psidev-ms-dev — Mass spectroscopy standard development

Re: [Psidev-ms-dev] More MzData Converters ?

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

On Thu, 2006-03-02 at 17:45 +0100, Cannataro_Mario wrote:
> Dear Steffen
> in our proteomics laboratory we have two mass spectrometry instruments:
[...]
> In this case, is it able to collect all experiment information or do you need
> to fill by hand some missing field?
You can add some fields (such as experiment, person, organization
manually in the converter. I have attached a (pruned) testfile
if you want to look at the other fields in <instrument>.

We have an mzData Editor based on Eclipse EMF available, 
which can edit & validate mzData files. 
We can create command line tools for batch-modifying mzData files:
http://www.ipb-halle.de/english/stress-and-developm-biolology/research/bioinformatics/research-projects/metabolomics-platform/

> We are developing a specialized spectra database
Our database is up and running, we have a web upload,
and http://metlin.scripps.edu/download/ can read mzData.

Yours,
Steffen

Re: [Psidev-ms-dev] More MzData Converters ?

[Cannataro_Mario <can...@un...>]

Dear Steffen
in our proteomics laboratory we have two mass spectrometry instruments:

a) Applied Biosystems  Voyager DE-STR MALDI-TOF, interfaced with BioExplo=
rer
software

b) Applied Biosystems  Hybrid QSTAR XL LC-MS/MS QTOF interfaced to Analys=
t QS
software.

Is the software you mentioned able to convert the binary dataset files sa=
ved
by such instruments in the mzData format?

In this case, is it able to collect all experiment information or do you =
need
to fill by hand some missing field?

We are developing a specialized spectra database and we also are interest=
ed
in mzData converters

Thank you in advance
Mario Cannataro

--
Prof. Mario Cannataro
Informatics and Biomedical Engineering,Faculty of Medicine,
University "Magna Gr=E6cia" of Catanzaro,
Via T. Campanella, 115
88100 CATANZARO, ITALY
Tel: 0961-369 4100
Fax: 0961-369 4070
Email: can...@un...


Quoting Steffen Neumann <sne...@IP...>:

> Hi,
>
> We successfully obtained an mzData Converter from Applied
> for our Qstar LC QTOF, and now we're looking for pointers/Contacts
> to MzData Converters for any one of the following machines:
>
> - Bruker Reflex III (MALDI) running FlexControl 1.2
> - Bruker Apex III 70e (FTICR)
> - Agilent 5975 inert MS
> - Thermo Finnigan TSQ Quantum Ultra AM
>   LC-MS with XCalibur software
>
> Thanks in advance
>
> Yours,
> Steffen
>
>





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Re: [Psidev-ms-dev] More MzData Converters ?

[Cannataro_Mario <can...@un...>]

Dear Steffen
in our proteomics laboratory we have two mass spectrometry instruments:

a) Applied Biosystems  Voyager DE-STR MALDI-TOF, interfaced with BioExplo=
rer
software

b) Applied Biosystems  Hybrid QSTAR XL LC-MS/MS QTOF interfaced to Analys=
t QS
software.

Is the software you mentioned able to convert the binary dataset files sa=
ved
by such instruments in the mzData format?

In this case, is it able to collect all experiment information or do you =
need
to fill by hand some missing field?

We are developing a specialized spectra database and we also are interest=
ed
in mzData converters

Thank you in advance
Mario Cannataro

--
Prof. Mario Cannataro
Informatics and Biomedical Engineering,Faculty of Medicine,
University "Magna Gr=E6cia" of Catanzaro,
Via T. Campanella, 115
88100 CATANZARO, ITALY
Tel: 0961-369 4100
Fax: 0961-369 4070
Email: can...@un...


Quoting Steffen Neumann <sne...@IP...>:

> Hi,
>
> We successfully obtained an mzData Converter from Applied
> for our Qstar LC QTOF, and now we're looking for pointers/Contacts
> to MzData Converters for any one of the following machines:
>
> - Bruker Reflex III (MALDI) running FlexControl 1.2
> - Bruker Apex III 70e (FTICR)
> - Agilent 5975 inert MS
> - Thermo Finnigan TSQ Quantum Ultra AM
>   LC-MS with XCalibur software
>
> Thanks in advance
>
> Yours,
> Steffen
>
>





----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.

[Psidev-ms-dev] More MzData Converters ?

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

Hi,

We successfully obtained an mzData Converter from Applied=20
for our Qstar LC QTOF, and now we're looking for pointers/Contacts=20
to MzData Converters for any one of the following machines:

- Bruker Reflex III (MALDI) running FlexControl 1.2
- Bruker Apex III 70e (FTICR)
- Agilent 5975 inert MS=20
- Thermo Finnigan TSQ Quantum Ultra AM
  LC-MS with XCalibur software

Thanks in advance

Yours,
Steffen

[Psidev-ms-dev] Revised InsilicosViewer of interest to mzData users

[Brian P. <bri...@in...>]

Those of you using our free InsilicosViewer software to look at mzData files might want to grab the new version 1.4.2 from
www.insilicos.com - there was a problem loading very small mzData files for viewing.

Hope this helps,
Brian Pratt
www.insilicos.com

[Psidev-ms-dev] Teleconference minutes

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

The minutes from the 7 Feb 2006 teleconference are now on the docstore:

http://psidev.sourceforge.net/docstore/download.php?sess=0&parent=4&expand=1&order=name&binary=1&id=67

The next teleconference is 21 Feb 2006 at 1600 GMT.  Dialing 
instructions can be obtained from Randy Julian (rkj...@in...) 
or Kent Laursen (Ken...@ge...)

Re: [Psidev-ms-dev] PSI-MS teleconference 21 Feb 1600 GMT

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

Hi Randy,
Thanks for the agenda.
Unfortunately, I will be unable to attend, as I will be in the middle of 
the night on my way back from Japan.
Please forward me the discussion outcome on the viewpoints. One thing to 
do is to try and make sure someone from each journal will be in San 
Francisco to discuss and define commonly their viewpoints and heir 
matching to MIAPE. I could take care of  Proteomics. Who can for MCP and 
the others?

Another topic, maybe to announce and then to plan for next: define the 
goals and deliverables to reach in San Francisco. 

Cheers,
Pierre-Alain

Randy Julian wrote:

> We have some left over topics from the Feb 7 PSI-MS teleconference and 
> a couple of new items:
>
> The topics I have for the 21 Feb call are:
>
> 1. Review of requirements questionnaire posted by Kent
> 2. Discussion of W3C "HCLSIG" - Sean Martin
> 3. Follow-up on LSID demo at Geneva and use of LSID in mzData/analysisXML
> 4. Discussion of the Viewpoint in Proteomics "Guidelines" (* See link 
> below)
> 5. Planning for a mzData/mzXML feature analysis in preparation for 
> merging
> 6. Discussion of CV development - all IUPAC terms are in - what's next?
>
> * Viewpoint in Proteomics  2006, vol 6, 4-8, 
> http://viewpoint.proteomics-journal.com, 'Guidelines for the next 10 
> years of proteomics'.  It is Proteomics journal's version of the draft 
> MCP Guidelines. But much more concise. It covers 2D PAGE, MS-based 
> experiments, Protein ID & characterisation, Bioinformatics & 
> Supplementary material.
>
> Anything else?
>
> If you need the call-in information contact either me 
> (rkj...@in...) or Kent Laursen (ken...@ge...) 
> for the numbers.
>
> Thanks,
> Randy
>
>
> -------------------------------------------------------
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-- 
--
 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] PSI-MS teleconference 21 Feb 1600 GMT

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

We have some left over topics from the Feb 7 PSI-MS teleconference and a 
couple of new items:

The topics I have for the 21 Feb call are:

1. Review of requirements questionnaire posted by Kent
2. Discussion of W3C "HCLSIG" - Sean Martin
3. Follow-up on LSID demo at Geneva and use of LSID in mzData/analysisXML
4. Discussion of the Viewpoint in Proteomics "Guidelines" (* See link below)
5. Planning for a mzData/mzXML feature analysis in preparation for merging
6. Discussion of CV development - all IUPAC terms are in - what's next?

* Viewpoint in Proteomics  2006, vol 6, 4-8, 
http://viewpoint.proteomics-journal.com, 'Guidelines for the next 10 
years of proteomics'.  It is Proteomics journal's version of the draft 
MCP Guidelines. But much more concise. It covers 2D PAGE, MS-based 
experiments, Protein ID & characterisation, Bioinformatics & 
Supplementary material.

Anything else?

If you need the call-in information contact either me 
(rkj...@in...) or Kent Laursen (ken...@ge...) 
for the numbers.

Thanks,
Randy

[Psidev-ms-dev] CV File

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

The latest version of the PSI-MS CV file is in the document management 
system:

http://psidev.sourceforge.net/docstore/download.php?sess=0&parent=7&expand=1&order=name&binary=1&id=64

There are now 373 terms in the CV - there are many yet to be added from 
the IUPAC list, however, all of the definitions of previously existing 
terms have been updated with the IUPAC definitions.

We need to review all of the terms and determine if there are any 
redundancies or problems with term usage.  The OBO-Edit program seems 
helpful in this regard.

This latest version now uses the "part_of" relationship (defined as a 
'type' at the top of the file) to indicate that most terms a 'part_of' 
the ontology, and some terms have a 'is_a' relationship with other terms 
('Quadrupole' is_a 'Analyzer Type').  There are some connecting terms 
(like 'Mass Spectrometer') which probably need to be added to create the 
proper relationships between some terms and there are a large number of 
terms from the technical mass spectrometry literature which may only 
rarely appear in a HUPO file, however, since the IUPAC terms were given 
no relationships or accession numbers, it seemed wise to import their 
list /en masse/.

Take a look and post any questions or comments to the list or send them 
to Randy.

Thanks

[Psidev-ms-dev] mzData 1.05 Specification Document

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

The formal specification of mzData version 1.05 is nearing completion 
and needs the attention of the entire PSI to help complete the final 
editing.

The document can be downloaded from our document management system using 
the following link:

http://psidev.sourceforge.net/docstore/download.php?sess=0&parent=7&expand=1&order=name&binary=1&id=63

We need to add additional detail just about everywhere in the document.  
Anyone developing programs using the format should be able to help with 
ensuring that the document would help a new developer in creating a file 
of this format.  Look for where the explanations are confusing or where 
someone is known to have had trouble.  Since most of the questions I 
have seen revolve around the CV and the base64binary implementation, I 
have added details and examples there - this may or may not be enough 
detail and there are other areas which could benefit from the same type 
of explanations.

One thing to note is that during the last PSI-MS teleconference, we 
decided that a 'Guide' document was needed to explain which CV terms 
were allowed under which elements and which CV terms were required for a 
mzData file to meet the expectations of "MIAPE-MS".  So you will not 
find this in the specification document itself.

Please review this specification and send comments, suggestions, and any 
clarifying ideas to Randy Julian (rkj...@in...).

Thanks,
Randy Julian

[Psidev-ms-dev] PSI-MS Teleconference agenda Feb 7 1600 GMT

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

The PSI-MS teleconference is on for Tuesday Feb 7.  The topics for 
dicussion this week:

1. Progress on the CV, new term addition mechanism, relationship 
specifications, etc.
2. Discussion on specification document
3. Review of requirements questionnaire posted by Kent
4. Planning for a mzData/mzXML feature analysis in preparation for merging
5. Feedback on 'Informatics' WG and the general 'WG' creation process

Anything else?

If you need the call-in information contact either me 
(rkj...@in...) or Kent Laursen (ken...@ge...) 
for the numbers.

Thanks,
Randy

[Psidev-ms-dev] requirements survey results

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

The responses to the PSI-MS requirements survery sent out some time ago =
are aggregated below.
=20
Regards,
Kent Laursen
GenoLogics
=20
PSI-MS Requirements Questionnaire

=20

=20

Requirements

=20

At the most technical level of detail the deliverables of PSI-MS will =
include a codified rendering of information interchange structure in the =
form of UML models and/or XML Schema that can be utilized as a basis for =
a variety of computerized implementations.  However PSI-MS has the goal =
to publish its work at three levels of abstraction in order clearly =
represent its value to a broader audience ranging from scientists and =
decision makers to technologists. These three levels of abstraction are =
the conceptual, the logical and the physical.  This questionnaire asks =
you to categorize your ideas for requirements with this leveling =
applied.  When collated your responses will be a valued input in =
describing mzData in both specification and codified form.  Some =
characteristics of these three levels of abstraction are listed below:

=20

Conceptual =96 visionary, science driven, computationally independent, =
expressing an aim, justifying and or explaining the basis for the effort

=20

Logical - expressed clearly in human understandable terms, logically =
complete without implementation dependence, providing satisfactory =
rendering of what the solution is, delineating the contract(s) that the =
solution must fulfill

=20

Physical =96 having a direct relationship to a codified or machine =
processable form, describing detail sufficient for implementation

=20

We utilize the notion of requirements to simply state a set of aims, =
qualities, rules, constraints, shapes and functionality to which the =
published work of PSI-MS must adhere.   In addition PSI-MS will provide =
a response or mapping describing how its publications address the =
requirements and concerns represented by MCP and MIAPE.=20

=20

=20

=20

Questions

=20

1. What is your aim in participating with the PSI-MS working group

=20

*	Get an in-depth understanding and early information of how the =
proposed standards are to be used.
*	Contribute to the standards by sharing of our expertise in proteomics =
experimentation and data analysis.
*	To contribute with our experience in using the proposed standards in =
software developed by us.
*	We have adopted mzData as our internal mass spec data format and have =
developed tools to convert other ms data formats - eg, mzXML - to it.  I =
participate primarily as an interested consumer of the standards =
developed by the working group.
*	We have interests in ms data that go beyond proteomics.  I would like =
to add a voice to the discussions that might allow the standard to =
encompass a broader discipline, eg glycoproteomics.
*	The creation of data interchange formats and utilities which enhance =
access to raw data for the development and use of informatics tools.  My =
research depends on high throughput and automated mass spectrometry and =
easy access to a full representation of data from instruments is =
critical.
*	To participate in establishing guidelines, defining and evaluating =
object models and derived schemes, and elaborating terminological =
resources in the context of existing initiatives including PSI
*	I am responsible for the standardization of the proteomics platform in =
our research center. Therefore, I am interested in the advancement of =
PSI-MS work concerning mzData and analysisXML.

=20

2. What would you like to see PSI-MS accomplish or stated another way =
what should be the goals of PSI-MS in your view?



*	To create data transport standards =96 for publication repositories, =
between software and database applications.
*	Create guidelines on what data should be retrieved and stored for easy =
access (call it an object model if you will) in proteomics =
experimentation.
*	Make vendors understand that proprietary data formats are not a key =
for success.
*	Define a standard that can capture ms data acquired by most models of =
ms instruments.
Define a standard that can capture the semantics of the ms data within =
any of numerous discipline contexts.
The first standard provides for the raw data, devoid of contextual =
semantics.  The second adds the contextual semantics
*	The goal should be to create a community standard which addresses the =
needs of as many stakeholders as possible.  To me this means recognizing =
several key facts: a) instrument vendors own their data formats and an =
interchange format is not the same as a operational or native format; b) =
there is no single, correct proteomics or mass spectrometry =91work =
flow=92 and as many of these uses need to be considered as possible for =
an interchange specification to become a standard.
*	From the data producer=92s point of view, to ensure common practices =
by sharing experimental data and results thru publications (i.e. =
supplementary materials) and repositories, and finally to be able to =
understand unambiguously and to reproduce proteomics experiments.
*	From the software engineer=92s point of view, to deliver standard =
format (and associated handling tools) that encompasses the following =
types of data: raw, processed and identification. To make it daily used, =
the issued standards might be open and well-documented; moreover, widely =
accepted and supported (especially by vendors and manufacturers).
*	In order to make people use PSI-MS standards, PSI-MS should not only =
define them but also provide users with free open source software tools =
such as MS spectra viewers, MS analysis viewers, parsers, converters, =
=85

=20

3. If you have any general suggestions as to how to accomplish these =
goals, please state them here.

 =20

*	What I think is lacking in PSI-MS is the lack of communication of =
progress and changes in the development. The PSI-dev web pages should be =
a natural place to look for the current status of PSI-MS development. As =
it is now, I get the feeling that a small group knows where PSI-MS is =
going. Since the bi-weekly teleconfs are not scalable to a large =
audience, information must be spread in some other way. I think this is =
a key issue if we want the community to take our work seriously, and in =
the long run adopting standards created by us.
*	Incremental revisions of standards, i.e. do not try to solve =
everything in one shot. Also, be more pragmatic, tests with real data =
during specification development. As it is now, we have problems knowing =
what should be changed in the proposed standards.
*	Get funding to key people so they can focus on PSI-MS
*	Concentrate first on the raw data standard.  You should be able to =
achieve widespread agreement on it rather quickly.  The bun-fight starts =
when the contextual semantics standard is attempted.  This is because =
each research group will have their own context and will want it =
represented.  If the contextual semantics standard can be made abstract =
enough, individual contextual subclasses will be straightforward to =
develop and most groups will be happy.
*	Define the process by which decisions are made.  Formalize the =
structure of the organization and give everyone a chance to contribute.  =
Provide better public interaction, communication and documentation
*	it seems fruitful to allow wide participation and create a transparent =
process for establishing standards. The main point remains the barrier =
of language which can lead to misunderstanding and sometimes, make it =
difficult to explicit semantic concept. For these reasons, frequent =
exchange by mailing list and conf call reports should ensure a good =
communication level between each participant. Besides, document revision =
tracking would be favored by making it frequently available. Two =
meetings per year seem to be enough

=20

4. What conceptual requirements should be fulfilled by PSI-MS/mzData?


=20

*	I think the most important goal for PSI-MS specifications is that they =
should support and enable sharing of data.
*	It should be possible to answer the question =93I=92ve done an =
experiment with 67 samples, MS and MSMS. I need to send these to a =
publication repository, how do I use PSI-MS stuff?=94
*	The formats of the PSI should allow experimental quality to be =
evaluated.
*	They should allow scientists to share information across instrument =
types, time and space.
*	The formats of the PSI should allow the accumulation of a community =
wisdom represented by the ability to reanalyze data indefinitely.

=20

5. What logical requirements should be fulfilled by PSI-MS/mzData?

=20

*	The standards should be implement-able, i.e. don=92t overdo them.
*	Examples of use of the standard should be created, i.e. real data in =
files following specifications created by PSI-MS. Use cases describing =
real world scenarios.
*	The aim of any standard is to promote interchange.  It is also to =
promote computability.  By creating, promoting, and enforcing a =
standard, researchers will be able to share data, build on previous =
findings, and construct useful databases and archives.
*	Something akin to the W3C (HYPERLINK "http://www.w3.org/"www.w3.org).
*	It should not break when new instruments or experiments are developed.
*	mzData should perform the function of being a full representation of =
data from mass spectrometry-based experiments.
*	The formats should be able to be generated by the instrument data =
systems directly and used by users without expertise in programming to =
submit data to repositories, or to interchange results between groups.
*	The solution should be the unique reference: produced by raw data =
processing software as well as identification (search) engines.=20
*	The solution must be pragmatic: for instance, xsl transformation from =
a given format to another one is time- and space-consuming, therefore =
unrealistic in a =93true=94 proteomics pipeline. Another example is =
illustrated by the amount of data daily produced by proteomics center =
(in our case around 30 Go/day of raw data): a human-readable format =
seems to be inappropriate for such volume.

=20

6. What physical requirements should be fulfilled by PSI-MS/mzData?

=20

*	Use LSID to reference data residing in known data providers, e.g. when =
a Swissprot entry is references do something like =
urn:lsid:expasy.ch:swissprot:p12345:41, and this should be possible to =
validate with an parser. This would also remove the need for storing =
information such as sequences, since these will be automatically =
retrievable. Bottom line: embrace LSID.
*	The PSI-MS working group thanks you for your participation in this =
survey.  Your entries will be examined, collated and included in the =
shaping of the published specifications of mzData and analysisXML.
*	Development and maintenance of a schema, eg .xsd, or collection =
thereof
*	Development of tools that can be used to move data from an earlier =
version of the schema to a later version
*	Development of documentation that helps people build datasets that =
conform to the schema
*	Maintenance of a repository of open source tools that have been =
developed by PSI or 3rd parties that operate on dataset conforming to =
the schema
*	It should be compact enough to allow reasonable computer systems to =
move and operate on files of the format.
*	The format should be open and self describing.
*	Files in the format should be verifiable, support concepts like =
digital security and allow for the management of data integrity.
*	To answer properly, we just wonder whether it is expected one (and =
only one) implementation (such as XML) or several (XML, SQL, Object =
oriented language) derived from a unique model?
*	As said in 2., for mzData, PSI-MS should do a work similar to the one =
done by Sashimi for mzXML standards cf:  =
http://sashimi.sourceforge.net/software_glossolalia.html.
*	That is provide free converters from native binary formats (RAW, wiff, =
=85) into mzData and parsers to get spectra objects from an mzData file =
in Perl, Java,=85
*	Same for analysisXML: provide converters from common formats: Sequest, =
Mascot, Tandem, =85 into analysisXML.
*	It should also provide a free portable viewer (cf msInspect =
http://proteomics.fhcrc.org/CPAS/Wiki/home/help/page.view?name=3Dviewer) =
to display MS spectra. InSilicos does the job but is available on =
Windows only.


--=20
No virus found in this outgoing message.
Checked by AVG Free Edition.
Version: 7.1.375 / Virus Database: 267.15.1/250 - Release Date: 2/3/2006
=20

[Psidev-ms-dev] Teleconference Minutes

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

The minutes from the last two PSI-MS teleconferences are now on the PSI 
DocStore:

10 Jan 2006:

http://psidev.sourceforge.net/docstore/download.php?sess=0&parent=4&expand=1&order=name&binary=1&id=59

24 Jan 2006:

http://psidev.sourceforge.net/docstore/download.php?sess=0&parent=4&expand=1&order=name&binary=1&id=60

The next teleconference is scheduled for Feb 7 at 1600 GMT - please 
forward any agenda items for discussion.

The mzData specification is being completed so that review can occur at 
the April PSI meeting.  We are collecting "Use Cases", "Goals" and 
"Non-Goals" for the document so that common uses of the format can be 
explained.  Our idea of 'use case' is more like a scenario than a formal 
document.  Goals should state what the specification should achieve and 
non-goals should describe what is considered out of scope for the 
specification

Some examples that have been collected so far:

_Use cases for mzData: _
Store spectral data collected from an HPLC-MS experiment

Store tandem mass spectrum

Store processed peak list

Store Time-domain data supporting TOF peak list

Store FID data from FTICR to support peak list

Store continuous, high resolution spectra

Store selected ion monitoring experimental data

Compare spectra from the same sample analysed by two instruments from 
different manufacturers using a third party tool.

_Goals:_
Provide a vendor-independent representation of mass spectral data 
collected for use in proteomics analysis

Allow new experiments and new instruments to be represented via an 
expansion of a controlled vocabulary rather than a format change

Provide a controlled vocabulary derived from the standard IUPAC 
terminology for analytical chemistry and other standards groups

_Non-Goals:_
Representation of sample preparation methods and steps

Representation of biological sample origins

The format is not intended to be suitable as an internal file format for 
a mass spectrometry application that works with peak lists and/or raw 
mass spec data.


Please either post to this list, or send comments to Randy Julian 
rkj...@in...

Thanks,
Randy

[Psidev-ms-dev] Proposed PSI Process for Review

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

During the 2005 PSI Fall Meeting in Geneva, it was widely suggested that 
the PSI mission would benefit from better documenting its processes and 
clarifying roles and responsibilities.

Given that we now have multiple standards which are being adopted by the 
proteomics community, the PSI leadership recognizes the need for more 
structure in creating, maintaining, and changing specifications.  At the 
same time, the group desires to remain approachable, inclusive and 
transparent while the size of the group and the complexity of the tasks 
both increase.

During the Geneva meeting, Prof. Norman Paton (Univ. Manchester) 
suggested that we look at the process used by the Global Grid Forum 
(GGF) to create and maintain recommendations.  These processes have been 
demonstrated to be both reasonable and productive having been used to 
create stable and useful specifications in modest time frames.

During the last few months a small team undertook editing several 
documents provided by the GGF founders to adapt them to the smaller size 
and narrower scope of the PSI.  The result is a proposed process 
described in three documents (structure, management and documents), and 
summarized in an overview paper.

In an nutshell, it is proposed that PSI formalize the current 'working 
groups', asking each one to create a charter, a set of deliverables and 
a time-line.  Working groups would generate documents which are either 
community practice descriptions, or recommendations.  A Steering Group 
will be created from the Working group chairs as well as other PSI 
members who will help with coordination between groups, organizing 
meetings and management of the PSI.  A formal PSI-Editor role will be 
created and an approval and review process for new recommendations is 
proposed.

Below are links to these documents for public review by the community:

Overview: 
http://psidev.sourceforge.net/docstore/download.php?sess=0&parent=16&expand=1&order=name&sortname=ASC&binary=1&id=57

Structure: 
http://psidev.sourceforge.net/docstore/download.php?sess=0&parent=16&expand=1&order=name&sortname=ASC&binary=1&id=58

Management: 
http://psidev.sourceforge.net/docstore/download.php?sess=0&parent=16&expand=1&order=name&sortname=ASC&binary=1&id=56

Document Process: 
http://psidev.sourceforge.net/docstore/download.php?sess=0&parent=16&expand=1&order=name&sortname=ASC&binary=1&id=55

We would like to collect comments on the processes outlined in these 
documents (and editorial comments on the documents themselves) by April 
14, 2006 (the week before the Spring PSI meeting April 21, 2006), with 
the goal of approving a final process during the Spring meeting.

Please send comments to either Randy Julian (rkj...@in...) or 
Henning Hermjakob (hh...@eb...).

Thanks,
Randy Julian

[Psidev-ms-dev] Re: [Psidev-gps-dev] Reminder, MIAPE GE call today at 4pm GMT

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

Hiya.

On the new parent (aligned with Norm's forms of words on intent=20
and taking into account all else that was said in relation to=20
MIAPE: GE and other stuff) and the module template (requires=20
Word); these have been on the GPS page for a little while now.=20
Please do comment on them direct to me.

http://psidev.sourceforge.net/gps/#miape (parent v2.0, module v1.0).

Cheers, Chris.

Btw we seriously need to work out what is going on with MCP (and=20
now Proteomics); while we wait for others we lose the initiative=20
and I really want to publish _at least_ the parent, ideally in=20
Nature Biotech, very soon. It'd be nice to start putting out the=20
modules also; MS has been done for nearly a _year_ now, sat on a=20
shelf while the world moved around it, and MSI has been done for=20
a good while too.


Pierre-Alain Binz wrote:
> Dear Andy,
> As I've been asked to take care of the MIAPE MS and MSinformatics MIAPE=
=20
> docs for the tow MS and MSInformatics working groups, I would have like=
d=20
> to participate to the next ccall. My input would have of course been=20
> mainly to coordinate the homogeneity in the format and content of the=20
> MIAPE docs in the different groups.But I unfortunately have a agenda=20
> clash and cannot attend.
>=20
> So I will be happy to get  in touch after it, and maybe then be part of=
=20
> the expert review, or even before if there is anything to be coordinate=
d=20
> (and maybe modified in the MS and MSI docs) before to be sent.
>=20
> Just one thing:
> At a recent ccall in the MS group, Chris Taylor has proposed to build a=
=20
> new draft of the parent doc, which should take in consideration the=20
> comments made I think last november in one of the Gel ccalls, where=20
> duplication of information and level of detail of the format was=20
> discussed. In case he is participating, could you ask him the status of=
=20
> this doc?
>=20
> Thanks
>=20
> Pierre-Alain
>=20
>=20
>=20
> Andy Jones wrote:
>=20
>> Hi all,
>>
>> This is a reminder we have a conference call to discuss MIAPE Gel=20
>> electrophoresis at 4pm GMT today=20
>> (http://www.timeanddate.com/worldclock/fixedtime.html?day=3D23&month=3D=
1&year=3D2006&hour=3D16&min=3D0&sec=3D0&p1=3D0=20
>> <http://www.timeanddate.com/worldclock/fixedtime.html?day=3D23&month=3D=
1&year=3D2006&hour=3D16&min=3D0&sec=3D0&p1=3D0>)=20
>>
>>
>> =20
>>
>> We now have several completed examples, demonstrating 1D and 2D gels=20
>> so we will discuss the changes that need to be made to the document=20
>> prior to expert review. If you still need the example documents or the=
=20
>> call access code, please send me an email (aj...@cs...=20
>> <mailto:aj...@cs...>).
>>
>> Best wishes,
>>
>> Andy
>>
>> =20
>>
>> =20
>>
>>    =20
>>
>> **Conference Details**
>>
>>    =20
>>
>> Right-click here to download pictures. To help protect your privacy,=20
>> Outlook prevented automatic download of this picture from the Internet.
>>
>> =20
>>
>> =20
>>
>> Scheduled Conference Date:
>>
>>    =20
>>
>> 23 January 2006
>>
>> Scheduled Start Time:
>>
>>    =20
>>
>> 4:00 p.m. Greenwich Mean Time
>>
>> Scheduled End Time:
>>
>>    =20
>>
>> 5:25 p.m. Greenwich Mean Time
>>
>> Scheduled # of Participants:
>>
>>    =20
>>
>> 10
>>
>> Type of Conference:
>>
>>    =20
>>
>> Web-Scheduled Standard
>>
>> Primary Dial-in Number:
>>
>>    =20
>>
>> 0844.888.8888 (UK 5p National Rate)
>>
>> Alternate Dial-in Numbers:
>>
>>    =20
>>
>> If your conference includes Participants located outside of the U.K.,=20
>> you can choose more than one dial-in phone number. As long as everyone=
=20
>> participating in your conference enters the same Participant Access=20
>> Code, they will be joined together.
>>
>> =20
>>
>>    =20
>>
>> =B7  +44.870.088.5706 (For Callers Outside of the U.K.)
>>
>> =20
>>
>>    =20
>>
>> =B7  01805.004.102 (For Callers in Germany)
>>
>> =20
>>
>=20

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

[Psidev-ms-dev] Testing spML milestone 1

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

Hello all, 

Following the release of spML (sample processing) milestone 1 last month,
the next stage of validation involves populating the model with real data to
see how it can be accommodated and if changes are required to the model.
Therefore, we would like to recruit people willing to validate the format by
providing some test data. The release contains models for column-based
separations (e.g. liquid chromatography), capillary electrophoresis,
rotofors, centrifugation and generic separations (for other types populated
by controlled vocab terms).  

 

We can provide a version of the model that loads in the Pedro software
(http://pedrodownload.man.ac.uk/) for entering data. If you are interested
in contributing to the development of spML by entering some protocol
information into the software or by providing the information for us to
enter, please get in touch (aj...@cs...),

Best wishes,

Andy

[Psidev-ms-dev] RE: Psidev-ms-dev digest, Vol 1 #83 - 1 msg

[Richard C. <rc...@eb...>]

The PSI-MI ontology uses the approach I've suggested. For example:

[Term]
id: MI:0016
name: circular dichroism
exact_synonym: "cd" []
synonym: "CD" []

[Term]
id: MI:0018
name: two hybrid
synonym: "2H" []

[Term]
id: MI:0019
name: coimmunoprecipitation
exact_synonym: "coip" []

[Term]
id: MI:0020
name: transmission electron microscopy
exact_synonym: "tem" []

--
Richard Cote
Software Engineer - PRIDE Project Team (Sequence Database Group)
             
European Bioinformatics Institute             
Wellcome Trust Genome Campus            RC...@eb...      
Hinxton                                 
Cambridge CB10 1SD                      Phone: (+44) 1223 492610  
United Kingdom                          Fax  : (+44) 1223 494468 

-----Original Message-----
From: Randy Julian [mailto:rkj...@in...] 
Sent: 11 January 2006 12:13
To: Richard Cote
Cc: psi...@li...; hh...@eb...; 'Philip Jones';
'Chris Taylor'
Subject: Re: Psidev-ms-dev digest, Vol 1 #83 - 1 msg


Richard,

All acronyms require context.  I like the idea of expanding them.  Are 
there other ontologies being developed by the PSI that have the same 
problem?

Randy





Richard Cote wrote:

>Hi Randy
>
>A quick comment on the ontology. I believe that the use of acronyms as 
>term names should be avoided if possible. The OBO format allows for the 
>use of synonyms and I believe that the acronyms should be placed there, 
>with the full name as the primary term name. In other ontolgies that I 
>have seen, this is common practice. The mzData/analysisXML files will 
>not have the definitions and some of these acronyms, taken out of 
>context, quickly become meaningless.
>
>id: PSI:1000070
>name: APCI
>
>id: PSI:1000071
>name: CI
>
>id: PSI:1000072
>name: EI
>
>id: PSI:1000073
>name: ESI
>
>id: PSI:1000074
>name: FAB
>
>id: PSI:1000075
>name: MALDI
>
>id: PSI:1000079
>name: FT-ICR
>
>id: PSI:1000084
>name: TOF
>
>id: PSI:1000086
>name: FWHM
>
>id: PSI:1000111
>name: EMT
>
>id: PSI:1000117
>name: ADC
>
>id: PSI:1000119
>name: TDC
>
>id: PSI:1000133
>name: CID
>
>id: PSI:1000134
>name: PD
>
>id: PSI:1000135
>name: PSD
>
>id: PSI:1000136
>name: SID
>
>Best regards,
>Richard
>--
>Richard Cote
>Software Engineer - PRIDE Project Team (Sequence Database Group)
>             
>European Bioinformatics Institute             
>Wellcome Trust Genome Campus            RC...@eb...      
>Hinxton                                 
>Cambridge CB10 1SD                      Phone: (+44) 1223 492610  
>United Kingdom                          Fax  : (+44) 1223 494468 
>
>
>  
>

Re: [Psidev-ms-dev] Updated Ontology File

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

Hello Randy,

I have two suggestions for the mzData ontology. My first suggestion is th=
e
use of "instance_of". I think it would be more practical to define, for
example,
"Channeltron" as follows:
[Term]
id: PSI:1000107
name: Channeltron
def: ...
instance_of: PSI:1000026 ! DetectorType
I'm not saying that "is_a=10" is wrong in this and other cases, but
considering this snippet of XML (addmittedly a bit silly):
<detector>
<cvParam cvLabel=3D"psi" accession=3D"PSI:1000026" name=3D"mzOntology"
value=3D"DetectorType"/>
</detector>
a program would validate this a correct use of the ontology (unless
additional "intelligence" is programmed into it).
This leads me to another problem:
<source>
<cvParam cvLabel=3D"psi" accession=3D"PSI:1000026" name=3D"mzOntology"
value=3D"DetectorType"/>
</source>
is also quite difficult to spot as incorrect, as the ontology doesn't
define where the terms can be used. The use of "part_of" could resolve
this:
[Term]
id: PSI:1000026
name: DetectorType
def: ...
part_of: PSI:... ! Detector

Regards
 Kai

Randy Julian wrote:
> There is a new PSI Ontology File (for use with mzData) on the docstore:
>
> http://psidev.sourceforge.net/docstore/view.php?sess=3D0&parent=3D7&exp=
and=3D1&order=3Dname&sortname=3DASC&id=3D53&action=3Dfile_details
>
> There have been no new terms added (there are 204 entries).  But there
is now a definition section for every term, and the MS group is
> currently editing definitions.  Have a look and send any comments you h=
ave.
>
> The file can be viewed and edited in the beta version of the OBO-Edit
program:
>
> http://sourceforge.net/project/showfiles.php?group_id=3D36855&package_i=
d=3D148487
>
> or you can use a text editor...
>
> The next step is to reconcile the ontology with the second draft of the
IUPAC nomenclature (2006 draft):
>
> http://www.msterms.com/wiki/index.php?title=3DIUPAC_Task_Group_MS_Terms=
_Second_Draft
>
> There are terms which are needed by mzData and analysisXML which are no=
t
on this list, so any other instrument or data processing parameters
which are desired by the PSI membership can be send to Randy
> (rkj...@in...) or any other PSI-MS group member.
>
> The goal of the PSI-MS group is to update this file frequently, with th=
e
possibility of the human readable text changing to correct spelling or
to adjust to IUPAC norms, but the accession number assigned to the
concept is fixed and will not be changed, removed or reused.
>
> Thanks,
> Randy Julian
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log
files
> for problems?  Stop!  Download the new AJAX search engine that makes
searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
http://ads.osdn.com/?ad_id=3D7637&alloc_id=3D16865&op=3Dclick
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
>
>


--
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
****************************************************************

Re: [Psidev-ms-dev] Re: Psidev-ms-dev digest, Vol 1 #83 - 1 msg

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

Hiya. There aren't yet, but there very soon will be. I like this 
as a general policy; I'll suggest it on the FuGO call later 
today also.

Cheers, Chris.

P.S. We had our second 'MetaboMeeting' Monday/Tuesday and in the 
standards breakout we (for the second time) affirmed that mzData 
would be the weapon of choice for moving mass spec Mbx data 
around (helped enormously by recent moves by Thermo (Thomas 
McClure) et al. to reimplement proteomics-based mzData-related 
libraries in chem software). Also we agreed to coordinate on 
vocabulary (/FuGO), to codevelop spML (sample prep -- 
separations++) and to develop from FuGE as far as humanly 
possible (esp. for their NMR format).

Randy Julian wrote:
> Richard,
> 
> All acronyms require context.  I like the idea of expanding them.  Are 
> there other ontologies being developed by the PSI that have the same 
> problem?
> 
> Randy
> 
> 
> 
> 
> 
> Richard Cote wrote:
> 
>> Hi Randy
>>
>> A quick comment on the ontology. I believe that the use of acronyms as 
>> term
>> names should be avoided if possible. The OBO format allows for the use of
>> synonyms and I believe that the acronyms should be placed there, with the
>> full name as the primary term name. In other ontolgies that I have seen,
>> this is common practice. The mzData/analysisXML files will not have the
>> definitions and some of these acronyms, taken out of context, quickly 
>> become
>> meaningless.
>> id: PSI:1000070
>> name: APCI
>>
>> id: PSI:1000071
>> name: CI
>>
>> id: PSI:1000072
>> name: EI
>>
>> id: PSI:1000073
>> name: ESI
>>
>> id: PSI:1000074
>> name: FAB
>>
>> id: PSI:1000075
>> name: MALDI
>>
>> id: PSI:1000079
>> name: FT-ICR
>>
>> id: PSI:1000084
>> name: TOF
>>
>> id: PSI:1000086
>> name: FWHM
>>
>> id: PSI:1000111
>> name: EMT
>>
>> id: PSI:1000117
>> name: ADC
>>
>> id: PSI:1000119
>> name: TDC
>>
>> id: PSI:1000133
>> name: CID
>>
>> id: PSI:1000134
>> name: PD
>>
>> id: PSI:1000135
>> name: PSD
>>
>> id: PSI:1000136
>> name: SID
>>
>> Best regards,
>> Richard
>> -- 
>> Richard Cote
>> Software Engineer - PRIDE Project Team (Sequence Database Group)
>>             European Bioinformatics Institute             Wellcome 
>> Trust Genome Campus            RC...@eb...      
>> Hinxton                                 Cambridge CB10 
>> 1SD                      Phone: (+44) 1223 492610  United 
>> Kingdom                          Fax  : (+44) 1223 494468
>>
>>  
>>
> 
> 
> 
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log 
> files
> for problems?  Stop!  Download the new AJAX search engine that makes
> searching your log files as easy as surfing the  web.  DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
> _______________________________________________
> Psidev-ms-dev mailing list
> Psi...@li...
> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> 

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

[Psidev-ms-dev] Re: Psidev-ms-dev digest, Vol 1 #83 - 1 msg

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

Richard,

All acronyms require context.  I like the idea of expanding them.  Are 
there other ontologies being developed by the PSI that have the same 
problem?

Randy





Richard Cote wrote:

>Hi Randy
>
>A quick comment on the ontology. I believe that the use of acronyms as term
>names should be avoided if possible. The OBO format allows for the use of
>synonyms and I believe that the acronyms should be placed there, with the
>full name as the primary term name. In other ontolgies that I have seen,
>this is common practice. The mzData/analysisXML files will not have the
>definitions and some of these acronyms, taken out of context, quickly become
>meaningless. 
>
>id: PSI:1000070
>name: APCI
>
>id: PSI:1000071
>name: CI
>
>id: PSI:1000072
>name: EI
>
>id: PSI:1000073
>name: ESI
>
>id: PSI:1000074
>name: FAB
>
>id: PSI:1000075
>name: MALDI
>
>id: PSI:1000079
>name: FT-ICR
>
>id: PSI:1000084
>name: TOF
>
>id: PSI:1000086
>name: FWHM
>
>id: PSI:1000111
>name: EMT
>
>id: PSI:1000117
>name: ADC
>
>id: PSI:1000119
>name: TDC
>
>id: PSI:1000133
>name: CID
>
>id: PSI:1000134
>name: PD
>
>id: PSI:1000135
>name: PSD
>
>id: PSI:1000136
>name: SID
>
>Best regards,
>Richard
>--
>Richard Cote
>Software Engineer - PRIDE Project Team (Sequence Database Group)
>             
>European Bioinformatics Institute             
>Wellcome Trust Genome Campus            RC...@eb...      
>Hinxton                                 
>Cambridge CB10 1SD                      Phone: (+44) 1223 492610  
>United Kingdom                          Fax  : (+44) 1223 494468 
>
>
>  
>

[Psidev-ms-dev] RE: Psidev-ms-dev digest, Vol 1 #83 - 1 msg

[Richard C. <rc...@eb...>]

Hi Randy

A quick comment on the ontology. I believe that the use of acronyms as =
term
names should be avoided if possible. The OBO format allows for the use =
of
synonyms and I believe that the acronyms should be placed there, with =
the
full name as the primary term name. In other ontolgies that I have seen,
this is common practice. The mzData/analysisXML files will not have the
definitions and some of these acronyms, taken out of context, quickly =
become
meaningless.=20

id: PSI:1000070
name: APCI

id: PSI:1000071
name: CI

id: PSI:1000072
name: EI

id: PSI:1000073
name: ESI

id: PSI:1000074
name: FAB

id: PSI:1000075
name: MALDI

id: PSI:1000079
name: FT-ICR

id: PSI:1000084
name: TOF

id: PSI:1000086
name: FWHM

id: PSI:1000111
name: EMT

id: PSI:1000117
name: ADC

id: PSI:1000119
name: TDC

id: PSI:1000133
name: CID

id: PSI:1000134
name: PD

id: PSI:1000135
name: PSD

id: PSI:1000136
name: SID

Best regards,
Richard
--
Richard Cote
Software Engineer - PRIDE Project Team (Sequence Database Group)
            =20
European Bioinformatics Institute            =20
Wellcome Trust Genome Campus            RC...@eb...     =20
Hinxton                                =20
Cambridge CB10 1SD                      Phone: (+44) 1223 492610 =20
United Kingdom                          Fax  : (+44) 1223 494468=20

[Psidev-ms-dev] Updated Ontology File

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

There is a new PSI Ontology File (for use with mzData) on the docstore:

http://psidev.sourceforge.net/docstore/view.php?sess=0&parent=7&expand=1&order=name&sortname=ASC&id=53&action=file_details

There have been no new terms added (there are 204 entries).  But there 
is now a definition section for every term, and the MS group is 
currently editing definitions.  Have a look and send any comments you have.

The file can be viewed and edited in the beta version of the OBO-Edit 
program:

http://sourceforge.net/project/showfiles.php?group_id=36855&package_id=148487

or you can use a text editor...

The next step is to reconcile the ontology with the second draft of the 
IUPAC nomenclature (2006 draft):

http://www.msterms.com/wiki/index.php?title=IUPAC_Task_Group_MS_Terms_Second_Draft

There are terms which are needed by mzData and analysisXML which are not 
on this list, so any other instrument or data processing parameters 
which are desired by the PSI membership can be send to Randy 
(rkj...@in...) or any other PSI-MS group member.

The goal of the PSI-MS group is to update this file frequently, with the 
possibility of the human readable text changing to correct spelling or 
to adjust to IUPAC norms, but the accession number assigned to the 
concept is fixed and will not be changed, removed or reused.

Thanks,
Randy Julian

[Psidev-ms-dev] PSI-MS Teleconfernce 10 January 2006

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

The first teleconference for the new year is scheduled for tomorrow (10 
Jan 2006) at 1600 GMT.  The usual call-in number will be used.  Contact 
Kent Laursen (ken...@ge...) if you need the number.

So far the topics for this call are:

1. Formalization of the Mass Spectrometry Data Working Group (MSD)
2. Formalization of the Mass Spectrometry Informatics Working Group (MSI)
3. Role of MIAPE chair, PSI-Editor and WG members responsible for MIAPE
4. Finalizing the mzData 1.05 specification document
5. Schedule for analysisXML 1.0 specification document
6. Review of mzData ontology (OBO format definitions file)
7. Planning for Spring PSI meeting

Other topics?

Thanks,
Randy

[Psidev-ms-dev] Minutes from 20 December 2005 Teleconference

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

The minutes from the 20 December Teleconference are now in the docstore:

http://psidev.sourceforge.net/docstore/view.php?sess=0&parent=4&expand=1&order=name&sortname=ASC&id=52&action=file_details

Please forward any corrections or comments.

Thanks,
Randy

[Psidev-ms-dev] Re: dta2mzData converter

[Jayson F. <jfa...@um...>]

 > I'm looking for a free dta2mzData converter, but I can't find one
 > (although I found several mzData2dta/mgf converters).
 > Does anybody knows such a tool? (dta/mgf2mzData or dta/mgf2mzXML)

Try the ProteomeCommons.org conversion utility. It can convert between 
DTA and mzXML and mzData. The link should run the application straight 
from your web browser.

http://www.proteomecommons.org/current/531/ConvertPeakList.jnlp

The program can also read and write many other formats.

Jayson Falkner
jfa...@um...

psi...@li... wrote:
> Send Psidev-ms-dev mailing list submissions to
> 	psi...@li...
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev
> or, via email, send a message with subject or body 'help' to
> 	psi...@li...
> 
> You can reach the person managing the list at
> 	psi...@li...
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Psidev-ms-dev digest..."
> 
> 
> Today's Topics:
> 
>    1. dta2mzData converter (Patricia Hernandez)
> 
> --__--__--
> 
> Message: 1
> Date: Fri, 06 Jan 2006 11:57:14 +0100
> From: Patricia Hernandez <pat...@is...>
> To: psi...@li...
> Subject: [Psidev-ms-dev] dta2mzData converter
> 
> Hi all,
> I'm looking for a free dta2mzData converter, but I can't find one 
> (although I found several mzData2dta/mgf converters).
> Does anybody knows such a tool? (dta/mgf2mzData or dta/mgf2mzXML)
> Thanks,
>