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From: Kent L. <Ken...@ge...> - 2005-09-30 14:18:10
|
Some have had problems with the attatchment, so I am resending 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 |
|
From: Sean L S. <Sey...@ap...> - 2005-09-30 00:26:31
|
Hi all,
Is it just my email system or are others seeing Kent's message transformed
into white noise? Is this a problem with the listserver is what I'm
getting at? If so, we should all know what these limits are (no html
mail?).
Sean
____________________________
Sean L. Seymour, Ph.D.
Staff Scientist
MS Informatics R&D
Applied Biosystems|MDS Sciex
510-708-9483
psi...@li...
Sent by: psi...@li...
09/28/2005 08:14 PM
Please respond to
psi...@li...
To
psi...@li...
cc
Subject
Psidev-ms-dev digest, Vol 1 #52 - 1 msg
Send Psidev-ms-dev mailing list submissions to
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Psidev-ms-dev digest..."
Today's Topics:
1. PSI-MS Requirements Questionnaire - attached as Word doc file this
time (Kent Laursen)
--__--__--
Message: 1
Date: Wed, 28 Sep 2005 08:42:20 -0700
From: "Kent Laursen" <Ken...@ge...>
To: <psi...@li...>
Subject: [Psidev-ms-dev] PSI-MS Requirements Questionnaire - attached as
Word doc file this time
This is a multi-part message in MIME format.
------_=_NextPart_001_01C5C443.37915470
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boundary="----_=_NextPart_002_01C5C443.37915470"
------_=_NextPart_002_01C5C443.37915470
Content-Type: text/plain;
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Content-Transfer-Encoding: quoted-printable
Dear Colleague,
=20
The PSI-MS working group is soliciting requirements for its mzData
standard efforts. Please take the time to fill out the simple
requirements questionnaire attached to this email. Your input is
appreciated and will help ensure the standard more accurately meets the
needs of the community.
=20
Thank You,
=20
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
------_=_NextPart_002_01C5C443.37915470
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charset="us-ascii"
Content-Transfer-Encoding: quoted-printable
<html xmlns:o=3D"urn:schemas-microsoft-com:office:office" =
xmlns:w=3D"urn:schemas-microsoft-com:office:word" =
xmlns=3D"http://www.w3.org/TR/REC-html40">
<head>
<META HTTP-EQUIV=3D"Content-Type" CONTENT=3D"text/html; =
charset=3Dus-ascii">
<meta name=3DGenerator content=3D"Microsoft Word 11 (filtered medium)">
<style>
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<div class=3DSection1>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Dear Colleague,<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>The PSI-MS working group is soliciting requirements =
for its
mzData standard efforts. Please take the time to fill out the =
simple
requirements questionnaire attached to this email. Your input is
appreciated and will help ensure the standard more accurately meets the =
needs
of the community.<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Thank You,<o:p></o:p></span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p><strong><b><font size=3D1 face=3DVerdana><span =
style=3D'font-size:7.5pt;
font-family:Verdana'>Kent Laursen</span></font></b></strong><b><font =
size=3D1
face=3DVerdana><span =
style=3D'font-size:7.5pt;font-family:Verdana;font-weight:bold'><br>
<strong><b><font face=3DVerdana><span =
style=3D'font-family:Verdana'>Senior Software
Architect</span></font></b></strong><br>
<strong><b><font face=3DVerdana><span =
style=3D'font-family:Verdana'>GenoLogics Life
Sciences Software Inc.</span></font></b></strong><br>
<strong><b><font face=3DVerdana><span style=3D'font-family:Verdana'>p: =
250.483.7011</span></font></b></strong><br>
</span></font></b><a
href=3D"file:///C:\Documents%20and%20Settings\kent\Application%20Data\Mic=
rosoft\Signatures\www.genologics.com"
title=3D"file:///C:/Documents%20and%20Settings/kent/Application%20Data/Mi=
crosoft/Signatures/www.genologics.com"><strong><b><font
size=3D2 face=3DVerdana
title=3D"file:///C:/Documents%20and%20Settings/kent/Application%20Data/Mi=
crosoft/Signatures/www.genologics.com"><span
title=3D"file:///C:/Documents%20and%20Settings/kent/Application%20Data/Mi=
crosoft/Signatures/www.genologics.com"><span
style=3D'font-size:10.0pt;font-family:Verdana;text-decoration:none'>www.g=
enologics.com</span></span></font></b></strong></a><o:p></o:p></p>
<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
</body>
</html>
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Psi...@li...
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End of Psidev-ms-dev Digest
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From: Randy J. <rkj...@in...> - 2005-09-23 03:40:20
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PSI-MS Teleconference 13 September 2005 (10:00 EST) Attendees: Patrick Pedrioli, Swiss Institute of Technology Sean Seymour, Applied Biosystems David Creasy, Matrix Science Limited David Horn, Agilent Technologies Mike Niemi, IBM Pierre-Alain Binz, Swiss Institute of Bioinformatics Andy Jones, University of Manchester Angel Pizarro, University of Pennsylvania Kent Laursen, GenoLogics Life Scences Software, Inc. Randy Julian, Indigo Biosystems Pre-meeting agenda: 1. Discuss our statement of mission 2. Explicitly declare our deliverables 3. Discuss the use of the documentation of the Global Grid Forum as a=20 possible template for PSI-MS 4. Discuss the extension mechanism in analysisXML (see attached .tgz=20 file with the schema) - what's the right balance between cvParam and sub-schema 5. Setting the next few calls agenda Discussion: #1 Mission: PSI-MS to oversee two standards; mzData and analysisXML A first step is to establish a concise statement of the group mission t= o=20 begin to establish a charter for the PSI-MS =91Working Group=92. The ne= xt=20 step is to gather requirements including MIAPE and MCP alignment Assigments/Dates: Specific mission/charter statements to be sent to Angel=20 (an...@ma...) for discussion at next teleconference=20 (9/27/2005). #2 Deliverables Improve the ability to describe our process and define specific roles,=20 deliverables in a process description document. MIAPE/MCP Alignment: Pierre-Alain is gathering input on the alignment=20 between MIAPE and MCP. Contact him (pie...@is...) to=20 request a current copy of the documents. We will discuss this document=20 and the role it has in the documentation process at the next=20 teleconference (9/27/2005). Assignment/Dates: Randy to review GGF documentation and provide summary for next=20 teleconference (9/27/2005) #3 Process: Improve process for standards development Need to define process for work, leveraging others such as IETF and GGF Once roles and deliverables ascertained, we can assign work to=20 participants for review Process needs to specifically address community =91marketing=92 needs. = David=20 Horn to discuss specific PSI goals and standards with a key MCP editor.= =20 Kent will develop and distribute a requirements survey form as part of=20 early requirements gathering effort Web pages need to be improved. There is a possibility of third party to= =20 resource website, IT to aid PSI via disease-state specific projects=20 which are already funded. Kent will check on this. #4 Extension mechanism for mzData, analysisXML, mzXML integration proje= ct Best mechanism for extension and CV still being discussed The group agrees that we need to reach out to the mzXML user community=20 and define unification and interoperability Need to answer how analysisXML would look/change to become FuGE-based Assignments/Dates: An off-line group (Randy, Patrick, Angel) will hold a teleconference to= =20 create a proposal for extension based on the current=20 mzData/analysisXML/mzXML approaches. The lack of a decision on this is=20 seen as a major distraction. There are =91best practices=92 for this =96= we=20 need to adopt them. This call will be held before the next teleconferen= ce. Angel will provide some examples of analysisXML modified to use=20 =46UGE-like ontologies in appropriate places. Please send corrections or comments to rkj...@in... |
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From: Randy J. <rkj...@in...> - 2005-09-22 03:55:38
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The next PSI-MS teleconference is scheduled for 9/27/2005 at 15:00 UTC (8:00 PDT, 10:00 EST, 11:00 EDT...16:00 BST, 17:00 CEST) The conference call number will be the same as the previous call - contact Kent Laursen (ken...@ge...) for the dialing instructions, including international call-in numbers. The proposed agenda for the 9/27 call is: 1. Discussion of the GGF process and roles we would have to assign to implement it 2. Expected documents from new GGF-based PSI process and how MIAPE fits in 3. Specific suggestions for MCP response (needed by October 15) 4. Review of the extension mechanism off-line meeting 5. Draft initial charter *** Other information *** The minutes to the previous meeting (9/13/2005) are being finalized and will be posted this week. We are starting a new list: psidev-ms-wg which stands for 'working group'. This will be a small list for circulating drafts of documents in progress. If you'd like to help with the editing and reviewing, subscribe at: http://lists.sourceforge.net/lists/listinfo/psidev-ms-wg *** Upcoming teleconferences *** During the 10/11 call, we need to: Finalize our MCP response Make specific 'spec team' assignments - Develop schedule for reaching draft status on analysisXML by end of year - Establish clear schedule/plan for mzXML/mzData integration |
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From: Angel P. <an...@ma...> - 2005-09-21 14:23:11
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Hello all, I was assigned to collate and edit our mission statements, both on a high-level and mid-level deliverables. Please forward me any copy that you may have lying around. Thanks, Angel -- 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 |
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From: Brian P. <bri...@in...> - 2005-09-19 22:05:12
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You're quite welcome! (And thanks for "stonking", an excellent word.) A couple of us at Insilicos have had experience with data standards efforts in other industries and we've found that there's nothing like a viewer and some freely available source code to encourage adoption of a format. (Speaking of which, another useful bit of code is at http://cvs.sourceforge.net/viewcvs.py/sashimi/readmzXML/ which you can use to convert your mzData files to ASCII text - a useful debugging tool when writing an mzData output.) The mzData reader code was tested using the example files which the mzData community has made available, but I won't be surprised when wildtype mzData files expose some issues. I'll be grateful to anyone who lets me know about any problems that crop up. And here's a shout-out to Patrick Pedrioli who wrote the original mzXML reader code which was so readily extended to read mzData. - Brian > -----Original Message----- > From: Chris Taylor [mailto:chr...@eb...] > Sent: Monday, September 19, 2005 2:18 PM > To: bri...@in... > Cc: psi...@li... > Subject: Re: [Psidev-ms-dev] mzData Viewer now available > > Wow!!! > > That is just fantastic. On behalf of all involved in the project over > the last few years can I express our deep gratitutde for > committing the > person-hours to get this to the public. Just plain fantastic. > Now anyone > can get 'touchy-feely' with their (mz)data :D > > For those who want a quick play, the best example file to grab is at > http://prdownloads.sourceforge.net/psidev/myo_full_1.05cv.zip?download > (although I wouldn't go trying it on a 56k modem as it is 8-odd meg). > > Stonking (if you'll forgive a little vernacular *). > > Cheers, Chris. > > * Courtesy of 'Wordweb'... > Adjective: Stonking > Usage: Brit. > Meaning: (informal, for emphasis) excellent > Example: "a stonking good read" > > > Brian Pratt wrote: > > Greetings All, > > > > A while back I posted a notice about some work I was doing > to integrate mzData reading capability into the ISB Sashimi > tools. That > > work is now included in our InsilicosViewer MS data viewing > software, which is available at > > http://www.insilicos.com/free_downloads.html. > > > > The source code for the mzData reading part of the viewer > is available at > > > http://cvs.sourceforge.net/viewcvs.py/sashimi/trans_proteomic_ > pipeline/src/Parsers/ramp/ > > > > Hopefully these resources will be of use to folks > implementing systems using mzData. > > > > Enjoy! > > > > Brian Pratt > > Insilicos LLC > > > > > > > > > > ------------------------------------------------------- > > SF.Net email is sponsored by: > > Tame your development challenges with Apache's Geronimo App Server. > > Download it for free - -and be entered to win a 42" plasma > tv or your very > > own Sony(tm)PSP. Click here to play: > http://sourceforge.net/geronimo.php > > _______________________________________________ > > Psidev-ms-dev mailing list > > Psi...@li... > > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > > > > -- > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Chris Taylor (ch...@eb...) > HUPO PSI: GPS -- psidev.sf.net > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > |
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From: Chris T. <chr...@eb...> - 2005-09-19 21:18:26
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Wow!!! That is just fantastic. On behalf of all involved in the project over the last few years can I express our deep gratitutde for committing the person-hours to get this to the public. Just plain fantastic. Now anyone can get 'touchy-feely' with their (mz)data :D For those who want a quick play, the best example file to grab is at http://prdownloads.sourceforge.net/psidev/myo_full_1.05cv.zip?download (although I wouldn't go trying it on a 56k modem as it is 8-odd meg). Stonking (if you'll forgive a little vernacular *). Cheers, Chris. * Courtesy of 'Wordweb'... Adjective: Stonking Usage: Brit. Meaning: (informal, for emphasis) excellent Example: "a stonking good read" Brian Pratt wrote: > Greetings All, > > A while back I posted a notice about some work I was doing to integrate mzData reading capability into the ISB Sashimi tools. That > work is now included in our InsilicosViewer MS data viewing software, which is available at > http://www.insilicos.com/free_downloads.html. > > The source code for the mzData reading part of the viewer is available at > http://cvs.sourceforge.net/viewcvs.py/sashimi/trans_proteomic_pipeline/src/Parsers/ramp/ > > Hopefully these resources will be of use to folks implementing systems using mzData. > > Enjoy! > > Brian Pratt > Insilicos LLC > > > > > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App Server. > Download it for free - -and be entered to win a 42" plasma tv or your very > own Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Chris Taylor (ch...@eb...) HUPO PSI: GPS -- psidev.sf.net ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
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From: Brian P. <bri...@in...> - 2005-09-19 20:38:09
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Greetings All, A while back I posted a notice about some work I was doing to integrate mzData reading capability into the ISB Sashimi tools. That work is now included in our InsilicosViewer MS data viewing software, which is available at http://www.insilicos.com/free_downloads.html. The source code for the mzData reading part of the viewer is available at http://cvs.sourceforge.net/viewcvs.py/sashimi/trans_proteomic_pipeline/src/Parsers/ramp/ Hopefully these resources will be of use to folks implementing systems using mzData. Enjoy! Brian Pratt Insilicos LLC |
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From: Kent L. <Ken...@ge...> - 2005-09-17 21:28:41
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Hi All, =20 At the meetings that occurred in Geneva in September there was generally a positive response to the idea of improving and more accurately defining the methods whereby the PSI MS working group would produce standards in the forms of documents, specifications and implementations. Stated another way, a conclusion was made that in order to increase the velocity of standards production, the quality of the standards and the breadth of their usage in both the academic and commercial realms, we might best begin with a candid reevaluation and re-modulation of our development process. In short, we will increase our chances of reaching the desired destination if we share a common understanding of how we get there and where we are going. In order to crystallize this understanding into a persistent and shareable form, its writing down should be undertaken. And so this little exposition is catalyzed. =20 A development process is a guidance that organizes participants into a workflow of deliverables leading to a desired product or set of products. In our case these products are standards for bioinformatics interchange. Development processes range from the simple to very complex. The trick is to honor both sufficiency and necessity. We should seek to introduce enough rigor to foster timely publishing of quality work, while avoiding overburdening the process with steps that reduce agility and do not possess a clear value.=20 =20 A development process consists of a set of process components that operate both in sequence and often in parallel. A fairly comprehensive process component from which we might derive a simpler configuration for PSI-MS might have the following properties =20 * Description - A description defining the process and providing an overview. * Entry Conditions - A list of conditions that should be met before starting into this process. * Exit Conditions - A list of conditions that have been met by completing this process. * Steps - A list of the steps that are followed to complete the process. * Planning Notes - Constraints and notes that will be useful to project managers and the team. Notes about complex dependencies that should be considered during the planning stage will be noted here. * Prerequisites - A list of the products from other processes that will be needed to conduct this process efficiently. * Products - The products are the artifacts created by the process, i.e. the deliverables. * Risks - Risks associated with the process are documented in this section. Any strategies that can be used to mitigate the risk are also documented here. * Metrics - These are the metrics that will be collected by users of the process. These processes will be used for aiding in process improvement. There are two sorts of metrics; sizing metrics are used to help determine the size of the task, whereas productivity metrics are used to measure the resources that are expended in completing the process. * Forces - The forces or constraints which affect the process and define why this process is structured in the way that it is. * Resources - The resources needed for this development. This section should be used in conjunction with the planning notes (if available). * Techniques - A collection of techniques that can be used to help facilitate the process. * Tools - Recommended tools that might prove useful during this stage of development. * Patterns - Recommended patterns that might prove useful during this stage of development. * References - A collection of references for further information. These references may have hotlinks to supplementary files or documents. * Related Principles - A list of principles that are in some way connected to this process. This section is used to help understand how this process fits into this development process (and other processes) as a whole. =20 The most minimal process consists of resources and products, which means we assign the responsibility of a deliverable to a participant and offer no other guidance and observability as to how the participant creates this deliverable. While this simplicity can work in cases where scope is constrained and the resource possesses sufficient knowledge to reliably produce, this simple of a process granularity does not engender reproducibility, manageability or scalability. For PSI-MS (and hopefully other standards working groups) we should foster a reusable process with the right levels of definition and rigor that lie somewhere in between the simple and complex. =20 As is the case with any technological development, we seek to provide a mechanism for automating particular aspects of a problem space to serve the needs of stakeholders. Stated another way, we want to devise a complete and accurate rendering of artifacts that satisfies the use cases of our customer. This need leads to a few essential questions: =20 * Who are the stakeholders? * What do they want? * Why do they want it? * How do we work together to answer stakeholder requirements? * How do we describe our solution separate from its physical/machine process-able form in a way that is human understandable while allowing for evolutionary/incremental implementation? * How do we encode or describe our end deliverable with sufficient technical accuracy, i.e. it works =20 A universal problem in technological development is the management of scope. The classic dimensions where scope applies include time, cost, size and complexity. Generally speaking it is this last dimension, complexity, which is the ruler/constrainer of the other dimensions. For this reason, addressing the layers of abstraction is a primary concern for any development process. =20 Well, dear reader, if you have made it this far, the writer expresses his gratitude for both your patience and tolerance. He will now endeavor to "get a grip on things" and drive more toward the pragmatic. =20 Regardless of domain, most development processes can be organized into three overarching layers of abstraction. These are observable from various roles and perspectives and have been expressed in ways such as: =20 Conceptual --> Logical --> Physical Business --> User --> Technical CIM --> PIM --> PSM Why --> What --> How =20 So now let's merge these toward a development process for PSI-MS, remembering that we should have traceability between the levels. For example: A stakeholder in the first level should be able to navigate to the relevant artifacts in the second level, and be able to have a reasonable understanding that these second level constructs address the needs he or she expressed at the first level. Correspondingly a party in the second level should be able to quickly find what implementing artifacts exist in the third level, while a person in the third level should have sufficient logical completeness from level 2 to encode a working solution. The conceptual and navigational gaps between the levels should be such that a resource from one level can communicate effectively with a role one level up or down for such purposes as review and change requests. =20 First what are some important characteristics of these three levels? =20 Level 1 - Visionary, business (Science in our case) driven, computationally independent, expressing an aim, justifying and or explaining the basis for the effort =20 Level 2 - 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 Level 3 - Providing sufficient technical detail leading to a machine process-able implementation or an automated transformation to it, providing the level of design necessary to bring the solution "into the physical" =20 Second, what sorts of roles exist at the levels? =20 Conceptual/Science - domain expert, subject matter expert, financial backer, evangelist, decision maker, PR, marketing Logical/User - domain expert, analyst, technical writer, modeler, quality assurance Physical/Technical - analyst, technologist, software architect, programmer Umbrella (existing at any level or step) - administration and project management along with the broader public community who might provide useful input/feedback aligned with their interest and knowledge =20 Third what are the deliverables? =20 Conceptual/Science - Charter or mission statement, high level requirements, statement of problem or opportunity Logical/User - Specifications, functional requirements, test specifications, manuals Physical/Technical - Schemas, models, code, test implementations, examples Umbrella - mailing list discussion, milestone/review/candidate releases of documentation and schemas/models, web site, communications, meeting and conference plans, "real world" examples or implementation links =20 While the above perspectives expressed in three levels of abstraction in no way pretend to represent the state of the art of development processes, they can help us in providing some shape to the expression of a process for PSI standards work. Given the bespoke philosophies and principles, the next step will be the publishing of an actual process definition we can use to guide the workgroup's activities. Because our group is comprised of a wide variety of backgrounds and experience, it was appropriate to "get on the same page" conceptually, prior to the actual definition of our process. =20 Regards, =20 Kent =20 |
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From: Chris T. <chr...@eb...> - 2005-09-14 08:50:58
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Hiya. It's unfortunate that I had to keep this most recent version of MS from view until the MCP business had been discussed in Geneva; not sure things really got fully cleared up there but anyway we can move forwards now. The revision of MS that comes after all the dust has settled from this MCP business will indeed as you say have to be v2.1... I hope that as well as your specific conversations about the commentary to go to Ralph Bradshaw you will find time to discuss the various general options available to us (MCP + MIAPE: MSI independently, MIAPE: MSI for reporting & MCP for quality, MCP and MIAPE: MSI to be the same thing, 'owned' by either PSI or ASBMB, etc etc). Cheers, Chris. Pierre-Alain Binz wrote: > Hi Chris, > as the MIAPE MS document being matched to the MCP draft guidelines is a > version that was available in Geneva, I will consider the doc (your > version 2.0) you has made available afterwards as being part of your > comments. The result of the comments from the people already having the > mapping documents or from those who still want to go through them (send > me an email for getting theem) will be compiled by the end of september. > I would ask all comments back to me by Sept 23rd. The resulting MIAPE-MS > doc will then have to have a version higher as 2.0 as a matter of fact > and to avoid any missunderstanding > Thanks in advance. > Pierre-Alain > > > Chris Taylor wrote: > >> Great. Thanks for the info. Sorry for being a pest :) >> >> I've reposted the 'final' (ha) MIAPE: MS document at >> http://psidev.sourceforge.net/gps/miape/MIAPE_MS_2.0.doc >> but rather than chop the bits I mentioned in the list post earlier >> today to make a v2.1, I have simply coloured parts red as things >> turned out not to be so simple; I think it should be something for >> discussion on that call whether (4) is moved wholesale to MSI or only >> partially. >> >> A particular issue is that the 'quantitation' section (4b) serves >> partly to annotate the spectra described, to alert people to the fact >> that something 'funny' is going on (i.e. expect to see cleaved iTRAQ >> tags or allow for isotope-label/ICAT related mass shifts etc.). It is >> only partly there to address (in a limited way) the informatics >> process of quantitation itself if you see what I mean, therefore the >> overlap with MCP is patchy. Clearly (4a) overlaps heavily except for >> the location of the (infamous) raw data (e.g. parameters triggering >> the generation of peak lists etc.). >> >> Anyway I'll hang on to post the MS document until I hear opinions from >> people, perhaps till after the call (on the 17th?). The colour coding >> reflects my own preference... >> >> Cheers, Chris. >> >> >> Pierre-Alain Binz wrote: >> >>> Hi Chris (and all psidev members) >>> The MS group has decided to talk about the MCP-MIAPE docs at the next >>> phone call. >>> I had prepared a set of mapping documents between MIAPE MS, MSI and >>> MCP guidelines draft July 14th. >>> For those interested in commenting on the mapping and on the content, >>> it's been decided that I send them the documents and will collect the >>> comments. >>> So if I get emails I send the docs... >>> Cheers, >>> Pierre-Alain >>> >>> Chris Taylor wrote: >>> >>>> Hi all. I'll try to make this call if I can; regardless though I >>>> wonder if a small addition to the agenda might be desirable, namely >>>> to mention the 'reponse' (or whatever) to MCP? I'm assuming that as >>>> owner of the MIAPE: MSI document, Pierre-Alain will have a hand in >>>> this along with Sean and others with an interest? It may be in order >>>> to actually draw up a list of drafters who can do the point-by-point >>>> offline. >>>> >>>> To do my bit I will later today post the MIAPE: MS document as a >>>> final version, but with any sniff of informatics removed (i.e. >>>> profile to peak list), with a view to putting it into the MSI >>>> module, to better align that document with the MCP proposal. MIAPE: >>>> MS has been sitting around for some time now though, and so I think >>>> it is only fair to the contribtors to that document that they see >>>> something come from it. >>>> >>>> We should have by early next year MIAPE modules for gels and gel >>>> informatics, and should be moving forwards with general separations >>>> (everything that is not a 'classical' 1 or 2D gel) and study design. >>>> I'd like to see something equivalent for mass spec informatics >>>> sooner rather than later, whether 'owned' by MCP or us or whatever >>>> gets it done quickest (this is also something for the call). I'd >>>> also underline as several people restated in Geneva, that what might >>>> come under the MIAPE banner shouldn't include prescriptive methods >>>> for doing the work, just for reporting it. >>>> >>>> Cheers, Chris. >>>> >>>> >>>> Randy Julian wrote: >>>> >>>>> The PSI-MS working group would like to organize a weekly (or >>>>> bi-weekly) teleconference to further the development of both the >>>>> mzData format as well as push forward on the results interchange >>>>> format proposed at Geneva as 'analysisXML'. >>>>> >>>>> We are new to this type of interaction, but it works well in other >>>>> standards organization and seems like a good way to allow wide >>>>> participation and create a transparent process for establishing >>>>> standards. >>>>> >>>>> The first teleconference was discussed at the Geneva meeting and >>>>> despite the late notice, we would like to have a 60 minute call >>>>> tomorrow (13 Sept) at 11:00 EST. >>>>> >>>>> The first call is organized by Genologics so if you would like to >>>>> attend, please e-mail Kent Laursen (ken...@ge...) >>>>> for the dialing instructions. >>>>> >>>>> We are planning to have these calls every two weeks, so if you miss >>>>> this one (due to the late notice...), we are planning another for >>>>> Sept 27. >>>>> >>>>> For the first call, I would propose the following agenda: >>>>> >>>>> 1. Discuss our statement of mission >>>>> 2. Explicitly declare our deliverables >>>>> 3. Discuss the use of the documentation of the Global Grid Forum as >>>>> a possible template for PSI-MS >>>>> 4. Discuss the extension mechanism in analysisXML (see attached >>>>> .tgz file with the schema) >>>>> - what's the right balance between cvParam and sub-schema >>>>> 5. Setting the next few calls agenda >>>>> >>>>> We will take notes at this call and post them to this list. >>>>> >>>>> Please contact me (rkj...@in...) with questions, and Kent >>>>> (ken...@ge...) for dialing instructions. >>>>> >>>>> Thanks, >>>>> Randy Julian for the PSI-MS group >>>> >>>> >>>> >>>> >>>> >>> >> > -- ~~~~~~~~~~~~~~~~~~~~~~~~ chr...@eb... http://psidev.sf.net/ ~~~~~~~~~~~~~~~~~~~~~~~~ |
|
From: Pierre-Alain B. <pie...@is...> - 2005-09-14 08:40:10
|
Hi Chris, as the MIAPE MS document being matched to the MCP draft guidelines is a version that was available in Geneva, I will consider the doc (your version 2.0) you has made available afterwards as being part of your comments. The result of the comments from the people already having the mapping documents or from those who still want to go through them (send me an email for getting theem) will be compiled by the end of september. I would ask all comments back to me by Sept 23rd. The resulting MIAPE-MS doc will then have to have a version higher as 2.0 as a matter of fact and to avoid any missunderstanding Thanks in advance. Pierre-Alain Chris Taylor wrote: > Great. Thanks for the info. Sorry for being a pest :) > > I've reposted the 'final' (ha) MIAPE: MS document at > http://psidev.sourceforge.net/gps/miape/MIAPE_MS_2.0.doc > but rather than chop the bits I mentioned in the list post earlier > today to make a v2.1, I have simply coloured parts red as things > turned out not to be so simple; I think it should be something for > discussion on that call whether (4) is moved wholesale to MSI or only > partially. > > A particular issue is that the 'quantitation' section (4b) serves > partly to annotate the spectra described, to alert people to the fact > that something 'funny' is going on (i.e. expect to see cleaved iTRAQ > tags or allow for isotope-label/ICAT related mass shifts etc.). It is > only partly there to address (in a limited way) the informatics > process of quantitation itself if you see what I mean, therefore the > overlap with MCP is patchy. Clearly (4a) overlaps heavily except for > the location of the (infamous) raw data (e.g. parameters triggering > the generation of peak lists etc.). > > Anyway I'll hang on to post the MS document until I hear opinions from > people, perhaps till after the call (on the 17th?). The colour coding > reflects my own preference... > > Cheers, Chris. > > > Pierre-Alain Binz wrote: > >> Hi Chris (and all psidev members) >> The MS group has decided to talk about the MCP-MIAPE docs at the next >> phone call. >> I had prepared a set of mapping documents between MIAPE MS, MSI and >> MCP guidelines draft July 14th. >> For those interested in commenting on the mapping and on the content, >> it's been decided that I send them the documents and will collect the >> comments. >> So if I get emails I send the docs... >> Cheers, >> Pierre-Alain >> >> Chris Taylor wrote: >> >>> Hi all. I'll try to make this call if I can; regardless though I >>> wonder if a small addition to the agenda might be desirable, namely >>> to mention the 'reponse' (or whatever) to MCP? I'm assuming that as >>> owner of the MIAPE: MSI document, Pierre-Alain will have a hand in >>> this along with Sean and others with an interest? It may be in order >>> to actually draw up a list of drafters who can do the point-by-point >>> offline. >>> >>> To do my bit I will later today post the MIAPE: MS document as a >>> final version, but with any sniff of informatics removed (i.e. >>> profile to peak list), with a view to putting it into the MSI >>> module, to better align that document with the MCP proposal. MIAPE: >>> MS has been sitting around for some time now though, and so I think >>> it is only fair to the contribtors to that document that they see >>> something come from it. >>> >>> We should have by early next year MIAPE modules for gels and gel >>> informatics, and should be moving forwards with general separations >>> (everything that is not a 'classical' 1 or 2D gel) and study design. >>> I'd like to see something equivalent for mass spec informatics >>> sooner rather than later, whether 'owned' by MCP or us or whatever >>> gets it done quickest (this is also something for the call). I'd >>> also underline as several people restated in Geneva, that what might >>> come under the MIAPE banner shouldn't include prescriptive methods >>> for doing the work, just for reporting it. >>> >>> Cheers, Chris. >>> >>> >>> Randy Julian wrote: >>> >>>> The PSI-MS working group would like to organize a weekly (or >>>> bi-weekly) teleconference to further the development of both the >>>> mzData format as well as push forward on the results interchange >>>> format proposed at Geneva as 'analysisXML'. >>>> >>>> We are new to this type of interaction, but it works well in other >>>> standards organization and seems like a good way to allow wide >>>> participation and create a transparent process for establishing >>>> standards. >>>> >>>> The first teleconference was discussed at the Geneva meeting and >>>> despite the late notice, we would like to have a 60 minute call >>>> tomorrow (13 Sept) at 11:00 EST. >>>> >>>> The first call is organized by Genologics so if you would like to >>>> attend, please e-mail Kent Laursen (ken...@ge...) >>>> for the dialing instructions. >>>> >>>> We are planning to have these calls every two weeks, so if you miss >>>> this one (due to the late notice...), we are planning another for >>>> Sept 27. >>>> >>>> For the first call, I would propose the following agenda: >>>> >>>> 1. Discuss our statement of mission >>>> 2. Explicitly declare our deliverables >>>> 3. Discuss the use of the documentation of the Global Grid Forum as >>>> a possible template for PSI-MS >>>> 4. Discuss the extension mechanism in analysisXML (see attached >>>> .tgz file with the schema) >>>> - what's the right balance between cvParam and sub-schema >>>> 5. Setting the next few calls agenda >>>> >>>> We will take notes at this call and post them to this list. >>>> >>>> Please contact me (rkj...@in...) with questions, and Kent >>>> (ken...@ge...) for dialing instructions. >>>> >>>> Thanks, >>>> Randy Julian for the PSI-MS group >>> >>> >>> >>> >> > -- -- 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 |
|
From: Chris T. <chr...@eb...> - 2005-09-13 14:37:36
|
Great. Thanks for the info. Sorry for being a pest :) I've reposted the 'final' (ha) MIAPE: MS document at http://psidev.sourceforge.net/gps/miape/MIAPE_MS_2.0.doc but rather than chop the bits I mentioned in the list post earlier today to make a v2.1, I have simply coloured parts red as things turned out not to be so simple; I think it should be something for discussion on that call whether (4) is moved wholesale to MSI or only partially. A particular issue is that the 'quantitation' section (4b) serves partly to annotate the spectra described, to alert people to the fact that something 'funny' is going on (i.e. expect to see cleaved iTRAQ tags or allow for isotope-label/ICAT related mass shifts etc.). It is only partly there to address (in a limited way) the informatics process of quantitation itself if you see what I mean, therefore the overlap with MCP is patchy. Clearly (4a) overlaps heavily except for the location of the (infamous) raw data (e.g. parameters triggering the generation of peak lists etc.). Anyway I'll hang on to post the MS document until I hear opinions from people, perhaps till after the call (on the 17th?). The colour coding reflects my own preference... Cheers, Chris. Pierre-Alain Binz wrote: > Hi Chris (and all psidev members) > The MS group has decided to talk about the MCP-MIAPE docs at the next > phone call. > I had prepared a set of mapping documents between MIAPE MS, MSI and MCP > guidelines draft July 14th. > For those interested in commenting on the mapping and on the content, > it's been decided that I send them the documents and will collect the > comments. > So if I get emails I send the docs... > Cheers, > Pierre-Alain > > Chris Taylor wrote: > >> Hi all. I'll try to make this call if I can; regardless though I >> wonder if a small addition to the agenda might be desirable, namely to >> mention the 'reponse' (or whatever) to MCP? I'm assuming that as owner >> of the MIAPE: MSI document, Pierre-Alain will have a hand in this >> along with Sean and others with an interest? It may be in order to >> actually draw up a list of drafters who can do the point-by-point >> offline. >> >> To do my bit I will later today post the MIAPE: MS document as a final >> version, but with any sniff of informatics removed (i.e. profile to >> peak list), with a view to putting it into the MSI module, to better >> align that document with the MCP proposal. MIAPE: MS has been sitting >> around for some time now though, and so I think it is only fair to the >> contribtors to that document that they see something come from it. >> >> We should have by early next year MIAPE modules for gels and gel >> informatics, and should be moving forwards with general separations >> (everything that is not a 'classical' 1 or 2D gel) and study design. >> I'd like to see something equivalent for mass spec informatics sooner >> rather than later, whether 'owned' by MCP or us or whatever gets it >> done quickest (this is also something for the call). I'd also >> underline as several people restated in Geneva, that what might come >> under the MIAPE banner shouldn't include prescriptive methods for >> doing the work, just for reporting it. >> >> Cheers, Chris. >> >> >> Randy Julian wrote: >> >>> The PSI-MS working group would like to organize a weekly (or >>> bi-weekly) teleconference to further the development of both the >>> mzData format as well as push forward on the results interchange >>> format proposed at Geneva as 'analysisXML'. >>> >>> We are new to this type of interaction, but it works well in other >>> standards organization and seems like a good way to allow wide >>> participation and create a transparent process for establishing >>> standards. >>> >>> The first teleconference was discussed at the Geneva meeting and >>> despite the late notice, we would like to have a 60 minute call >>> tomorrow (13 Sept) at 11:00 EST. >>> >>> The first call is organized by Genologics so if you would like to >>> attend, please e-mail Kent Laursen (ken...@ge...) for >>> the dialing instructions. >>> >>> We are planning to have these calls every two weeks, so if you miss >>> this one (due to the late notice...), we are planning another for >>> Sept 27. >>> >>> For the first call, I would propose the following agenda: >>> >>> 1. Discuss our statement of mission >>> 2. Explicitly declare our deliverables >>> 3. Discuss the use of the documentation of the Global Grid Forum as a >>> possible template for PSI-MS >>> 4. Discuss the extension mechanism in analysisXML (see attached .tgz >>> file with the schema) >>> - what's the right balance between cvParam and sub-schema >>> 5. Setting the next few calls agenda >>> >>> We will take notes at this call and post them to this list. >>> >>> Please contact me (rkj...@in...) with questions, and Kent >>> (ken...@ge...) for dialing instructions. >>> >>> Thanks, >>> Randy Julian for the PSI-MS group >> >> >> > -- ~~~~~~~~~~~~~~~~~~~~~~~~ chr...@eb... http://psidev.sf.net/ ~~~~~~~~~~~~~~~~~~~~~~~~ |
|
From: Pierre-Alain B. <pie...@is...> - 2005-09-13 13:57:13
|
Hi Chris (and all psidev members) The MS group has decided to talk about the MCP-MIAPE docs at the next phone call. I had prepared a set of mapping documents between MIAPE MS, MSI and MCP guidelines draft July 14th. For those interested in commenting on the mapping and on the content, it's been decided that I send them the documents and will collect the comments. So if I get emails I send the docs... Cheers, Pierre-Alain Chris Taylor wrote: > Hi all. I'll try to make this call if I can; regardless though I > wonder if a small addition to the agenda might be desirable, namely to > mention the 'reponse' (or whatever) to MCP? I'm assuming that as owner > of the MIAPE: MSI document, Pierre-Alain will have a hand in this > along with Sean and others with an interest? It may be in order to > actually draw up a list of drafters who can do the point-by-point > offline. > > To do my bit I will later today post the MIAPE: MS document as a final > version, but with any sniff of informatics removed (i.e. profile to > peak list), with a view to putting it into the MSI module, to better > align that document with the MCP proposal. MIAPE: MS has been sitting > around for some time now though, and so I think it is only fair to the > contribtors to that document that they see something come from it. > > We should have by early next year MIAPE modules for gels and gel > informatics, and should be moving forwards with general separations > (everything that is not a 'classical' 1 or 2D gel) and study design. > I'd like to see something equivalent for mass spec informatics sooner > rather than later, whether 'owned' by MCP or us or whatever gets it > done quickest (this is also something for the call). I'd also > underline as several people restated in Geneva, that what might come > under the MIAPE banner shouldn't include prescriptive methods for > doing the work, just for reporting it. > > Cheers, Chris. > > > Randy Julian wrote: > >> The PSI-MS working group would like to organize a weekly (or >> bi-weekly) teleconference to further the development of both the >> mzData format as well as push forward on the results interchange >> format proposed at Geneva as 'analysisXML'. >> >> We are new to this type of interaction, but it works well in other >> standards organization and seems like a good way to allow wide >> participation and create a transparent process for establishing >> standards. >> >> The first teleconference was discussed at the Geneva meeting and >> despite the late notice, we would like to have a 60 minute call >> tomorrow (13 Sept) at 11:00 EST. >> >> The first call is organized by Genologics so if you would like to >> attend, please e-mail Kent Laursen (ken...@ge...) for >> the dialing instructions. >> >> We are planning to have these calls every two weeks, so if you miss >> this one (due to the late notice...), we are planning another for >> Sept 27. >> >> For the first call, I would propose the following agenda: >> >> 1. Discuss our statement of mission >> 2. Explicitly declare our deliverables >> 3. Discuss the use of the documentation of the Global Grid Forum as a >> possible template for PSI-MS >> 4. Discuss the extension mechanism in analysisXML (see attached .tgz >> file with the schema) >> - what's the right balance between cvParam and sub-schema >> 5. Setting the next few calls agenda >> >> We will take notes at this call and post them to this list. >> >> Please contact me (rkj...@in...) with questions, and Kent >> (ken...@ge...) for dialing instructions. >> >> Thanks, >> Randy Julian for the PSI-MS group > > -- -- 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 |
|
From: Chris T. <chr...@eb...> - 2005-09-13 09:01:37
|
Hi all. I'll try to make this call if I can; regardless though I wonder if a small addition to the agenda might be desirable, namely to mention the 'reponse' (or whatever) to MCP? I'm assuming that as owner of the MIAPE: MSI document, Pierre-Alain will have a hand in this along with Sean and others with an interest? It may be in order to actually draw up a list of drafters who can do the point-by-point offline. To do my bit I will later today post the MIAPE: MS document as a final version, but with any sniff of informatics removed (i.e. profile to peak list), with a view to putting it into the MSI module, to better align that document with the MCP proposal. MIAPE: MS has been sitting around for some time now though, and so I think it is only fair to the contribtors to that document that they see something come from it. We should have by early next year MIAPE modules for gels and gel informatics, and should be moving forwards with general separations (everything that is not a 'classical' 1 or 2D gel) and study design. I'd like to see something equivalent for mass spec informatics sooner rather than later, whether 'owned' by MCP or us or whatever gets it done quickest (this is also something for the call). I'd also underline as several people restated in Geneva, that what might come under the MIAPE banner shouldn't include prescriptive methods for doing the work, just for reporting it. Cheers, Chris. Randy Julian wrote: > The PSI-MS working group would like to organize a weekly (or bi-weekly) > teleconference to further the development of both the mzData format as > well as push forward on the results interchange format proposed at > Geneva as 'analysisXML'. > > We are new to this type of interaction, but it works well in other > standards organization and seems like a good way to allow wide > participation and create a transparent process for establishing standards. > > The first teleconference was discussed at the Geneva meeting and despite > the late notice, we would like to have a 60 minute call tomorrow (13 > Sept) at 11:00 EST. > > The first call is organized by Genologics so if you would like to > attend, please e-mail Kent Laursen (ken...@ge...) for the > dialing instructions. > > We are planning to have these calls every two weeks, so if you miss this > one (due to the late notice...), we are planning another for Sept 27. > > For the first call, I would propose the following agenda: > > 1. Discuss our statement of mission > 2. Explicitly declare our deliverables > 3. Discuss the use of the documentation of the Global Grid Forum as a > possible template for PSI-MS > 4. Discuss the extension mechanism in analysisXML (see attached .tgz > file with the schema) > - what's the right balance between cvParam and sub-schema > 5. Setting the next few calls agenda > > We will take notes at this call and post them to this list. > > Please contact me (rkj...@in...) with questions, and Kent > (ken...@ge...) for dialing instructions. > > Thanks, > Randy Julian for the PSI-MS group -- ~~~~~~~~~~~~~~~~~~~~~~~~ chr...@eb... http://psidev.sf.net/ ~~~~~~~~~~~~~~~~~~~~~~~~ |
|
From: Randy J. <rkj...@in...> - 2005-09-12 22:19:16
|
The PSI-MS working group would like to organize a weekly (or bi-weekly)
teleconference to further the development of both the mzData format as
well as push forward on the results interchange format proposed at
Geneva as 'analysisXML'.
We are new to this type of interaction, but it works well in other
standards organization and seems like a good way to allow wide
participation and create a transparent process for establishing standards.
The first teleconference was discussed at the Geneva meeting and despite
the late notice, we would like to have a 60 minute call tomorrow (13
Sept) at 11:00 EST.
The first call is organized by Genologics so if you would like to
attend, please e-mail Kent Laursen (ken...@ge...) for the
dialing instructions.
We are planning to have these calls every two weeks, so if you miss this
one (due to the late notice...), we are planning another for Sept 27.
For the first call, I would propose the following agenda:
1. Discuss our statement of mission
2. Explicitly declare our deliverables
3. Discuss the use of the documentation of the Global Grid Forum as a
possible template for PSI-MS
4. Discuss the extension mechanism in analysisXML (see attached .tgz
file with the schema)
- what's the right balance between cvParam and sub-schema
5. Setting the next few calls agenda
We will take notes at this call and post them to this list.
Please contact me (rkj...@in...) with questions, and Kent
(ken...@ge...) for dialing instructions.
Thanks,
Randy Julian for the PSI-MS group
|
|
From: David C. <dc...@ma...> - 2005-08-23 14:52:38
|
Simon,
I can't see any downside in your suggestion. In fact, the following
validates using Xerces and XMLSpy using the current schema:
<mzArrayBinary>
<data precision="64" endian="little" length="0">
</data>
</mzArrayBinary>
<intenArrayBinary>
<data precision="64" endian="little" length="0">
</data>
</intenArrayBinary>
Looks as though
http://www.w3.org/TR/2004/PER-xmlschema-2-20040318/datatypes.html#base64Binary
specifies that an empty field is OK for base64Binary
David
simon andrews (BI) wrote:
>
> On 23 Aug 2005, at 13:38, Tom Blackwell wrote:
>
>> Simon and Randy -
>>
>> Both of you are pointing to the need for explicit "missing value" codes
>> in the schema -- in this case, a "missing spectrum" code. Either it's
>> a separate field, "spectrum supplied" which is normally true, or it's a
>> reserved value in some other field, say 'length="0"' as below, with an
>> explanation in the schema explaining that 'length="0"' MEANS that the
>> actual spectrum is missing, and what's there in its place should have
>> length 1 and should be ignored.
>
>
> It certainly seems odd to me to have this extra check value which
> doesn't always function as expected. At the very least this behaviour
> should be documented in the annotated schema files (which I don't think
> it is at the moment).
>
> At the risk of baring my ignorance of XML - if there are legitimate
> cases where this field is not supplied would this not suggest that the
> field shouldn't be mandatory in the schema? As long as the
> mzArrayBinary and internArrayBindary elements are present a parser
> should be able to cope with the data element being absent or having a
> length of 0.
>
> Simon.
--
David Creasy
Matrix Science
8 Wyndham Place
London W1H 1PP
Tel +44 (0)20 7723 2142
Fax +44 (0)20 7725 9360
dc...@ma...
http://www.matrixscience.com
|
|
From: simon a. (B. <sim...@bb...> - 2005-08-23 13:17:39
|
On 23 Aug 2005, at 13:38, Tom Blackwell wrote: > Simon and Randy - > > Both of you are pointing to the need for explicit "missing value" codes > in the schema -- in this case, a "missing spectrum" code. Either it's > a separate field, "spectrum supplied" which is normally true, or it's a > reserved value in some other field, say 'length="0"' as below, with an > explanation in the schema explaining that 'length="0"' MEANS that the > actual spectrum is missing, and what's there in its place should have > length 1 and should be ignored. It certainly seems odd to me to have this extra check value which doesn't always function as expected. At the very least this behaviour should be documented in the annotated schema files (which I don't think it is at the moment). At the risk of baring my ignorance of XML - if there are legitimate cases where this field is not supplied would this not suggest that the field shouldn't be mandatory in the schema? As long as the mzArrayBinary and internArrayBindary elements are present a parser should be able to cope with the data element being absent or having a length of 0. Simon. -- Simon Andrews PhD Bioinformatics Dept. The Babraham Institute sim...@bb... +44 (0) 1223 496463 |
|
From: Tom B. <tb...@um...> - 2005-08-23 12:38:44
|
Simon and Randy - Both of you are pointing to the need for explicit "missing value" codes in the schema -- in this case, a "missing spectrum" code. Either it's a separate field, "spectrum supplied" which is normally true, or it's a reserved value in some other field, say 'length="0"' as below, with an explanation in the schema explaining that 'length="0"' MEANS that the actual spectrum is missing, and what's there in its place should have length 1 and should be ignored. I'm not much of an xml hacker, but I should think that the preference among these two representations is clearly in favor of an additional field, since this allows straightforward validation logic, even though the extra field may seem pointless in normal usage. Tom Blackwell Univ Michigan Bioinformatics Ann Arbor, Michigan USA On Mon, 22 Aug 2005, Randy Julian wrote: > This question is a good one to address again as we consider various changes > to the schema. The essential goal is to allow schema-level validation where > the content of the <data> element is required in the schema definition. > Thus, the element cannot be left empty, but what should we do when the mass > spectrometer reports (and records) a totally empty spectrum? Currently we > are suggesting this be handled as given below - report a 0 length data array > and put 0 in for mass and intensity. Several instrument vendor do it this > way (and report this information using their API's). This seems preferable > over not recording the spectrum, or putting length="1" and then having an > invalid mass value of 0. This most often occurs when the export from the > vendor format file is performed with a threshold which sets a minimum > intensity value on what is exported - a spectrum full of noise might be > reported as 'empty'. Even when no user threshold is set, I have seen 'empty' > spectra recorded in the raw binary data for an instrument even through > electronically this makes almost no sense. > > Does anyone have any other suggestions which improve the reporting of an > empty (but recorded) spectrum? > > Your other question is language dependent. If you map to Java, > precision="32" is a float, and precision="64" is a double. Other languages > have other precisions for internal representations, but the idea is the "32" > is an IEEE 4 byte float and "64" is an IEEE 8 byte float. > > Has anyone else had any problems using the precision attribute? > > Randy > >> I'm writing a viewer for mzData files and have come across a small >> problem where I'm not sure if it's me or the data files which are wrong. >> >> I'm decoding the Base64 data in the spectra and am using the myo_ms2.xml >> file from sourceforge as an example. However my parser is falling over >> on the following lines: >> >> <mzArrayBinary> >> <data precision="32" endian="little" >> length="0">AAAAAA==</data> >> </mzArrayBinary> >> <intenArrayBinary> >> <data precision="32" endian="little" >> length="0">AAAAAA==</data> >> </intenArrayBinary> >> >> In these cases the file specifies a length of 0, despite there being 1 >> value in the entry (albeit 0 and 0). Is this the correct way of >> denoting an empty spectrum, or should this file really quote a length of >> 1? >> >> Also whilst I'm asking - can anyone point me to a reference for the >> correct way to handle 64 bit precision data on a 32bit machine and vice >> versa? I'm kind of new to a lot of this low level binary stuff! >> >> Cheers >> >> Simon. >> >> -- >> Simon Andrews PhD >> Bioinformatics Dept >> The Babraham Institute >> >> sim...@bb... >> +44 (0)1223 496463 >> >> >> >> ------------------------------------------------------- >> SF.Net email is Sponsored by the Better Software Conference & EXPO >> September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices >> Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA >> Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf >> _______________________________________________ >> Psidev-ms-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >> > > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > > > |
|
From: Randy J. <rkj...@in...> - 2005-08-22 15:50:05
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This question is a good one to address again as we consider various changes to the schema. The essential goal is to allow schema-level validation where the content of the <data> element is required in the schema definition. Thus, the element cannot be left empty, but what should we do when the mass spectrometer reports (and records) a totally empty spectrum? Currently we are suggesting this be handled as given below - report a 0 length data array and put 0 in for mass and intensity. Several instrument vendor do it this way (and report this information using their API's). This seems preferable over not recording the spectrum, or putting length="1" and then having an invalid mass value of 0. This most often occurs when the export from the vendor format file is performed with a threshold which sets a minimum intensity value on what is exported - a spectrum full of noise might be reported as 'empty'. Even when no user threshold is set, I have seen 'empty' spectra recorded in the raw binary data for an instrument even through electronically this makes almost no sense. Does anyone have any other suggestions which improve the reporting of an empty (but recorded) spectrum? Your other question is language dependent. If you map to Java, precision="32" is a float, and precision="64" is a double. Other languages have other precisions for internal representations, but the idea is the "32" is an IEEE 4 byte float and "64" is an IEEE 8 byte float. Has anyone else had any problems using the precision attribute? Randy > I'm writing a viewer for mzData files and have come across a small > problem where I'm not sure if it's me or the data files which are wrong. > > I'm decoding the Base64 data in the spectra and am using the myo_ms2.xml > file from sourceforge as an example. However my parser is falling over > on the following lines: > > <mzArrayBinary> > <data precision="32" endian="little" > length="0">AAAAAA==</data> > </mzArrayBinary> > <intenArrayBinary> > <data precision="32" endian="little" > length="0">AAAAAA==</data> > </intenArrayBinary> > > In these cases the file specifies a length of 0, despite there being 1 > value in the entry (albeit 0 and 0). Is this the correct way of > denoting an empty spectrum, or should this file really quote a length of > 1? > > Also whilst I'm asking - can anyone point me to a reference for the > correct way to handle 64 bit precision data on a 32bit machine and vice > versa? I'm kind of new to a lot of this low level binary stuff! > > Cheers > > Simon. > > -- > Simon Andrews PhD > Bioinformatics Dept > The Babraham Institute > > sim...@bb... > +44 (0)1223 496463 > > > > ------------------------------------------------------- > SF.Net email is Sponsored by the Better Software Conference & EXPO > September 19-22, 2005 * San Francisco, CA * Development Lifecycle > Practices > Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA > Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > |
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From: simon a. \(BI\) <sim...@bb...> - 2005-08-22 15:07:58
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I'm writing a viewer for mzData files and have come across a small problem where I'm not sure if it's me or the data files which are wrong. I'm decoding the Base64 data in the spectra and am using the myo_ms2.xml file from sourceforge as an example. However my parser is falling over on the following lines: <mzArrayBinary> <data precision=3D"32" endian=3D"little" = length=3D"0">AAAAAA=3D=3D</data> </mzArrayBinary> <intenArrayBinary> <data precision=3D"32" endian=3D"little" = length=3D"0">AAAAAA=3D=3D</data> </intenArrayBinary> In these cases the file specifies a length of 0, despite there being 1 value in the entry (albeit 0 and 0). Is this the correct way of denoting an empty spectrum, or should this file really quote a length of 1? Also whilst I'm asking - can anyone point me to a reference for the correct way to handle 64 bit precision data on a 32bit machine and vice versa? I'm kind of new to a lot of this low level binary stuff! Cheers Simon. --=20 Simon Andrews PhD Bioinformatics Dept The Babraham Institute sim...@bb... +44 (0)1223 496463 =20 |
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From: HOOGLAND C. <chr...@is...> - 2005-08-19 09:19:04
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Dear PSI participants, this autumn brings the opportunity for feedback and participation in the Proteomics Standards Initiative to all of you! On August 28, we will have a PSI session in the context of the HUPO congress in Munich. This is a relatively short session, providing an opportunity to report the current state of the PSI, and to gather feedback from a wider audience of HUPO congress participants. For detailed information, please see http://www.hupo2005.com/pc_initiatives.htm#PSI September 4-6, the Swiss Institute of Bioinformatics will host the PSI autumn workshop, following the =93tradition=94 of the PSI spring workshop= s. The aim is to do concrete work in the various PSI work groups, and to further PSI standardisation efforts. For detailed information and (free) registration, please see http://psidev.sourceforge.net/meetings/2005-09/index.html The registration is free of cost, but please do register for logistics organisation, in particular if you plan to have lunches! Whether Munich or Geneva is more convenient to you, please attend the PSI meetings to make your requirements count in Proteomics Data Standardisation! --=20 -------------------------------------------------------- Christine Hoogland Swiss Institute of Bioinformatics CMU - 1, rue Michel Servet Tel. (+41 22) 379 58 28 CH - 1211 Geneva 4 Switzerland Fax (+41 22) 379 58 58 Chr...@is... http://www.expasy.org/ -------------------------------------------------------- |
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From: Brian P. <bri...@in...> - 2005-08-05 17:36:59
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Greetings from mzXML-land!
I just wanted to drop a note to the mzData community saying that I've =
completed a first cut (not yet committed to CVS) at extending the =
Sashimi RAMP mzXML reader code to transparently handle mzData, thereby =
adding mzData compatiblity to future versions of the ISB's Trans =
Proteomic Pipeline and anything else using RAMP. As our free =
InsilicosViewer also uses RAMP you'll be seeing mzData capability there =
soon as well.
I'd like to ask for a bit of help - there are a few examples of mzData =
to be found on the net, but I could use more. Just within the handful =
I found through Google there's a fair amount of variability ("mz" vs =
MassToChargeRatio", for example) so I'd like to look at as many examples =
from the field as possible - the schema is obviously helpful but the =
devil is in the various writer implementations, which all need to be =
supported by a reader.
BTW is there any agreement on the proper filename extension for an =
mzData file? In the mzXML world we tend to go with ".mzXML", as ".xml" =
is not very informative. I've been assuming ".mzData" in my work so =
far, which several examples tend to support. What say the mzData =
community and/or its gurus?
Thanks,
Brian Pratt
Insilicos LLC
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From: Chris T. <chr...@eb...> - 2005-07-20 16:19:26
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Hi Jian. The particular converters to which you refer are not currently being supported, although the original codebase is still available, albeit for an older version of the schema. Sorry for that. We will soon be in a position where most vendor software directly exports mzData you see, hence the failure to updating the PSI-generated converters... The only route for conversion currently is to go via mzXML (they have many converters to that format) then through the converter developed by Proteome Systems available from the page at psidev.sf.net/ms under the heading 'Software supporting mzData'. I will if you like forward details of a 'wrapped up' version of this script that runs without it being necessary to get Java correctly configured (this app is in beta at the moment); do let me know if that would be useful to you (we are trying to speed it up a bit by expoiting some features of Xalan). Cheers, Chris. ji...@vb... wrote: > Hi, > > I've check out the mzData conventer from cvs, I think it was for old > version of mzData schema, I am wondering how soon it will be updated to > the most updated version of mzData format? > > Thanks, > Jian > > > > ------------------------------------------------------- > SF.Net email is sponsored by: Discover Easy Linux Migration Strategies > from IBM. Find simple to follow Roadmaps, straightforward articles, > informative Webcasts and more! Get everything you need to get up to > speed, fast. http://ads.osdn.com/?ad_id=7477&alloc_id=16492&op=click > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > > -- ~~~~~~~~~~~~~~~~~~~~~~~~ chr...@eb... http://psidev.sf.net/ ~~~~~~~~~~~~~~~~~~~~~~~~ |
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From: <ji...@vb...> - 2005-07-20 13:39:41
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Hi, I've check out the mzData conventer from cvs, I think it was for old version of mzData schema, I am wondering how soon it will be updated to the most updated version of mzData format? Thanks, Jian |
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From: Henning H. <hh...@eb...> - 2005-07-01 09:38:08
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Dear Juha, I forward your message to the PSI MS developers list, who will hopefully be able to answer you. Juha Vahokoski wrote: > I got your name from sourceforge web pages in context of mzData converters. > I am looking native data -> mzData converter/s for following mass specs: >Applied Biosystems: >*Q-Star Pulsar >*Voyager DE Pro >Bruker: >*Ultraflex I &II >*Esquire HCT >So far, no success. Would you help us in this issue? >Any information regarding mzData converters would be valuable. >Looking forward hearing from you. >Kind Regards, >Juha Vahokoski |
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