables
    d. Schedule

4. Discuss dependencies between WG's:
    a. MIAPE/Reporting & MS/MSI/Separations
    b. Extensions & mzData/analysisXML/...

5. Comments/Feedback/Next Steps for MCP response

6. New website & Document management system feedback


Here is a proposed 'summary' charter for the work of the mzData 
Specification team:

mzData Charter:

The group will focus on improvements to the mzData format and creation 
of documentation.  Changes to the format should be backward compatible 
with mzData 1.05 as much as possible with new features added as 
extensions. Some desired extensions are:

    * Reduced redundancy of parameters through experiment descriptions
    * Representation of mass chromatograms for direct support of 
SIM/SRM/MRM experiments
    * Improved ontology support
    * Improved extension capability

Goals and Milestones:

   1. Publish mzData 1.05 format document as an official PSI document - 
by PSI Spring 2006 Meeting (PSI6)
   2. Collect and discuss list of improvements to mzData 1.05 - by 
Spring 2006 Meeting (PSI6)
   3. Produce mzData v1.1 format - Spring 2006 Meeting (PSI6)
   4. Draft merger of mzData with mzXML - Fall 2006 Meeting (PSI7)


Thanks,
Randy Julian

[Psidev-ms-dev] Minutes from the 11 Oct PSI-MS teleconference

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

The minutes from the 11 Oct PSI-MS teleconference are in the document 
archive:

http://psidev.sourceforge.net/docstore/browse.php?sess=0&parent=4

Let me know if you have any questions or comments.

Thanks,
Randy

[Psidev-ms-dev] [Fwd: RE: [Psidev-gps-dev] [Fwd: [Fwd: [Fwd: Skype]]]]

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

Maybe not that good then...

-------- Original Message --------
Subject: RE: [Psidev-gps-dev] [Fwd: [Fwd: [Fwd: Skype]]]
Date: Mon, 17 Oct 2005 13:07:45 +0100
From: Andy Jones <aj...@cs...>
Reply-To: psi...@li...
To: <psi...@li...>

Hi Chris,
Skype is not bad, although they are currently limited to 4 
people per call
so generally it would not be applicable. They may up this limit 
at some
point. There is also a bit of a time delay that might make 
complicated
discussions a bit confusing.
Cheers
Andy

> -----Original Message-----
> From: psi...@li... [mailto:psidev-gps-dev-
> ad...@li...] On Behalf Of Chris Taylor
> Sent: 17 October 2005 12:42
> To: PSI MS Dev; PSI GPS Dev
> Subject: [Psidev-gps-dev] [Fwd: [Fwd: [Fwd: Skype]]]
> 
> Possble future telcon mechanism? PC to PC it is free (only pay
> when interacting with landlines) http://www.skype.com/
> 
> I have had a quick look to see why they might be doing stuff for
> free, but couldn't see much beyond the usual 'news' spam excuse.
> Maybe it'll become not-free in six months from now...
> 
> Cheers, Chris.
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~
>   chr...@eb...
>   http://psidev.sf.net/
> ~~~~~~~~~~~~~~~~~~~~~~~~
> 
> 
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads, discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> Psidev-gps-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-gps-dev



-------------------------------------------------------
This SF.Net email is sponsored by:
Power Architecture Resource Center: Free content, downloads, 
discussions,
and more. http://solutions.newsforge.com/ibmarch.tmpl
_______________________________________________
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-- 
~~~~~~~~~~~~~~~~~~~~~~~~
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  http://psidev.sf.net/
~~~~~~~~~~~~~~~~~~~~~~~~

[Psidev-ms-dev] [Fwd: [Fwd: [Fwd: Skype]]]

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

Possble future telcon mechanism? PC to PC it is free (only pay 
when interacting with landlines) http://www.skype.com/

I have had a quick look to see why they might be doing stuff for 
free, but couldn't see much beyond the usual 'news' spam excuse. 
Maybe it'll become not-free in six months from now...

Cheers, Chris.

~~~~~~~~~~~~~~~~~~~~~~~~
  chr...@eb...
  http://psidev.sf.net/
~~~~~~~~~~~~~~~~~~~~~~~~

[Psidev-ms-dev] RE: [Fuge-devel] Article about data model development

[Miller, M. D (Rosetta) <Mic...@Ro...>]

Hi Andy,
 
Great review, gives a good perspective on the standards.
 
The only thing I wanted to add is about the intent of the NVT.  
 
As I mentioned previously at the meeting for developing the FuGE milestone,
one of our key use cases is the ability to use MAGE in pipeline situations.
Typically the use of the format in these circumstances is in no-way complete
in terms of repository export for any particular pipeline but we have been
very successful in getting a diverse amount of data from various
instruments, wet labs and third party annotation that end up being connected
together in our application.
 
The NVT is documented as "Allows specification of name/value pairs.  Meant
to primarily help in-house, pipeline processing of instances by providing a
place for values that aren't part of the specification proper."  So best
practice says don't use NVTs for anything that has biological significance.
But we have indeed used these for many processing purposes, one of the
primary ones being for specifying what action to take if a record already
exists.
 
cheers,
Michael

-----Original Message-----
From: fug...@li...
[mailto:fug...@li...] On Behalf Of Andy Jones
Sent: Friday, October 14, 2005 6:16 AM
To: fug...@li...; psi...@li...;
psi...@li...
Subject: [Fuge-devel] Article about data model development



Hello all,

 

Norman Paton and I have written an article that reviews the current models
in functional genomics and the kinds of tasks that must be performed over
data formats. It then presents a set of guidelines about the kinds of
modelling structures that are suitable for particular tasks. I think the
guidelines may be of interest to people currently involved in data model
development. The article is in BMC Bioinformatics
(http://www.biomedcentral.com/1471-2105/6/235
<http://www.biomedcentral.com/1471-2105/6/235> ).

 

Apologies for the blatant self-publicity!

Best wishes,

Andy

[Psidev-ms-dev] MCP reponse submitted

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

According to the plan finalized during the 11 Oct 2005 PSI-MS 
teleconference, the final versions of the PSI-MS response to the MCP 
guidelines "request for comment" was completed and submitted before the 
deadline (15 October 2005).

The files which were submitted include a cover letter, the MIAPE 
principles document and highlighted versions of the MIAPE-MS, and 
MIAPE-MSI documents as well as a highlighted copy of the MCP 
guidelines.  The highlighting was done to show the relationship between 
the HUPO-PSI MS formats (mzData) and the minimum expected information in 
those formats (MIAPE).

Instead of attaching the documents to this e-mail, I am attaching a link 
to these documents in our new document system:

http://psidev.sourceforge.net/docstore/browse.php?sess=0&parent=10

If you go to:

http://psidev.sourceforge.net/docstore

You will see the login page - click on "(Anonymous Access)" to browse 
the entire collection of documents in the system.

Thanks to everyone on the PSI-MS team who helped with the submission and 
thanks to everyone who worked on the original MIAPE documents, the 
HUPO-PSI formats and reporting standards represent a significant 
contribution to the proteomics community which should help journals like 
MCP to archive high quality electronic data reporting.

Randy

p.s. Let me know if you have any problems with the document archive.

[Psidev-ms-dev] Article about data model development

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

Hello all,

 

Norman Paton and I have written an article that reviews the current models
in functional genomics and the kinds of tasks that must be performed over
data formats. It then presents a set of guidelines about the kinds of
modelling structures that are suitable for particular tasks. I think the
guidelines may be of interest to people currently involved in data model
development. The article is in BMC Bioinformatics
(http://www.biomedcentral.com/1471-2105/6/235).

 

Apologies for the blatant self-publicity!

Best wishes,

Andy

[Psidev-ms-dev] Hello from Tennessee

[David L. T. <dav...@va...>]

I've recently joined this list, and I wanted to introduce myself.  I'm 
Dave Tabb, a new assistant professor at Vanderbilt University.  I have 
been working in different areas of shotgun proteome informatics for 
about nine years.  My interest in PSI comes from several motivations:

1) I want to develop software that can make use of data from several 
instrument platforms.  The Mass Spec Research Center here has QTOFs, 
TOF/TOFs, QITs, and other types of instruemnts.  If it can produce 
tandem mass spectra, I'll want to push its spectra through the software 
my group develops.  As such, seeing mzData export available from 
instrument manufacturers' software would pose a real benefit to me.

2) I want the analytical results from my tools to be legible by other 
software packages.  If I write a database identifier (a la Sequest or 
Mascot), I want its identifications to be readable by (for example) 
PeptideProphet.  I've had only a cursory look at mzIdent, but I'm 
hopeful that it or another format will mature to be usable for that purpose.

3) I met Chris Taylor at a workshop in Michigan, and I figure any group 
that he participates in is likely to be entertaining.

Thanks!

Dave Tabb

[Psidev-ms-dev] deadlne for feedback on MCP response tomorrow

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

Dear all,
according to our ccall today, I would ask you all to feedback on the MCP 
answer by tomorrow 5pm Central Europe time, so that enough time is 
available for a last round with the final version before friday.
For those with limited time availability, concentrate on
- the cover letter, particularly the summary, list of supporting bodies 
and relationships paragraph
- the MCP guidelines, particularly the agreement on the information not 
to include in MIAPE  (red-labeled in the MCP doc)

Thanks again,
Pierre-Alain

-- 
--
 Dr. 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
 Pie...@is...
 http://www.expasy.org/people/Pierre-Alain.Binz.html

Re: [Psidev-ms-dev] PSI-MS teleconference agenda (11 Oct 2005)

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

Hi all. First of all, really great job on the pairwise=20
comparisons. Nice clinical laying out of the issues.

And on the MIAPE 'ownership' thing; clearly the MS workgroup own=20
both MIAPE: MS and MSI and are the responsible body in this=20
interaction with MCP.

But... I would like nonetheless to comment on the cover=20
letter/document. As I say I think the comparison is very clear=20
in the actual comparison documents themselves (MS/MSI/MCP) but=20
the cover letter is too long and doesn't make the main point=20
clearly enough up front. It is good to lay out the various=20
aspects of our work, but what should be clear throughout is that=20
the issue is the overlap between MIAPE and MCP. The first page=20
or so talks about using PSI formats to supply data to meet=20
journal quality measures, but doesn't actually mention or define=20
MIAPE. The first clear mention of MIAPE is halfway down page 2...

Towards the end the message becomes clearer, but is still=20
embedded in a lot of verbiage and discussion of our other work=20
(which is essentially irrelevant and potentially confusing).=20
Overall I think the premises and proposed resolution need to be=20
up front, almost in an abstract-style front end summary,=20
followed by clear supporting arguments and (minimally) detailed=20
proposals. The background info about formats etc. needs to be=20
drastically cut back and generally it needs tightening.

We will obviously chat about this shortly; I would be happy to=20
contribute some time to redrafting this document in the light of=20
discussions this afternoon if that appeals..?

Cheers, Chris.


Angel Pizarro wrote:
> Pierre-Alain Binz wrote:
>=20
>> Thanks Angel.
>> I would add, even if we decide that MIAPE is a group on its own, that=20
>> the MS working group also generates the corresponding MIAPE modules,=20
>> which are high-level (end-user and software-vendor) minimal=20
>> requirements to be supported by the formats
>>
> Good point. Revised:
>=20
> The PSI Mass Spectrometry (PSI-MS) standards group consists of academic=
=20
> and industry researchers, software developers and instrument=20
> manufacturers. The goals of the group are: to provide a set of minimal=20
> reporting requirements which augment the \link{ MIAPE reporting=20
> guidelines }with respect to mass spectrometry experiments; to provide=20
> vendor-neutral standard formats for representing mass spectrometry=20
> experimental data and the results derived through analysis of those=20
> data;  to foster adoption of the format by highlighting efforts made by=
=20
> vendors and individuals that utilize the format in their \link{ product=
s }.
>=20
> -angel
>=20
>> Pierre-Alain
>>
>> Angel Pizarro wrote:
>>
>>> First stab at a mission statement:
>>>
>>> "The PSI Mass Spectrometry (PSI-MS) standards group consists of=20
>>> academic and industry researchers, software developers and instrument=
=20
>>> manufacturers. The goal of the group is to provide vendor-neutral=20
>>> standard formats for representing mass spectrometry experimental data=
=20
>>> and the results derived through analysis of those data. A secondary=20
>>> goal of the group is to foster adoption of the format by highlighting=
=20
>>> efforts made by vendors and individuals that utilize the format in=20
>>> their products."
>>>
>>> We could go on from here to highlight the current efforts and=20
>>> releases, as well as provide the mechanisms whereby we get things=20
>>> done. In addition we may want to touch on the boundaries with other=20
>>> PSI groups.
>>> Angel
>>>
>>> Randy Julian wrote:
>>>
>>>> The PSI-MS biweekly call is scheduled for 10:00 EST at the usual=20
>>>> call-in number. Please sent an e-mail to Kent Laursen=20
>>>> (Ken...@ge...) if you need dialing instructions for=20
>>>> the call.
>>>>
>>>> The agenda for the 11 Oct 2005 PSI-MS teleconference was essentially=
=20
>>>> set at the last meeting:
>>>>
>>>> 1. MCP response - This is essential since the reply is required by=20
>>>> 15 Oct 2005
>>>> 2. Review of feedback on the Requirements Survey
>>>> 3. Review of mission statement
>>>> 4. Approval of working groups and recommendations for chairs & spec=20
>>>> teams.
>>>>
>>>> On this last point, the recommendation for working groups looks like=
=20
>>>> this:
>>>>
>>>> 1) MI
>>>> 2) Mass spec (mzData Spec)
>>>> 3) Separations (Prep, Columns, Gels)
>>>> 4) Protein Modifications
>>>> 5) Informatics/Identification/Analysis (analysisXML spec)
>>>> 6) GPS (deliverable Document is the Object Model used by all WGs)
>>>> 7) Extensions, CV=92s & Ontology Methodology
>>>> 8) Reporting Recommendations (MIAPE documents)
>>>>
>>>> Each group needs at least two chairs who are committed to keeping=20
>>>> the communication active and providing reports.
>>>>
>>>> According to the minutes, the draft of the document process should=20
>>>> have been completed, but is still underway with good feedback being=20
>>>> provided by several members (but not enough time to do all the=20
>>>> editing yet). We will discuss the state of these documents and the=20
>>>> overall process if time allows.
>>>>
>>>> Thanks,
>>>> Randy Julian
>>>>
>>>>
>>>>
>>>> -------------------------------------------------------
>>>> This SF.Net email is sponsored by:
>>>> Power Architecture Resource Center: Free content, downloads,=20
>>>> discussions,
>>>> and more. http://solutions.newsforge.com/ibmarch.tmpl
>>>> _______________________________________________
>>>> Psidev-ms-dev mailing list
>>>> Psi...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by:
>>> Power Architecture Resource Center: Free content, downloads,=20
>>> discussions,
>>> and more. http://solutions.newsforge.com/ibmarch.tmpl
>>> _______________________________________________
>>> Psidev-ms-dev mailing list
>>> Psi...@li...
>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>>
>>
>=20
>=20

--=20
~~~~~~~~~~~~~~~~~~~~~~~~
  chr...@eb...
  http://psidev.sf.net/
~~~~~~~~~~~~~~~~~~~~~~~~

Re: [Psidev-ms-dev] PSI-MS teleconference agenda (11 Oct 2005)

[Angel P. <an...@ma...>]

Pierre-Alain Binz wrote:

> Thanks Angel.
> I would add, even if we decide that MIAPE is a group on its own, that 
> the MS working group also generates the corresponding MIAPE modules, 
> which are high-level (end-user and software-vendor) minimal 
> requirements to be supported by the formats
>
Good point. Revised:

The PSI Mass Spectrometry (PSI-MS) standards group consists of academic 
and industry researchers, software developers and instrument 
manufacturers. The goals of the group are: to provide a set of minimal 
reporting requirements which augment the \link{ MIAPE reporting 
guidelines }with respect to mass spectrometry experiments; to provide 
vendor-neutral standard formats for representing mass spectrometry 
experimental data and the results derived through analysis of those 
data;  to foster adoption of the format by highlighting efforts made by 
vendors and individuals that utilize the format in their \link{ products }.

-angel

> Pierre-Alain
>
> Angel Pizarro wrote:
>
>> First stab at a mission statement:
>>
>> "The PSI Mass Spectrometry (PSI-MS) standards group consists of 
>> academic and industry researchers, software developers and instrument 
>> manufacturers. The goal of the group is to provide vendor-neutral 
>> standard formats for representing mass spectrometry experimental data 
>> and the results derived through analysis of those data. A secondary 
>> goal of the group is to foster adoption of the format by highlighting 
>> efforts made by vendors and individuals that utilize the format in 
>> their products."
>>
>> We could go on from here to highlight the current efforts and 
>> releases, as well as provide the mechanisms whereby we get things 
>> done. In addition we may want to touch on the boundaries with other 
>> PSI groups.
>> Angel
>>
>> Randy Julian wrote:
>>
>>> The PSI-MS biweekly call is scheduled for 10:00 EST at the usual 
>>> call-in number. Please sent an e-mail to Kent Laursen 
>>> (Ken...@ge...) if you need dialing instructions for 
>>> the call.
>>>
>>> The agenda for the 11 Oct 2005 PSI-MS teleconference was essentially 
>>> set at the last meeting:
>>>
>>> 1. MCP response - This is essential since the reply is required by 
>>> 15 Oct 2005
>>> 2. Review of feedback on the Requirements Survey
>>> 3. Review of mission statement
>>> 4. Approval of working groups and recommendations for chairs & spec 
>>> teams.
>>>
>>> On this last point, the recommendation for working groups looks like 
>>> this:
>>>
>>> 1) MI
>>> 2) Mass spec (mzData Spec)
>>> 3) Separations (Prep, Columns, Gels)
>>> 4) Protein Modifications
>>> 5) Informatics/Identification/Analysis (analysisXML spec)
>>> 6) GPS (deliverable Document is the Object Model used by all WGs)
>>> 7) Extensions, CV’s & Ontology Methodology
>>> 8) Reporting Recommendations (MIAPE documents)
>>>
>>> Each group needs at least two chairs who are committed to keeping 
>>> the communication active and providing reports.
>>>
>>> According to the minutes, the draft of the document process should 
>>> have been completed, but is still underway with good feedback being 
>>> provided by several members (but not enough time to do all the 
>>> editing yet). We will discuss the state of these documents and the 
>>> overall process if time allows.
>>>
>>> Thanks,
>>> Randy Julian
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by:
>>> Power Architecture Resource Center: Free content, downloads, 
>>> discussions,
>>> and more. http://solutions.newsforge.com/ibmarch.tmpl
>>> _______________________________________________
>>> Psidev-ms-dev mailing list
>>> Psi...@li...
>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>
>>
>>
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by:
>> Power Architecture Resource Center: Free content, downloads, 
>> discussions,
>> and more. http://solutions.newsforge.com/ibmarch.tmpl
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>>
>


-- 

Angel Pizarro
Director, Bioinformatics Facility
Institute for Translational Medicine and Therapeutics
University of Pennsylvania
806 BRB II/III
421 Curie Blvd.
Philadelphia, PA 19104-6160

P: 215-573-3736
F: 215-573-9004

Re: [Psidev-ms-dev] PSI-MS teleconference agenda (11 Oct 2005)

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

Thanks Angel.
I would add, even if we decide that MIAPE is a group on its own, that=20
the MS working group also generates the corresponding MIAPE modules,=20
which are high-level (end-user and software-vendor) minimal requirements=20
to be supported by the formats

Pierre-Alain

Angel Pizarro wrote:

> First stab at a mission statement:
>
> "The PSI Mass Spectrometry (PSI-MS) standards group consists of=20
> academic and industry researchers, software developers and instrument=20
> manufacturers. The goal of the group is to provide vendor-neutral=20
> standard formats for representing mass spectrometry experimental data=20
> and the results derived through analysis of those data. A secondary=20
> goal of the group is to foster adoption of the format by highlighting=20
> efforts made by vendors and individuals that utilize the format in=20
> their products."
>
> We could go on from here to highlight the current efforts and=20
> releases, as well as provide the mechanisms whereby we get things=20
> done. In addition we may want to touch on the boundaries with other=20
> PSI groups.
> Angel
>
> Randy Julian wrote:
>
>> The PSI-MS biweekly call is scheduled for 10:00 EST at the usual=20
>> call-in number. Please sent an e-mail to Kent Laursen=20
>> (Ken...@ge...) if you need dialing instructions for=20
>> the call.
>>
>> The agenda for the 11 Oct 2005 PSI-MS teleconference was essentially=20
>> set at the last meeting:
>>
>> 1. MCP response - This is essential since the reply is required by 15=20
>> Oct 2005
>> 2. Review of feedback on the Requirements Survey
>> 3. Review of mission statement
>> 4. Approval of working groups and recommendations for chairs & spec=20
>> teams.
>>
>> On this last point, the recommendation for working groups looks like=20
>> this:
>>
>> 1) MI
>> 2) Mass spec (mzData Spec)
>> 3) Separations (Prep, Columns, Gels)
>> 4) Protein Modifications
>> 5) Informatics/Identification/Analysis (analysisXML spec)
>> 6) GPS (deliverable Document is the Object Model used by all WGs)
>> 7) Extensions, CV=92s & Ontology Methodology
>> 8) Reporting Recommendations (MIAPE documents)
>>
>> Each group needs at least two chairs who are committed to keeping the=20
>> communication active and providing reports.
>>
>> According to the minutes, the draft of the document process should=20
>> have been completed, but is still underway with good feedback being=20
>> provided by several members (but not enough time to do all the=20
>> editing yet). We will discuss the state of these documents and the=20
>> overall process if time allows.
>>
>> Thanks,
>> Randy Julian
>>
>>
>>
>> -------------------------------------------------------
>> This SF.Net email is sponsored by:
>> Power Architecture Resource Center: Free content, downloads,=20
>> discussions,
>> and more. http://solutions.newsforge.com/ibmarch.tmpl
>> _______________________________________________
>> Psidev-ms-dev mailing list
>> Psi...@li...
>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
>
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads, discussion=
s,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>

--=20
--
 Dr. 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
 Pie...@is...
 http://www.expasy.org/people/Pierre-Alain.Binz.html

Re: [Psidev-ms-dev] PSI-MS teleconference agenda (11 Oct 2005)

[Angel P. <an...@ma...>]

First stab at a mission statement:

"The PSI Mass Spectrometry (PSI-MS) standards group consists of academic 
and industry researchers, software developers and instrument 
manufacturers. The goal of the group is to provide vendor-neutral 
standard formats for representing mass spectrometry experimental data 
and the results derived through analysis of those data. A secondary goal 
of the group is to foster adoption of the format by highlighting efforts 
made by vendors and individuals that utilize the format in their products."

 We could go on from here to highlight the current efforts and releases, 
as well as provide the mechanisms whereby we get things done. In 
addition we may want to touch on the boundaries with other PSI groups.
Angel

 Randy Julian wrote:

> The PSI-MS biweekly call is scheduled for 10:00 EST at the usual 
> call-in number. Please sent an e-mail to Kent Laursen 
> (Ken...@ge...) if you need dialing instructions for the 
> call.
>
> The agenda for the 11 Oct 2005 PSI-MS teleconference was essentially 
> set at the last meeting:
>
> 1. MCP response - This is essential since the reply is required by 15 
> Oct 2005
> 2. Review of feedback on the Requirements Survey
> 3. Review of mission statement
> 4. Approval of working groups and recommendations for chairs & spec 
> teams.
>
> On this last point, the recommendation for working groups looks like 
> this:
>
> 1) MI
> 2) Mass spec (mzData Spec)
> 3) Separations (Prep, Columns, Gels)
> 4) Protein Modifications
> 5) Informatics/Identification/Analysis (analysisXML spec)
> 6) GPS (deliverable Document is the Object Model used by all WGs)
> 7) Extensions, CV’s & Ontology Methodology
> 8) Reporting Recommendations (MIAPE documents)
>
> Each group needs at least two chairs who are committed to keeping the 
> communication active and providing reports.
>
> According to the minutes, the draft of the document process should 
> have been completed, but is still underway with good feedback being 
> provided by several members (but not enough time to do all the editing 
> yet). We will discuss the state of these documents and the overall 
> process if time allows.
>
> Thanks,
> Randy Julian
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads, discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev

[Psidev-ms-dev] PSI-MS teleconference agenda (11 Oct 2005)

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

The PSI-MS biweekly call is scheduled for 10:00 EST at the usual call-i=
n=20
number. Please sent an e-mail to Kent Laursen=20
(Ken...@ge...) if you need dialing instructions for the =
call.

The agenda for the 11 Oct 2005 PSI-MS teleconference was essentially se=
t=20
at the last meeting:

1. MCP response - This is essential since the reply is required by 15=20
Oct 2005
2. Review of feedback on the Requirements Survey
3. Review of mission statement
4. Approval of working groups and recommendations for chairs & spec tea=
ms.

On this last point, the recommendation for working groups looks like th=
is:

1) MI
2) Mass spec (mzData Spec)
3) Separations (Prep, Columns, Gels)
4) Protein Modifications
5) Informatics/Identification/Analysis (analysisXML spec)
6) GPS (deliverable Document is the Object Model used by all WGs)
7) Extensions, CV=92s & Ontology Methodology
8) Reporting Recommendations (MIAPE documents)

Each group needs at least two chairs who are committed to keeping the=20
communication active and providing reports.

According to the minutes, the draft of the document process should have=
=20
been completed, but is still underway with good feedback being provided=
=20
by several members (but not enough time to do all the editing yet). We=20
will discuss the state of these documents and the overall process if=20
time allows.

Thanks,
Randy Julian

[Psidev-ms-dev] Minutes from

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

Everyone,

Attached are the minutes from the September 27, PSI-MS Teleconference.  
Please forward comments, questions or corrections to rkj...@in...

The next teleconference is scheduled for October 11, 2005 10:00 EST at 
the usual number.  Contact Kent Laursen (Ken...@ge...) 
for dialing instructions if you'd like to join the conference call.

Thanks,
Randy

Re: [Psidev-ms-dev] MCP response

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

Dear all,
as proposed in Geneva in the plenary session I have sent to the draft 
MCP, the MIAPE-MS and MIAPE-MSI all with mapping annotations those 
interested to comment on (8 people have asked). A few comments came back 
to me.
After the last MS-group ccall I have sent a draft of a response letter 
that would be addressed to Ralf Bradshaw..
It is planed that I collect the comments before the next ccall (next 
tuesday). I received one from Sean over the list until now. Then I 
reformulate the letter, distribute it before the next ccall together 
with the revised annotated MCP guiudelines and MIAPE-enriched docs and 
we can state on a final draft that can circulate again, at least again 
to the chairs of PSI, so that it can be sent to RB by the 15th.

What is clear from the modifications on the MIAPE docs is:
- no quality judgement are to be included. The MIAPE docs contain only 
min req to describe an experiment.
- The modifications to the MIAPE docs will generate a new version of the 
MIAPE doc, but this version is not the final release. As we have a 
procedure that comes into place to formalise the acceptance of 
documents, we can only say that it is a draft that has reached the 
reviewing status and will be finalised in its next development step.
- The letter will not be my private letter. It has a PSI dimension for 
which we still can decide who might sign it (are Rolf and Ruedi 
appropriate, at least this is a practical work of the MS group who has 
two chairs, and we have people in charge of the MIAPE-MS and MSI docs, 
which all together adds to 6 names)

Keep cool Chris, this is a work that is planed and made available to all 
interested people. So those who are still interested to actively 
participate with comments, please do...

Cheers to all,
Pierre-Alain

Chris Taylor wrote:

> Hi Pierre-Alain, all.
>
> I'm a little nervous that there doesn't seem to have been much list 
> traffic on the reponse to the MCP guidelines. The deadline is next 
> week (15th)...
>
> Maybe this is all in hand, or even done and already out the door, but 
> I am really worried that our big window of opportunity to get our 
> views in will lapse.
>
> Incidentally the separation of 'what was done' and 'was it any good' 
> was something raised (independently) at a recent proteomics PIs 
> meeting I attended in the UK. Opinions were strongly expressed (shall 
> we say) there that a HUPO-like community effort should determine 
> reporting requirements and that journals should only concern 
> themselves with assessing quality (internally, or maybe as a group).
>
> I think that we should propose a separation to the Paris group where 
> PSI in collaboration with them (re)drafts MIAPE: MSI as originally 
> conceived and that the quality measures are pulled out into a second 
> document that PSI can also support in a limited way for 'journal 
> publication standard' results. I say limited firstly because there are 
> a number of journals and we wouldn't want to be seen to siding with 
> anyone and secondly because quality measures have _never_ been part of 
> our remit; and I don't know about everyone else but I have talked to a 
> _lot_ of people at various things over the last few years and noone 
> has ever questioned our approach with MIAPE (i.e. to not address 
> quality).
>
> I may well draft something up myself next week anyway for submission 
> as an individual (clearly stating within that mine is not a PSI view), 
> but I'd really like to also see what is going to go from us as a 
> corporate body.
>
> Cheers, Chris.
>
> ~~~~~~~~~~~~~~~~~~~~~~~~
>  chr...@eb...
>  http://psidev.sf.net/
> ~~~~~~~~~~~~~~~~~~~~~~~~
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by:
> Power Architecture Resource Center: Free content, downloads, discussions,
> and more. http://solutions.newsforge.com/ibmarch.tmpl
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>

-- 
--
 Dr. 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
 Pie...@is...
 http://www.expasy.org/people/Pierre-Alain.Binz.html

[Psidev-ms-dev] MCP response

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

Hi Pierre-Alain, all.

I'm a little nervous that there doesn't seem to have been much 
list traffic on the reponse to the MCP guidelines. The deadline 
is next week (15th)...

Maybe this is all in hand, or even done and already out the 
door, but I am really worried that our big window of opportunity 
to get our views in will lapse.

Incidentally the separation of 'what was done' and 'was it any 
good' was something raised (independently) at a recent 
proteomics PIs meeting I attended in the UK. Opinions were 
strongly expressed (shall we say) there that a HUPO-like 
community effort should determine reporting requirements and 
that journals should only concern themselves with assessing 
quality (internally, or maybe as a group).

I think that we should propose a separation to the Paris group 
where PSI in collaboration with them (re)drafts MIAPE: MSI as 
originally conceived and that the quality measures are pulled 
out into a second document that PSI can also support in a 
limited way for 'journal publication standard' results. I say 
limited firstly because there are a number of journals and we 
wouldn't want to be seen to siding with anyone and secondly 
because quality measures have _never_ been part of our remit; 
and I don't know about everyone else but I have talked to a 
_lot_ of people at various things over the last few years and 
noone has ever questioned our approach with MIAPE (i.e. to not 
address quality).

I may well draft something up myself next week anyway for 
submission as an individual (clearly stating within that mine is 
not a PSI view), but I'd really like to also see what is going 
to go from us as a corporate body.

Cheers, Chris.

~~~~~~~~~~~~~~~~~~~~~~~~
  chr...@eb...
  http://psidev.sf.net/
~~~~~~~~~~~~~~~~~~~~~~~~

[Psidev-ms-dev] Requirements questionnaire reminder`

[Kent L. <Ken...@ge...>]

Thank you to those that have already sent back their requirements
questionnaire.  We are hoping to collate the results after the end of
this week.  We encourage those that would like their input factored into
the process to submit their questionnaires by end of this week, if
possible.  If anyone has trouble with the attachment from the original
questionnaire posting(s), please email me directly and I will send it to
you.

=20

Regards,

Kent Laursen
Senior Software Architect
GenoLogics Life Sciences Software Inc.
p: 250.483.7011
www.genologics.com
<file:///C:\Documents%20and%20Settings\kent\Application%20Data\Microsoft
\Signatures\www.genologics.com>=20

=20

RE: [Psidev-ms-dev] plain text email with attache PSI-MS Requirements questionnaire

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

Might be easier not to send attachments but give a url pointer for
download.=20

>-----Original Message-----
>From: psi...@li...=20
>[mailto:psi...@li...] On Behalf=20
>Of Kent Laursen
>Sent: 30 September 2005 15:18
>To: psi...@li...
>Subject: [Psidev-ms-dev] plain text email with attache PSI-MS=20
>Requirements questionnaire
>
>Some have had problems with the attatchment, so I am resending=20
>one more time with a plain text message.
>
>Kent Laursen
>Senior Software Architect
>GenoLogics Life Sciences Software Inc.
>p: 250.483.7011
>www.genologics.com
>
>
>