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From: Steffen N. <sne...@ip...> - 2010-04-06 10:33:08
|
Am Tuesday, den 23.03.2010, 09:30 -0700 schrieb Eric Deutsch: > - Bruker uses Lithium Fromiate; others? Just for the record: it is lithium formiate. Bye, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 |
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From: Steffen N. <sne...@ip...> - 2010-04-06 10:32:23
|
Am Tuesday, den 23.03.2010, 09:30 -0700 schrieb Eric Deutsch: > Present: Matt, Richard, Eric, Pierre-Alain, > > > > Agenda: > > 1) mzML 1.1.0 > > - Manuscript has been submitted > > - Matt will release updated 1.1.1 of indexedmzML schema: <indexList> > name attribute will be enumerated to “spectrum” or “chromatogram” > > - Matt will update the example files to reference mzML 1.1.0 but > indexedmzML 1.1.1 > > - How do we handle lock mass corrections? Matt will make an example > > - We should assemble list of calibrants and make them specific terms > > - Bruker uses Lithium Fromiate; others? > > - Jim will find out what Thermo is using > > - Matt will contact David Anderson and Mike Ashton and ask about a > date in lieu of checksum > > + Matt will follow up again > > - Other items? > > + What about FAIMS and mzML? > > + Might need a term for “compensation voltage” and for FAIMS itself? > > + Eric will ask Kristian > > > > ---- > > 2) MIAPE-MS revision > > - Pierre-Alain has submitted the latest MIAPE-MS to the doc proc > > + Need to have 3 examples to go along with a document submission > > + Until we provide the examples, it is not officially in the document > process > > + We can use the sample MIAPE-compliant mzML file > > + Pierre-Alain will contact Juan-Pablo to see if he has some suitable > examples in Proteo-Red > > + Richard will look into PRIDE to see if there may be a good example > there > > + When officially in the process, send out submitted document to > journal editors and everyone else to get the word out > > > > ---- > > 3) TraML development > > - Current version 0.9.3 is available at > http://www.psidev.info/index.php?q=node/405 > > - Fredrik sent out an inclusion list example. Everyone look and > comment. > > - Andreas also sent out an example > > - Need to finish writing the spec doc and submit to doc proc > > - Eric will update schema to 0.9.4 with previously-discussed updates > to <RetentionTime> > > - Eric will update the spec document with contributions from Steffen, > etc. > > - We will also need a few more example files > > - Andreas says he is up to date at 0.9.3 > > - Jim has an implementation but just will need to update to 0.9.4 > > - Implementations? > > - Matt will implement in ProteoWizard > > - Andreas will implement in OpenMS and update on-line validator > > - ISB implementation in ATAQS nearly done > > - Jim will implement as a test > > - David Cox at Sciex will test implement? > > - Are we ready to update validator page?: > http://www.psidev.info/index.php?q=node/304 > > + Draft manuscript in preparation > > + Will get the final changes made soon > > > > ---- > > 4) PSI workshop in Seoul preparation > > - Workshop is next week > > - Need to figure out who will give the PSI-MS WG activities summary > and otherwise represent the group > > + Andy Jones will present. Eric will send slides > > + Perhaps try to meet at ASMS briefly > > > > > > ---- > > 5) Working with ASMS on controlled vocabulary > > - Eric is coordinating with David Sparkman and others related to ASMS > who will contribute to our CV as the single standard CV > > - Eric will update this email list with activities and non-trivial > changes > > + Nothing new to report > > > > + Next meeting: April 6 at 8am PDT > > > > > > From: Eric Deutsch [mailto:ede...@sy...] > Sent: Monday, March 22, 2010 12:43 PM > To: Mass spectrometry standard development > Cc: Eric Deutsch > Subject: PSI-MSS WG call reminder > > > > > Hi everyone, the next PSI Mass Spectrometry Standards Working Group > call will be Tuesday 9am PDT: > > > > http://www.timeanddate.com/worldclock/fixedtime.html?day=23&month=3&year=2010&hour=16&min=0&sec=0&p1=136 > > > > Note: due to DST imbalance, the meeting time will be 1 hour later in > the US and regular time for Europe. > > > > 09:00 San Francisco > > 12:00 New York > > 16:00 London > > 17:00 Geneva > > > > + Germany: 08001012079 > > + Switzerland: 0800000860 > > + UK: 08081095644 > > + USA: 1-866-314-3683 > > Generic international: +44 2083222500 (UK number) > > > > access code: 297427 # > > > > Agenda: > > 1) mzML 1.1.0 > > - Manuscript has been submitted > > - Matt will release updated 1.1.1 of indexedmzML schema: <indexList> > name attribute will be enumerated to “spectrum” or “chromatogram” > > - Matt will update the example files to reference mzML 1.1.0 but > indexedmzML 1.1.1 > > - How do we handle lock mass corrections? Matt will make an example > > - We should assemble list of calibrants and make them specific terms > > - Bruker uses Lithium Fromiate; others? > > - Jim will find out what Thermo is using > > - Matt will contact David Anderson and Mike Ashton and ask about a > date in lieu of checksum > > - Other items? > > > > ---- > > 2) MIAPE-MS revision > > - Pierre-Alain has submitted the latest MIAPE-MS to the doc proc > > - And send out submitted document to journal editors and everyone else > to get the word out > > > > ---- > > 3) TraML development > > - Current version 0.9.3 is available at > http://www.psidev.info/index.php?q=node/405 > > - Fredrik sent out an inclusion list example. Everyone look and > comment. > > - Andreas also sent out an example > > - Need to finish writing the spec doc and submit to doc proc > > - Eric will update schema to 0.9.4 with previously-discussed updates > to <RetentionTime> > > - Eric will update the spec document with contributions from Steffen, > etc. > > - We will also need a few more example files > > - Andreas says he is up to date at 0.9.3 > > - Jim has an implementation but just will need to update to 0.9.4 > > - Implementations? > > - Matt will implement in ProteoWizard > > - Andreas will implement in OpenMS and update on-line validator > > - ISB implementation in ATAQS nearly done > > - Jim will implement as a test > > - David Cox at Sciex will test implement? > > - Are we ready to update validator page?: > http://www.psidev.info/index.php?q=node/304 > > > > ---- > > 4) PSI workshop in Seoul preparation > > - Workshop is next week > > - Need to figure out who will give the PSI-MS WG activities summary > and otherwise represent the group > > > > ---- > > 5) Working with ASMS on controlled vocabulary > > - Eric is coordinating with David Sparkman and others related to ASMS > who will contribute to our CV as the single standard CV > > - Eric will update this email list with activities and non-trivial > changes > > > > Next meeting: > > > > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ Psidev-ms-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 |
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From: Eric D. <ede...@sy...> - 2010-04-05 16:45:44
|
Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=6&month=4&year=2010&hour=16&min=0&sec=0&p1=136 08:00 San Francisco 11:00 New York 16:00 London 17:00 Geneva + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 Generic international: +44 2083222500 (UK number) access code: 297427 # Agenda: 1) mzML 1.1.0 - Manuscript has been reviewed and generally positive. Reviewers concerns can be addressed. In progress. - Matt will release updated 1.1.1 of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - How do we handle lock mass corrections? Matt will make an example - We should assemble list of calibrants and make them specific terms - Bruker uses Lithium Fromiate; others? - Jim will find out what Thermo is using - Matt will contact David Anderson and Mike Ashton and ask about a date in lieu of checksum - Need to test FAIMS support in mzML - Add term for “compensation voltage” to support FAIMS data - Other items? ---- 2) MIAPE-MS revision - Need to have 3 examples to go along with a document submission - Until we provide the examples, it is not officially in the document process - We can use the sample MIAPE-compliant mzML file - Pierre-Alain will contact Juan-Pablo to see if he has some suitable examples in Proteo-Red - Richard will look into PRIDE to see if there may be a good example there - When officially in the process, send out submitted document to journal editors and everyone else to get the word out ---- 3) TraML development - New version 0.9.4 released and is available at http://www.psidev.info/index.php?q=node/405 - Specification document is updated. Please examine. Is it ready for submission? http://www.peptideatlas.org/tmp/TraML/0.9.4/TraML_0.9.4.1_specificationDocument.doc - Implementations? Please update to 0.9.4 and test - Matt will implement in ProteoWizard - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim has an implementation but just will need to update to 0.9.4 - David Cox at Sciex will test implement? - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 - Manuscript is also in preparation ---- 4) PSI workshop in Seoul - Andy Jones presented the report. - Other reports? - Perhaps try to meet at ASMS briefly ---- 5) Working with ASMS on controlled vocabulary - Eric is coordinating with David Sparkman and others related to ASMS who will contribute to our CV as the single standard CV - Eric will update this email list with activities and non-trivial changes Next meeting: - In 3 weeks? Apr 27? |
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From: Jones, A. <And...@li...> - 2010-04-01 05:48:15
|
Hi all, I think this is one for the list, best wishes Andy ________________________________________ From: Mi-Youn Brusniak [mbr...@sy...] Sent: 31 March 2010 23:13 To: Jones, Andy Cc: 'Matthew Chambers'; 'Chris Paulse' Subject: One suggested item for mzML controlled vocabulary? Dear Andy, How is PSI meeting going in Seoul? I am not sure what is the exact procedure for requesting new controlled vocabulary for mzML but the current mzML1.1.0 doesn't have a controlled vocabulary for "FAIMS compensation voltage". I would appreciate if you can mention to PSI group for adding FAIMS compensation voltage to mzML controlled vocabulary with assigned MS:1000xxxx value. Thank you. Mi-Youn Mi-Youn Brusniak, Ph.D. Computational Biology Seattle Proteome Center mbr...@sy... Tel: (206) 732-1327 |
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From: Eric D. <ede...@sy...> - 2010-04-01 00:18:03
|
Hi Matt, I second the term (but maybe I'm biased?) (and I don't know a FAIMS CV from a tomato) but maybe a third opinion would be warranted, but I suggest this slightly edited entry: [Term] id: MS:1000XXX name: FAIMS compensation voltage def: "The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion." [PSI:MS] synonym: "FAIMS CV" EXACT [] is_a: MS:1000503 ! scan attribute Thanks, Eric > -----Original Message----- > From: Matthew Chambers [mailto:mat...@va...] > Sent: Wednesday, March 31, 2010 3:28 PM > To: Mass spectrometry standard development > Subject: [Psidev-ms-dev] Fwd: RE: thermo faims (yet again) > > Hello PSI folks, > > Can I get a second on adding this new term? Preferably from another > person that knows the meaning of FAIMS CV. :) > > -Matt > > > -------- Original Message -------- > Subject: RE: thermo faims (yet again) > Date: Wed, 31 Mar 2010 14:04:38 -0700 > From: Chris Paulse <cp...@sy...> > To: 'Matthew Chambers' <mat...@va...> > CC: 'Mi-Youn Brusniak' <mbr...@sy...> > > > I propose this as an entry for compensation voltage with definition > courtesy > of Rich Johnson: > > [Term] > id: MS:1000XXX > name: FAIMS compensation voltage > def: " The DC potential applied to the asymmetric waveform in FAIMS > that > compensates for the difference between high and low field mobility of > an > ion." [PSI:MS] > synonym: "FAIMS_CV" EXACT [] > is_a: MS:1000293 ! mass spectrometer > > > -----Original Message----- > From: Matthew Chambers [mailto:mat...@va...] > Sent: Wednesday, March 31, 2010 11:13 AM > To: Chris Paulse > Subject: Re: thermo faims (yet again) > > Hi Chris, can you propose a definition for a compensation voltage CV > term? > > -Matt > > > ----------------------------------------------------------------------- > ------- > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev |
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From: Eric D. <ede...@sy...> - 2010-03-31 23:14:14
|
Hi everyone, TraML version 0.9.4 has been posted at the development web page: http://www.psidev.info/index.php?q=node/405 The links to HTML documentation and examples files are all updated. Please examine the materials and respond. Major changes from 0.9.3: - <RetentionTime> is now permitted for each <Transition> and <Target> Please update your implementations and example files and validators and report. I think the OpenMS implementation is already at 0.9.4, and the on-line validator is up-to-date. It would be great if others would update their implementations and do some testing. We have three example files posted on the dev page. This is the minimum number required for submission, but it would be nice to collect a few more. Please implement and generate some files if you can! Thanks, Eric ---------------------------------- Eric Deutsch, Ph.D. Institute for Systems Biology 1441 North 34th Street Seattle WA 98103 Tel: 206-732-1397 Fax: 206-732-1260 Email: ede...@sy... WWW: http://www.systemsbiology.org/Senior_Research_Scientists/Eric_Deutsch |
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From: Matthew C. <mat...@va...> - 2010-03-31 22:27:45
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Hello PSI folks, Can I get a second on adding this new term? Preferably from another person that knows the meaning of FAIMS CV. :) -Matt -------- Original Message -------- Subject: RE: thermo faims (yet again) Date: Wed, 31 Mar 2010 14:04:38 -0700 From: Chris Paulse <cp...@sy...> To: 'Matthew Chambers' <mat...@va...> CC: 'Mi-Youn Brusniak' <mbr...@sy...> I propose this as an entry for compensation voltage with definition courtesy of Rich Johnson: [Term] id: MS:1000XXX name: FAIMS compensation voltage def: " The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion." [PSI:MS] synonym: "FAIMS_CV" EXACT [] is_a: MS:1000293 ! mass spectrometer -----Original Message----- From: Matthew Chambers [mailto:mat...@va...] Sent: Wednesday, March 31, 2010 11:13 AM To: Chris Paulse Subject: Re: thermo faims (yet again) Hi Chris, can you propose a definition for a compensation voltage CV term? -Matt |
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From: Matthew C. <mat...@va...> - 2010-03-30 19:26:22
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Don't everybody answer at once. :) Eric asked for this in pwiz 2.0. -Matt On 3/24/2010 2:35 PM, Matthew Chambers wrote: > I uploaded mzML1.1.1_idx.xsd. How do we copy it to: > http://psidev.info/files/ms/mzML/xsd/mzML1.1.1_idx.xsd ? > > -Matt > > > On 3/23/2010 11:30 AM, Eric Deutsch wrote: > >> Agenda: >> >> 1) mzML 1.1.0 >> >> - Matt will release updated 1.1.1 of indexedmzML schema:<indexList> >> name attribute will be enumerated to “spectrum” or “chromatogram” >> >> - Matt will update the example files to reference mzML 1.1.0 but >> indexedmzML 1.1.1 |
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From: Matthew C. <mat...@va...> - 2010-03-24 19:35:07
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I uploaded mzML1.1.1_idx.xsd. How do we copy it to: http://psidev.info/files/ms/mzML/xsd/mzML1.1.1_idx.xsd ? -Matt On 3/23/2010 11:30 AM, Eric Deutsch wrote: > > Agenda: > > 1) mzML 1.1.0 > > - Matt will release updated 1.1.1 of indexedmzML schema: <indexList> > name attribute will be enumerated to “spectrum” or “chromatogram” > > - Matt will update the example files to reference mzML 1.1.0 but > indexedmzML 1.1.1 > |
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From: Eric D. <ede...@sy...> - 2010-03-23 16:30:23
|
Present: Matt, Richard, Eric, Pierre-Alain, Agenda: 1) mzML 1.1.0 - Manuscript has been submitted - Matt will release updated 1.1.1 of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - How do we handle lock mass corrections? Matt will make an example - We should assemble list of calibrants and make them specific terms - Bruker uses Lithium Fromiate; others? - Jim will find out what Thermo is using - Matt will contact David Anderson and Mike Ashton and ask about a date in lieu of checksum + Matt will follow up again - Other items? + What about FAIMS and mzML? + Might need a term for “compensation voltage” and for FAIMS itself? + Eric will ask Kristian ---- 2) MIAPE-MS revision - Pierre-Alain has submitted the latest MIAPE-MS to the doc proc + Need to have 3 examples to go along with a document submission + Until we provide the examples, it is not officially in the document process + We can use the sample MIAPE-compliant mzML file + Pierre-Alain will contact Juan-Pablo to see if he has some suitable examples in Proteo-Red + Richard will look into PRIDE to see if there may be a good example there + When officially in the process, send out submitted document to journal editors and everyone else to get the word out ---- 3) TraML development - Current version 0.9.3 is available at http://www.psidev.info/index.php?q=node/405 - Fredrik sent out an inclusion list example. Everyone look and comment. - Andreas also sent out an example - Need to finish writing the spec doc and submit to doc proc - Eric will update schema to 0.9.4 with previously-discussed updates to <RetentionTime> - Eric will update the spec document with contributions from Steffen, etc. - We will also need a few more example files - Andreas says he is up to date at 0.9.3 - Jim has an implementation but just will need to update to 0.9.4 - Implementations? - Matt will implement in ProteoWizard - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim will implement as a test - David Cox at Sciex will test implement? - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 + Draft manuscript in preparation + Will get the final changes made soon ---- 4) PSI workshop in Seoul preparation - Workshop is next week - Need to figure out who will give the PSI-MS WG activities summary and otherwise represent the group + Andy Jones will present. Eric will send slides + Perhaps try to meet at ASMS briefly ---- 5) Working with ASMS on controlled vocabulary - Eric is coordinating with David Sparkman and others related to ASMS who will contribute to our CV as the single standard CV - Eric will update this email list with activities and non-trivial changes + Nothing new to report + Next meeting: April 6 at 8am PDT *From:* Eric Deutsch [mailto:ede...@sy...] *Sent:* Monday, March 22, 2010 12:43 PM *To:* Mass spectrometry standard development *Cc:* Eric Deutsch *Subject:* PSI-MSS WG call reminder Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 9am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=23&month=3&year=2010&hour=16&min=0&sec=0&p1=136 Note: due to DST imbalance, the meeting time will be 1 hour later in the US and regular time for Europe. 09:00 San Francisco 12:00 New York 16:00 London 17:00 Geneva + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 Generic international: +44 2083222500 (UK number) access code: 297427 # Agenda: 1) mzML 1.1.0 - Manuscript has been submitted - Matt will release updated 1.1.1 of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - How do we handle lock mass corrections? Matt will make an example - We should assemble list of calibrants and make them specific terms - Bruker uses Lithium Fromiate; others? - Jim will find out what Thermo is using - Matt will contact David Anderson and Mike Ashton and ask about a date in lieu of checksum - Other items? ---- 2) MIAPE-MS revision - Pierre-Alain has submitted the latest MIAPE-MS to the doc proc - And send out submitted document to journal editors and everyone else to get the word out ---- 3) TraML development - Current version 0.9.3 is available at http://www.psidev.info/index.php?q=node/405 - Fredrik sent out an inclusion list example. Everyone look and comment. - Andreas also sent out an example - Need to finish writing the spec doc and submit to doc proc - Eric will update schema to 0.9.4 with previously-discussed updates to <RetentionTime> - Eric will update the spec document with contributions from Steffen, etc. - We will also need a few more example files - Andreas says he is up to date at 0.9.3 - Jim has an implementation but just will need to update to 0.9.4 - Implementations? - Matt will implement in ProteoWizard - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim will implement as a test - David Cox at Sciex will test implement? - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 ---- 4) PSI workshop in Seoul preparation - Workshop is next week - Need to figure out who will give the PSI-MS WG activities summary and otherwise represent the group ---- 5) Working with ASMS on controlled vocabulary - Eric is coordinating with David Sparkman and others related to ASMS who will contribute to our CV as the single standard CV - Eric will update this email list with activities and non-trivial changes Next meeting: |
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From: Eric D. <ede...@sy...> - 2010-03-22 19:43:35
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Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 9am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=23&month=3&year=2010&hour=16&min=0&sec=0&p1=136 Note: due to DST imbalance, the meeting time will be 1 hour later in the US and regular time for Europe. 09:00 San Francisco 12:00 New York 16:00 London 17:00 Geneva + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 Generic international: +44 2083222500 (UK number) access code: 297427 # Agenda: 1) mzML 1.1.0 - Manuscript has been submitted - Matt will release updated 1.1.1 of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - How do we handle lock mass corrections? Matt will make an example - We should assemble list of calibrants and make them specific terms - Bruker uses Lithium Fromiate; others? - Jim will find out what Thermo is using - Matt will contact David Anderson and Mike Ashton and ask about a date in lieu of checksum - Other items? ---- 2) MIAPE-MS revision - Pierre-Alain has submitted the latest MIAPE-MS to the doc proc - And send out submitted document to journal editors and everyone else to get the word out ---- 3) TraML development - Current version 0.9.3 is available at http://www.psidev.info/index.php?q=node/405 - Fredrik sent out an inclusion list example. Everyone look and comment. - Andreas also sent out an example - Need to finish writing the spec doc and submit to doc proc - Eric will update schema to 0.9.4 with previously-discussed updates to <RetentionTime> - Eric will update the spec document with contributions from Steffen, etc. - We will also need a few more example files - Andreas says he is up to date at 0.9.3 - Jim has an implementation but just will need to update to 0.9.4 - Implementations? - Matt will implement in ProteoWizard - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim will implement as a test - David Cox at Sciex will test implement? - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 ---- 4) PSI workshop in Seoul preparation - Workshop is next week - Need to figure out who will give the PSI-MS WG activities summary and otherwise represent the group ---- 5) Working with ASMS on controlled vocabulary - Eric is coordinating with David Sparkman and others related to ASMS who will contribute to our CV as the single standard CV - Eric will update this email list with activities and non-trivial changes Next meeting: |
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From: Eric D. <ede...@sy...> - 2010-03-15 17:02:32
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Hi everyone, due to an unexpected schedule conflict, I need to defer the PSI-MSS WG call until next week. Due to DST imbalance the time will be a bit shifted. I propose Mar 23 at 8am PDT which is 15:00 in London. Let me know if this causes significant trouble. As before, please let me know if you plan on attending the PSI workshop in Seoul. The revised MIAPE-MS document has been submitted to the document process. Regards, Eric |
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From: Eric D. <ede...@sy...> - 2010-03-02 21:24:54
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Present: Matt, Steffen, Jim, Eric Agenda: 1) mzML 1.1.0 - Manuscript has been submitted - Matt will release updated 1.1.1 of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - How do we handle lock mass corrections? Matt will make an example - Eric will add term “calibration spectrum” to the CV + Added by Fredrik - We should assemble list of calibrants and make them specific terms - Bruker uses Lithium Fromiate; others? + Jim will find out what Thermo is using + Then figure out where to place the terms in the CV - Other items? + Several vendors are now requesting a mechanism to write mzML directly from a database instead of from a file. + How will we handle the now required file checksum? + Significant discussion about this. No clear solution. Can we just include a revision number managed by the RDBMS in lieu of a checksum? + Let’s add another checksum term which is “no checksum possible”. + then add a special rule that says if the term is a database record, only then allow that checksum + Or another idea: instead of checksum, allow a last modified date for that msrun record + Matt will contact David Anderson and Mike Ashton and ask about a date in lieu of checksum ---- 2) MIAPE-MS revision - Pierre-Alain will submit the latest to the doc proc - And send out submitted document to journal editors and everyone else to get the word out + Pierre-Alain says it will be submitted later this week and an announcement sent out ---- 3) TraML development - Current version 0.9.3 is available at http://www.psidev.info/index.php?q=node/405 - Fredrik sent out an inclusion list example. Everyone look and comment. - Andreas also sent out an example - Need to finish writing the spec doc and submit to doc proc - Eric will update schema to 0.9.4 with previously-discussed updates to <RetentionTime> - Eric will update the spec document with contributions from Steffen, etc. - We will also need a few more example files - Andreas says he is up to date at 0.9.3 - Jim has an implementation but just will need to update to 0.9.4 - Implementations? - Matt will implement in ProteoWizard - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim will implement as a test - David Cox at Sciex will test implement? - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 + No new progress to report on this front. Need to work on outstanding action items ---- 4) PSI workshop in Seoul preparation - Need to figure out who will give the PSI-MS WG activities summary and otherwise represent the group + No one from the working group able to attend. Jim may still be able to ---- 5) Working with ASMS on controlled vocabulary - Eric is coordinating with David Sparkman and others related to ASMS who will contribute to our CV as the single standard CV - Eric will update this email list with activities and non-trivial changes + Nothing new to report + Next meeting in two weeks: Mar 16 *From:* Eric Deutsch [mailto:ede...@sy...] *Sent:* Monday, March 01, 2010 10:44 PM *To:* 'Mass spectrometry standard development' *Cc:* 'Eric Deutsch' *Subject:* PSI-MSS WG call reminder Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=2&month=3&year=2010&hour=16&min=0&sec=0&p1=136 08:00 San Francisco 11:00 New York 16:00 London 17:00 Geneva + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 Generic international: +44 2083222500 (UK number) access code: 297427 # Agenda: 1) mzML 1.1.0 - Manuscript has been submitted - Matt will release updated 1.1.1 of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - How do we handle lock mass corrections? Matt will make an example - Eric will add term “calibration spectrum” to the CV - We should assemble list of calibrants and make them specific terms - Bruker uses Lithium Fromiate; others? - Other items? ---- 2) MIAPE-MS revision - Pierre-Alain will submit the latest to the doc proc - And send out submitted document to journal editors and everyone else to get the word out ---- 3) TraML development - Current version 0.9.3 is available at http://www.psidev.info/index.php?q=node/405 - Fredrik sent out an inclusion list example. Everyone look and comment. - Andreas also sent out an example - Need to finish writing the spec doc and submit to doc proc - Eric will update schema to 0.9.4 with previously-discussed updates to <RetentionTime> - Eric will update the spec document with contributions from Steffen, etc. - We will also need a few more example files - Andreas says he is up to date at 0.9.3 - Jim has an implementation but just will need to update to 0.9.4 - Implementations? - Matt will implement in ProteoWizard - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim will implement as a test - David Cox at Sciex will test implement? - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 ---- 4) PSI workshop in Seoul preparation - Need to figure out who will give the PSI-MS WG activities summary and otherwise represent the group ---- 5) Working with ASMS on controlled vocabulary - Eric is coordinating with David Sparkman and others related to ASMS who will contribute to our CV as the single standard CV - Eric will update this email list with activities and non-trivial changes |
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From: Eric D. <ede...@sy...> - 2010-03-02 07:04:57
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I have added this term exactly as shown below. [Term] id: MS:1000927 name: ion injection time def: "The length of time spent filling an ion trapping device." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000028 ! millisecond I have also added calibration spectrum: [Term] id: MS:1000928 name: calibration spectrum def: "A spectrum derived from a special calibration source, rather than from the primary injected sample. A calibration spectrum is typically derived from a substance that can be used to correct systematic shift in m/z for spectra of the primary inject sample." [PSI:MS] is_a: MS:1000559 ! spectrum type I don't have enough information to add calibrants yet. Initial users please advise. Also, where in the CV should calibrant and children go? Comments welcome. Eric > -----Original Message----- > From: Fredrik Levander [mailto:Fre...@im...] > Sent: Monday, March 01, 2010 1:37 AM > To: Mass spectrometry standard development > Subject: Re: [Psidev-ms-dev] Request for adding "ion injection time" term > to thePSI-MS CV > > Hi Andreas, > > This should definitely be added, maybe the 'before detection' can be > removed from the definition (it could be before other types o processing > as well). Milliseconds is probably appropriate as unit, or would seconds > be more in line with other entries even if it would typically mean e-6? > OK to add the following entry?: > > [Term] > id: MS:1000927 > name: ion injection time > def: "The length of time spent filling an ion trapping device." [PSI:MS] > xref: value-type:xsd\:float "The allowed value-type for this CV term." > is_a: MS:1000503 ! scan attribute > relationship: has_units UO:0000028 ! millisecond > > Regards > > Fredrik > > Andreas Römpp wrote: > > > > Hi there, > > > > > > > > This is an excellent idea. Although I would propose a somewhat more > > general definition (see below). This is not necessarily limited to > > (classical) ion trap mass spectrometers. > > > > > > > > "The length of time that ions were accumulated (in a trapping device) > > before detection. > > > > > > > > Regards, > > > > Andreas > > > > > > > > > > > > *Von:* Tahmina Baker [mailto:eva...@ho...] > > *Gesendet:* Dienstag, 23. Februar 2010 19:25 > > *An:* psi...@li... > > *Betreff:* [Psidev-ms-dev] Request for adding "ion injection time" > > term to thePSI-MS CV > > > > > > > > Hello, > > > > > > > > Can we please add a term to the PSI-MS CV for the ion injection > > time? Heres a proposed definition: > > > > > > > > "The length of time the mass spectrometer spent filling the ion trap > > after the selected ion was injected into it." > > > > > > > > Thanks, > > > > Eva > > > > > -------------------------------------------------------------------------- > ---- > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev |
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From: Eric D. <ede...@sy...> - 2010-03-02 06:44:43
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Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=2 <http://www.timeanddate.com/worldclock/fixedtime.html?day=2&month=3&year=201 0&hour=16&min=0&sec=0&p1=136> &month=3&year=2010&hour=16&min=0&sec=0&p1=136 08:00 San Francisco 11:00 New York 16:00 London 17:00 Geneva + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 Generic international: +44 2083222500 (UK number) access code: 297427 # Agenda: 1) mzML 1.1.0 - Manuscript has been submitted - Matt will release updated 1.1.1 of indexedmzML schema: <indexList> name attribute will be enumerated to "spectrum" or "chromatogram" - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - How do we handle lock mass corrections? Matt will make an example - Eric will add term "calibration spectrum" to the CV - We should assemble list of calibrants and make them specific terms - Bruker uses Lithium Fromiate; others? - Other items? ---- 2) MIAPE-MS revision - Pierre-Alain will submit the latest to the doc proc - And send out submitted document to journal editors and everyone else to get the word out ---- 3) TraML development - Current version 0.9.3 is available at <http://www.psidev.info/index.php?q=node/405> http://www.psidev.info/index.php?q=node/405 - Fredrik sent out an inclusion list example. Everyone look and comment. - Andreas also sent out an example - Need to finish writing the spec doc and submit to doc proc - Eric will update schema to 0.9.4 with previously-discussed updates to <RetentionTime> - Eric will update the spec document with contributions from Steffen, etc. - We will also need a few more example files - Andreas says he is up to date at 0.9.3 - Jim has an implementation but just will need to update to 0.9.4 - Implementations? - Matt will implement in ProteoWizard - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim will implement as a test - David Cox at Sciex will test implement? - Are we ready to update validator page?: <http://www.psidev.info/index.php?q=node/304> http://www.psidev.info/index.php?q=node/304 ---- 4) PSI workshop in Seoul preparation - Need to figure out who will give the PSI-MS WG activities summary and otherwise represent the group ---- 5) Working with ASMS on controlled vocabulary - Eric is coordinating with David Sparkman and others related to ASMS who will contribute to our CV as the single standard CV - Eric will update this email list with activities and non-trivial changes |
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From: Fredrik L. <Fre...@im...> - 2010-03-01 09:57:55
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Hi Andreas, This should definitely be added, maybe the 'before detection' can be removed from the definition (it could be before other types o processing as well). Milliseconds is probably appropriate as unit, or would seconds be more in line with other entries even if it would typically mean e-6? OK to add the following entry?: [Term] id: MS:1000927 name: ion injection time def: "The length of time spent filling an ion trapping device." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000503 ! scan attribute relationship: has_units UO:0000028 ! millisecond Regards Fredrik Andreas Römpp wrote: > > Hi there, > > > > This is an excellent idea. Although I would propose a somewhat more > general definition (see below). This is not necessarily limited to > (classical) ion trap mass spectrometers. > > > > "The length of time that ions were accumulated (in a trapping device) > before detection.” > > > > Regards, > > Andreas > > > > > > *Von:* Tahmina Baker [mailto:eva...@ho...] > *Gesendet:* Dienstag, 23. Februar 2010 19:25 > *An:* psi...@li... > *Betreff:* [Psidev-ms-dev] Request for adding "ion injection time" > term to thePSI-MS CV > > > > Hello, > > > > Can we please add a term to the PSI-MS CV for the “ion injection > time”? Here’s a proposed definition: > > > > "The length of time the mass spectrometer spent filling the ion trap > after the selected ion was injected into it." > > > > Thanks, > > Eva > |
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From: Andreas R. <And...@an...> - 2010-02-24 16:53:33
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Hi there, This is an excellent idea. Although I would propose a somewhat more general definition (see below). This is not necessarily limited to (classical) ion trap mass spectrometers. "The length of time that ions were accumulated (in a trapping device) before detection." Regards, Andreas Von: Tahmina Baker [mailto:eva...@ho...] Gesendet: Dienstag, 23. Februar 2010 19:25 An: psi...@li... Betreff: [Psidev-ms-dev] Request for adding "ion injection time" term to thePSI-MS CV Hello, Can we please add a term to the PSI-MS CV for the "ion injection time"? Here's a proposed definition: "The length of time the mass spectrometer spent filling the ion trap after the selected ion was injected into it." Thanks, Eva |
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From: Tahmina B. <eva...@ho...> - 2010-02-23 18:25:35
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Hello, Can we please add a term to the PSI-MS CV for the "ion injection time"? Here's a proposed definition: "The length of time the mass spectrometer spent filling the ion trap after the selected ion was injected into it." Thanks, Eva |
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From: Eric D. <ede...@sy...> - 2010-02-22 17:27:50
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Hi everyone, The PSI Spring meeting, now in its seventh year, is a hands-on workshop for the community-based development of data representation standards in Proteomics. Based on results of previous activities, the 2010 meeting in Seoul will focus on the further development of mzQuantML for the representation of quantitative mass spectrometry data, gelML and associated controlled vocabularies for protein separation, and PSICQUIC, a common query interface for molecular interaction data resources. The first day will be devoted to introductory talks and training sessions, the second and third day will focus on concrete, joint further development of the PSI standards. The meeting registration is FREE, thanks to generous support from our sponsors. For meeting details and registration, please see http://www.psidev.info/index.php?q=node/438 Regards, Eric |
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From: Eric D. <ede...@sy...> - 2010-02-16 16:40:50
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Notes from today’s call: Present: Richard, Andreas, Steffen, Eric, Pierre-Alain, Jim Agenda: 1) mzML 1.1.0 - Manuscript undergoing final editing + Final draft almost ready - Matt will release updated 1.1.1 of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - How do we handle lock mass corrections? Matt will make an example + Steffen has sent out new suggested CV term for “calibration spectrum” 1/19 + The place in the schema and mapping file is already there directly under spectrum element + Eric will add this to the CV, hearing no dissent + We should make the calibrants separate terms rather than in the value attribute + Bruker: Lithium fromiate; - Other items? ---- 2) MIAPE-MS revision - Pierre-Alain has sent out the revised MIAPE-MS draft 2.94 document to the list - Everyone: Please examine MIAPE-MS 2.94 in Pierre-Alain Binz’s email on 2009-12-22 and respond with comments - Deadline is Jan 12, after which the document will be submitted to the PSI document process + Pierre-Alain received only one comment + The changes have been made and other formatting changes made + Pierre-Alain will submit the document to the doc proc early next week + We should send the submitted document to all of the journal editors as a courtesy + In the cover letter, suggest some editors as official reviewers + Advertise the official web site of the MIAPE-MS draft for everyone to review ---- 3) TraML development - Current version 0.9.3 is available at http://www.psidev.info/index.php?q=node/405 - Fredrik sent out an inclusion list example. Everyone look and comment. - Andreas also sent out an example - Need to finish writing the spec doc and submit to doc proc + Eric will update schema to 0.9.4 with previously-discussed updates to <RetentionTime> + Eric will update the spec document with contributions from Steffen, etc. + We will also need a few more example files + Andreas says he is up to date at 0.9.3 + Jim has an implementation but just will need to update to 0.9.4 - Implementations? - Matt will implement in ProteoWizard - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim will implement as a test - David Cox at Sciex will test implement? - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 ---- 4) PSI workshop in Seoul preparation + Jim is hoping to be there + Henning and JuanAn will be there + Andy Jones will be giving MS-WG activities summary? ---- 5) Working with ASMS on controlled vocabulary + David Sparkman and others related to ASMS will contribute to our CV as the single standard CV + Eric is coordinating with them + Eric will update this email list with activities and non-trivial changes + Next call in two weeks, March 2 *From:* Eric Deutsch [mailto:ede...@sy...] *Sent:* Tuesday, February 16, 2010 12:40 AM *To:* Mass spectrometry standard development; Mark Christiansen *Cc:* ede...@sy... *Subject:* FW: PSI-MSS WG call reminder Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=16&month=2&year=2010&hour=16&min=0&sec=0&p1=136 08:00 San Francisco 11:00 New York 16:00 London 17:00 Geneva + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 Generic international: +44 2083222500 (UK number) access code: 297427 # Agenda: 1) mzML 1.1.0 - Manuscript undergoing final editing - Matt will release updated 1.1.1 of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - How do we handle lock mass corrections? Matt will make an example - Other items? ---- 2) MIAPE-MS revision - Pierre-Alain has sent out the revised MIAPE-MS draft 2.94 document to the list - Everyone: Please examine MIAPE-MS 2.94 in Pierre-Alain Binz’s email on 2009-12-22 and respond with comments - Deadline is Jan 12, after which the document will be submitted to the PSI document process ---- 3) TraML development - Current version 0.9.3 is available at http://www.psidev.info/index.php?q=node/405 - Fredrik sent out an inclusion list example. Everyone look and comment. - Andreas also sent out an example - Need to finish writing the spec doc and submit to doc proc - Implementations? - Matt will implement in ProteoWizard - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim will implement as a test - David Cox at Sciex will test implement? - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 ---- 4) PSI workshop in Seoul preparation ---- 5) Working with ASMS on controlled vocabulary |
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From: Eric D. <ede...@sy...> - 2010-02-16 08:40:25
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Hi everyone, the next PSI Mass Spectrometry Standards Working Group call will be Tuesday 8am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=16&month=2&year=2010&hour=16&min=0&sec=0&p1=136 08:00 San Francisco 11:00 New York 16:00 London 17:00 Geneva + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 Generic international: +44 2083222500 (UK number) access code: 297427 # Agenda: 1) mzML 1.1.0 - Manuscript undergoing final editing - Matt will release updated 1.1.1 of indexedmzML schema: <indexList> name attribute will be enumerated to “spectrum” or “chromatogram” - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 - How do we handle lock mass corrections? Matt will make an example - Other items? ---- 2) MIAPE-MS revision - Pierre-Alain has sent out the revised MIAPE-MS draft 2.94 document to the list - Everyone: Please examine MIAPE-MS 2.94 in Pierre-Alain Binz’s email on 2009-12-22 and respond with comments - Deadline is Jan 12, after which the document will be submitted to the PSI document process ---- 3) TraML development - Current version 0.9.3 is available at http://www.psidev.info/index.php?q=node/405 - Fredrik sent out an inclusion list example. Everyone look and comment. - Andreas also sent out an example - Need to finish writing the spec doc and submit to doc proc - Implementations? - Matt will implement in ProteoWizard - Andreas will implement in OpenMS and update on-line validator - ISB implementation in ATAQS nearly done - Jim will implement as a test - David Cox at Sciex will test implement? - Are we ready to update validator page?: http://www.psidev.info/index.php?q=node/304 ---- 4) PSI workshop in Seoul preparation ---- 5) Working with ASMS on controlled vocabulary |
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From: Trish W. <plw...@gm...> - 2010-02-09 08:21:56
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Special Issue - Second Call for Papers -- THE ONTOLOGY OF FUNCTIONS: BIOLOGY, ENGINEERING AND BEYOND -- http://www.loa-cnr.it/func_sp_issue2010 Applied Ontology Journal (IOS Press) Abstract Submission: 22-02-2010 Function and functionality play a central role not only in modern science but also in our extra-scientific understanding of the world. Unfortunately, the term 'function' is hereby used with a variety of meanings and is associated with a variety of views as to what functions are. This special issue is devoted to the foundation, the comparison and the application of functional theories in all areas, with particular attention to the biological and engineering domains. The goal is to publish state-of-the-art theoretical and technical contributions related to the description, characterization, and application of functions. We especially welcome contributions in which the theories are presented and motivated with an eye on the underlying ontological aspects and an introduction to their formalization. Contributions may include analyses of the different notions of function that have proven useful in science, proposals towards development of a unifying framework, or criticisms of existing frameworks. The goal is to provide materials for the creation of an ontological treatment of functions and functioning that will: 1) identify and describe functions in a consistent and comprehensive way; 2) list the arguments that lead to a preference of one notion of function over others; 3) make clear the basic assumptions and principles of classification that motivate a given notion of function; 4) discuss formalization issues and relevant application methodologies. TOPICS include, but are not limited to, the following: - comparison of functional theories and models - formalization of functional theories and models - basic functions, functional classification, functional (de)composition - assigning functions to natural and/or artificial entities - functional ontology - unified theory of biological and artifact functions - theory of artifacts - what kinds of biological entities have functions? - how are biological functions related to disease? IMPORTANT DATES ** Abstract Submission: 22-02-2010* * Invitation to submit a full paper (20/25 pages): 10-03-2010 * Full papers due: 12-05-2010 * Notification of acceptance/rejection: 24-06-2010 * Revised papers due: 21-07-2010 * Final review: 15-09-2010 * Camera-ready papers due: 12-10-2010 * Publication: Spring 2011 PAPER SUBMISSION Submissions to the first phase (deadline: 22 Feb 2010) should include an abstract of about 1000 words, a separate list of references and a cover page with title, name, address (including e-mail address) and affiliation of author(s) and a list of keywords. Authors are encouraged to submit high-quality, original work that has neither appeared in, nor is under consideration by, other journals. Manuscripts must be written in English. Manuscripts must be submitted to: functions (at) loa-cnr.it Please indicate in the email subject that you are submitting to the ''AOJ Special Issue on Functions''. GUEST EDITORS Stefano Borgo, ISTC-CNR Trento and FUB Bolzano, Italy Riichiro Mizoguchi, The Institute of Scientific and Industrial Research, Osaka University, Japan Barry Smith, University at Buffalo, USA REVIEW COMMITTEE Massimiliano Carrara, University of Padova Randall R. Dipert, University at Buffalo Pawel Garbacz, Katolicki Uniwersytet Lubelski Jana Pawla II John S. Gero, George Mason University Ashok K. Goel, Georgia Institute of Technology W.N. Houkes, Technische Universiteit Eindhoven Yoshinobu Kitamura, Osaka University Peter Kroes, Technische Universiteit Delft Ulrich Krohs, University of Bielefeld Pieter Vermaas, Technische Universiteit Delft |
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From: Eric D. <ede...@sy...> - 2010-02-09 07:20:27
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Hi everyone, I regret the late notice, but I just returned from a trip and am unable to do the call tomorrow as we had planned. Let us defer it until next week. There has been some progress on the mzML manuscript, however. We have a almost-final draft and we are hoping to submit by the end of the week. Regards, Eric > -----Original Message----- > From: Matthew Chambers [mailto:mat...@va...] > Sent: Thursday, January 21, 2010 8:08 AM > To: Mass spectrometry standard development > Subject: Re: [Psidev-ms-dev] PSI-MSS WG call reminder > > > Conference call notes: > > Present: Matt, Jim, Ree?, Mark, Steffen, Eric > > 1) mzML 1.1.0 > > - Manuscript now in active preparation > + draft available in a couple weeks > > - Matt will release updated 1.1.1 of indexedmzML schema: <indexList> > name attribute will be enumerated to "spectrum" or "chromatogram" > + not yet done > > - Matt will update the example files to reference mzML 1.1.0 but > indexedmzML 1.1.1 > + not yet done > > - Andreas will add "Replaced-by" field to the obsoleted MaRiMba term > + done > > - Matt added new terms for ABI TOF/TOF T2D file format > + done > > - How do we handle lock mass corrections? Matt will make an example > + Steffen wants lock mass spectra to be marked so they can be segregated > + Need an example of what lock mass spectra would look like in mzML, > also what do corrected spectra look like (e.g. processingMethod)? > + Steffen will start a ML thread with ideas on the topic. > + CompassXport beta version supports mzML > > - Other items? > > > ---- > > 2) MIAPE-MS revision > > - Pierre-Alain has sent out the revised MIAPE-MS draft 2.94 document to > the list > - Everyone: Please examine MIAPE-MS 2.94 in Pierre-Alain Binz's email on > 2009-12-22 and respond with comments > - Deadline is Jan 12, after which the document will be submitted to the > PSI document process > + Pierre-Alain will address minor comments and send doc process > > ---- > > 3) TraML development > > - Current version 0.9.3 is available at > http://www.psidev.info/index.php?q=node/405 > - Matt suggest changing "frag: y ion" to "product: y ion" > - But Andreas points out that the "frag" is supposed to differentiate > search parameter from resulting > - Andreas will rephrase all the definitions for "frag: y ion" to be better > + done > > - Fredrik sent out an inclusion list example. Everyone look and comment. > - Andreas also sent out an example > + not yet reviewed > > - What do we do about specifying retention times, i.e. where to allow > <RetentionTimeList> (see 1/14) > + because of semantic differences between predicted/observed retention > times (e.g. provided by public transition lists), should we move local > retention time to transition or configuration? > + local retention time under transition can override local retention > time in Peptide/Compound > + Eric will summarize the discussion to the list. Add <RetentionTime> to > <Transition> and <Target> > > - Do we try to merge <Transition> and <Target>? > + Keep them separate for now. > + Discussed the scope of TraML. We agreed that we would keep TraML 1.0 > limited to transitions and an additional add-on for inclusion/exclusion > lists. Steffen proposes a future TraML 2.0 or MethodsML that tries to > tackle a unified instrument input configuration or "methods file" format. > > - Implementations? > - Matt will implement in ProteoWizard > + mostly done > - Andreas will implement in OpenMS and update on-line validator > + done > - ISB implementation in ATAQS nearly done > - Jim will implement as a test > - David Cox at Sciex will test implement? > - Are we ready to update validator page?: http://www.psidev.info > > Next meeting: > + Eric is unavailable in two weeks, next meeting is in 3 weeks on > February 9th at regular time. > > -------------------------------------------------------------------------- > ---- > Throughout its 18-year history, RSA Conference consistently attracts the > world's best and brightest in the field, creating opportunities for > Conference > attendees to learn about information security's most important issues > through > interactions with peers, luminaries and emerging and established > companies. > http://p.sf.net/sfu/rsaconf-dev2dev > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev |
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From: Matthew C. <mat...@va...> - 2010-01-21 16:09:34
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Conference call notes: Present: Matt, Jim, Ree?, Mark, Steffen, Eric 1) mzML 1.1.0 - Manuscript now in active preparation + draft available in a couple weeks - Matt will release updated 1.1.1 of indexedmzML schema: <indexList> name attribute will be enumerated to "spectrum" or "chromatogram" + not yet done - Matt will update the example files to reference mzML 1.1.0 but indexedmzML 1.1.1 + not yet done - Andreas will add "Replaced-by" field to the obsoleted MaRiMba term + done - Matt added new terms for ABI TOF/TOF T2D file format + done - How do we handle lock mass corrections? Matt will make an example + Steffen wants lock mass spectra to be marked so they can be segregated + Need an example of what lock mass spectra would look like in mzML, also what do corrected spectra look like (e.g. processingMethod)? + Steffen will start a ML thread with ideas on the topic. + CompassXport beta version supports mzML - Other items? ---- 2) MIAPE-MS revision - Pierre-Alain has sent out the revised MIAPE-MS draft 2.94 document to the list - Everyone: Please examine MIAPE-MS 2.94 in Pierre-Alain Binz's email on 2009-12-22 and respond with comments - Deadline is Jan 12, after which the document will be submitted to the PSI document process + Pierre-Alain will address minor comments and send doc process ---- 3) TraML development - Current version 0.9.3 is available at http://www.psidev.info/index.php?q=node/405 - Matt suggest changing "frag: y ion" to "product: y ion" - But Andreas points out that the "frag" is supposed to differentiate search parameter from resulting - Andreas will rephrase all the definitions for "frag: y ion" to be better + done - Fredrik sent out an inclusion list example. Everyone look and comment. - Andreas also sent out an example + not yet reviewed - What do we do about specifying retention times, i.e. where to allow <RetentionTimeList> (see 1/14) + because of semantic differences between predicted/observed retention times (e.g. provided by public transition lists), should we move local retention time to transition or configuration? + local retention time under transition can override local retention time in Peptide/Compound + Eric will summarize the discussion to the list. Add <RetentionTime> to <Transition> and <Target> - Do we try to merge <Transition> and <Target>? + Keep them separate for now. + Discussed the scope of TraML. We agreed that we would keep TraML 1.0 limited to transitions and an additional add-on for inclusion/exclusion lists. Steffen proposes a future TraML 2.0 or MethodsML that tries to tackle a unified instrument input configuration or “methods file” format. - Implementations? - Matt will implement in ProteoWizard + mostly done - Andreas will implement in OpenMS and update on-line validator + done - ISB implementation in ATAQS nearly done - Jim will implement as a test - David Cox at Sciex will test implement? - Are we ready to update validator page?: http://www.psidev.info Next meeting: + Eric is unavailable in two weeks, next meeting is in 3 weeks on February 9th at regular time. |
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From: Steffen N. <sne...@ip...> - 2010-01-20 14:03:18
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On Tue, 2010-01-19 at 11:10 -0800, Eric Deutsch wrote: > Hi everyone, after a discussion at today's call, we came to a > conclusion that maybe it would be best to attach the specification of > local retention times to the <Transition> (and <Target>) and all the > others to <Peptide> (or <Compound>). and here is a little blurb that could go into the spec document: 1.3 Use Cases / 2.3 Design Decisions ... The retention times stored with the and compounds can be multiple measured or predicted retention times. They can be interpreted as input-, archived- or generic retention times. One step in the processing of a TraML file is the selection/merging (and optionally calibrating) of these retention times into the "local" retention time under the target- and transition lists. This local retention time SHOULD be used for the export to the instrument method in an export / conversion into e.g. a TSV file the instrument can import. Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 |
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