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From: Eric D. <ede...@sy...> - 2008-05-05 07:12:14
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Hi everyone, as previously mentioned, the PSI Mass Spectrometry Standards Working Group call is Tuesday May 6 at 9am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=6&month=5&year=2008&hour=17&min=0&sec=0&p1=136 + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 The agenda will be to review and discuss what remains to be done to finish up mzML, including the latest release and some recent issues discovered while making examples. Thanks, Eric |
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From: Eric D. <ede...@sy...> - 2008-05-06 17:04:01
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Hi everyone, here are the minutes for the telecon. Please see action items for you. Anyone not on the call willing to help out is welcome. Present: Darren, Matt, Eric, Jim, Pierre-Alain Thank you to Juan Antonio for setting up the call. Agenda: - What is the purpose of <mzML> id and accession attributes? + Make the id= attribute optional in schema + Recommend in the documentation that you use LSID or local identifiers + Make all sample instance documents use a psidev LSID + Leave accession= optional as is, perhaps with better documentation - Make <run> instrumentConfigurationRef optional or remove it: - if remove, then this attribute can be required in <scan> - if optional, semval must insure that it is provide either in <run> or <scan> + OR consensus opinion: rename <run> instrumentConfigurationRef to defaultInstrumentConfigurationRef and keep it required + Document the intrumentConfiguration a bit better. Applies to LTQ-FT but not LTQ, for example. For different modes, use ParamGroups + Discussion of issue of how to use ParamGroups without having to do two passes through the file. - Issue of exactly how other spectra are referenced in <acquisition> + We agree to move forward with Matt suggestion: spectrumRef (infer reference as current file and spectrumRef is IDREF pointing to an existing spectrum's id) sourceFileRef + externalNativeID (original file is native) sourceFileRef + externalSpectrumID (original file is mzML) For example external mzXML files, the externalNativeID would refer to mzXML scanNumber In fact, anything that's not mzML would have externNativeID Matt says that XML schema can enforce these various options - MIAPE spreadsheet? + Pierre-Alain has spreadsheet. Darren added some comments trying to implement it + Rename Darren's tiny2 to tiny5 or some other name since "tiny2" is used by another document + Get miape-ms.pwiz.mzML posted + Pierre-Alain will continue to work on the spreadsheet + Before next call, send out or post miape-ms.pwiz.mzML and spreadsheet of issues to discuss - CV? + Randy has pink teddy bear, but haven't heard from him + Eric will take it and work on some changes to the CV + Eric will create the CV spreadsheets and start sending to vendors + Some contacts: Bruker :Herbert Thiele? Waters: Ronan O'Malley? - documentation? + latest is posted without figures - schema? + Eric will add Darren & Matt as a developers (dkessner) (chambm) + Darren will update 0.99.10 to 0.99.11 with changes above + Matt can help with multiple accession configs in <acquisition> - website + Eric post 0.99.10 schemas + Darren verify that tiny.pwiz encodes all ideas of tiny1 and then post as a single tiny1 - example files + Jim has an example that he will send out + Jim will send out examples of the nativeIDs for Thermo ________________________________ From: Eric Deutsch Sent: Monday, May 05, 2008 12:12 AM To: 'Mass spectrometry standard development'; Juan Antonio Vizcaíno González Cc: Eric Deutsch Subject: RE: PSI-MSS WG call Tuesday Hi everyone, as previously mentioned, the PSI Mass Spectrometry Standards Working Group call is Tuesday May 6 at 9am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=6&month=5&year=2008&hour=17&min=0&sec=0&p1=136 + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 The agenda will be to review and discuss what remains to be done to finish up mzML, including the latest release and some recent issues discovered while making examples. Thanks, Eric |
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From: Matthew C. <mat...@va...> - 2008-05-06 21:45:03
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Hi all, It looks like I was wrong about the "choice" xsd concept. It only works on elements, not attributes. If we want to do this with schematic validation, we could make two acquisition types: <acquisition spectrumRef="..." /> <externalAcquisition sourceFileRef="..." spectrumRef="..." nativeID="(optional)" /> Or we can keep the current suggestion and leave it to the semantic validator to enforce the right attributes: spectrumRef (infer reference as current file and spectrumRef is IDREF pointing to an existing spectrum's id) sourceFileRef + externalNativeID (original file is native) sourceFileRef + externalSpectrumID (original file is mzML) -Matt Eric Deutsch wrote: > > Hi everyone, here are the minutes for the telecon. Please see action > items for you. Anyone not on the call willing to help out is welcome. > > Present: Darren, Matt, Eric, Jim, Pierre-Alain > > Thank you to Juan Antonio for setting up the call. > > Agenda: > > - What is the purpose of <mzML> id and accession attributes? > > + Make the id= attribute optional in schema > > + Recommend in the documentation that you use LSID or local identifiers > > + Make all sample instance documents use a psidev LSID > > + Leave accession= optional as is, perhaps with better documentation > > - Make <run> instrumentConfigurationRef optional or remove it: > > - if remove, then this attribute can be required in <scan> > > - if optional, semval must insure that it is provide either in <run> > or <scan> > > + OR consensus opinion: rename <run> instrumentConfigurationRef to > defaultInstrumentConfigurationRef and keep it required > > + Document the intrumentConfiguration a bit better. Applies to LTQ-FT > but not LTQ, for example. For different modes, use ParamGroups > > + Discussion of issue of how to use ParamGroups without having to do > two passes through the file. > > - Issue of exactly how other spectra are referenced in <acquisition> > > + We agree to move forward with Matt suggestion: > > spectrumRef (infer reference as current file and spectrumRef is IDREF > > pointing to an existing spectrum's id) > > sourceFileRef + externalNativeID (original file is native) > > sourceFileRef + externalSpectrumID (original file is mzML) > > For example external mzXML files, the externalNativeID would refer to > mzXML scanNumber > > In fact, anything that’s not mzML would have externNativeID > > Matt says that XML schema can enforce these various options > > - MIAPE spreadsheet? > > + Pierre-Alain has spreadsheet. Darren added some comments trying to > implement it > > + Rename Darren’s tiny2 to tiny5 or some other name since “tiny2” is > used by another document > > + Get miape-ms.pwiz.mzML posted > > + Pierre-Alain will continue to work on the spreadsheet > > + Before next call, send out or post miape-ms.pwiz.mzML and > spreadsheet of issues to discuss > > - CV? > > + Randy has pink teddy bear, but haven’t heard from him > > + Eric will take it and work on some changes to the CV > > + Eric will create the CV spreadsheets and start sending to vendors > > + Some contacts: Bruker :Herbert Thiele? Waters: Ronan O’Malley? > > - documentation? > > + latest is posted without figures > > - schema? > > + Eric will add Darren & Matt as a developers (dkessner) (chambm) > > + Darren will update 0.99.10 to 0.99.11 with changes above > > + Matt can help with multiple accession configs in <acquisition> > > - website > > + Eric post 0.99.10 schemas > > + Darren verify that tiny.pwiz encodes all ideas of tiny1 and then > post as a single tiny1 > > - example files > > + Jim has an example that he will send out > > + Jim will send out examples of the nativeIDs for Thermo > > ------------------------------------------------------------------------ > > *From:* Eric Deutsch > *Sent:* Monday, May 05, 2008 12:12 AM > *To:* 'Mass spectrometry standard development'; Juan Antonio Vizcaíno > González > *Cc:* Eric Deutsch > *Subject:* RE: PSI-MSS WG call Tuesday > > Hi everyone, as previously mentioned, the PSI Mass Spectrometry > Standards Working Group call is Tuesday May 6 at 9am PDT: > > http://www.timeanddate.com/worldclock/fixedtime.html?day=6&month=5&year=2008&hour=17&min=0&sec=0&p1=136 > <http://www.timeanddate.com/worldclock/fixedtime.html?day=6&month=5&year=2008&hour=17&min=0&sec=0&p1=136> > > + Germany: 08001012079 > > + Switzerland: 0800000860 > > + UK: 08081095644 > > + USA: 1-866-314-3683 > > + Generic international: +44 2083222500 (UK number) > > access code: 297427 > > The agenda will be to review and discuss what remains to be done to > finish up mzML, including the latest release and some recent issues > discovered while making examples. > > Thanks, > > Eric > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > This SF.net email is sponsored by the 2008 JavaOne(SM) Conference > Don't miss this year's exciting event. There's still time to save $100. > Use priority code J8TL2D2. > http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone > ------------------------------------------------------------------------ > > _______________________________________________ > 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...> - 2008-05-13 17:12:04
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Hi everyone, there are the minutes for the telecon of 2008-05-13. Present: Matt, Darren, Eric, Jim, Pierre-Alain Thank you to Juan Antonio for setting up the call. - Schema updated to 0.99.11 + Eric will update web site for that + Darren has updated the codebase and will check if the latest output validates - MIAPE example document? + A few small items left. + A final example document will be finished in the next week for inspection - CV status + Fredrik volunteers to help with the CV, too + Eric has updated the CV a couple times + Darren will send around a few examples of datatype and unittype - CV template updates to vendors + Eric has sent out and will follow up + Thermo and Waters have returned results - documentation + Check whether instrumentConfiguration is well defined in xsd + Eric will generate a HTML and .doc spec document for 0.99.11 and post - website + Eric will update web site for 0.99.11 - validator + Eric will contact Lennart and Fredrik and see how to proceed + Does the validator check that if there is a acquisition list, then there would be a combination type (like sum of spectra) provided - example files + Remove tiny4 and point to "small" which includes LTQ-FT demo usage + Fredrik sent out a nice example of dta -> mzML + Matt will generate an example MGF -> mzML using pwiz and post + Jim will send Eric some example RAW files and converted files (including PDA, SRM) - ASMS + Eric will follow up with Randy about ASMS "Computer applications interest group" + or try mark.sanders@therm - Amsterdam + Poster in Eric's name was submitted. No word on acceptance, but Eric cannot attend. + PSI session during the congress at Sunday 17th 9:30a-12 + Tentative presenter at PSI session is Jim Shofstahl with backups of Randy and Pierre-Alain - Open schema issue: where to put "centroided" and "deisotoped" + We will allow spectrum representation (like centroid/profile) in the fileContent section - Next call + Same time next week. Eric will figure how to start the call ________________________________ From: Eric Deutsch Sent: Tuesday, May 06, 2008 10:04 AM To: 'Mass spectrometry standard development' Cc: Eric Deutsch Subject: RE: RE: PSI-MSS WG call Tuesday Hi everyone, here are the minutes for the telecon of 2008-05-06. Please see action items for you. Anyone not on the call willing to help out is welcome. Present: Darren, Matt, Eric, Jim, Pierre-Alain Thank you to Juan Antonio for setting up the call. Agenda: - What is the purpose of <mzML> id and accession attributes? + Make the id= attribute optional in schema + Recommend in the documentation that you use LSID or local identifiers + Make all sample instance documents use a psidev LSID + Leave accession= optional as is, perhaps with better documentation - Make <run> instrumentConfigurationRef optional or remove it: - if remove, then this attribute can be required in <scan> - if optional, semval must insure that it is provide either in <run> or <scan> + OR consensus opinion: rename <run> instrumentConfigurationRef to defaultInstrumentConfigurationRef and keep it required + Document the intrumentConfiguration a bit better. Applies to LTQ-FT but not LTQ, for example. For different modes, use ParamGroups + Discussion of issue of how to use ParamGroups without having to do two passes through the file. - Issue of exactly how other spectra are referenced in <acquisition> + We agree to move forward with Matt suggestion: spectrumRef (infer reference as current file and spectrumRef is IDREF pointing to an existing spectrum's id) sourceFileRef + externalNativeID (original file is native) sourceFileRef + externalSpectrumID (original file is mzML) For example external mzXML files, the externalNativeID would refer to mzXML scanNumber In fact, anything that's not mzML would have externNativeID Matt says that XML schema can enforce these various options - MIAPE spreadsheet? + Pierre-Alain has spreadsheet. Darren added some comments trying to implement it + Rename Darren's tiny2 to tiny5 or some other name since "tiny2" is used by another document + Get miape-ms.pwiz.mzML posted + Pierre-Alain will continue to work on the spreadsheet + Before next call, send out or post miape-ms.pwiz.mzML and spreadsheet of issues to discuss - CV? + Randy has pink teddy bear, but haven't heard from him + Eric will take it and work on some changes to the CV + Eric will create the CV spreadsheets and start sending to vendors + Some contacts: Bruker :Herbert Thiele? Waters: Ronan O'Malley? - documentation? + latest is posted without figures - schema? + Eric will add Darren & Matt as a developers (dkessner) (chambm) + Darren will update 0.99.10 to 0.99.11 with changes above + Matt can help with multiple accession configs in <acquisition> - website + Eric post 0.99.10 schemas + Darren verify that tiny.pwiz encodes all ideas of tiny1 and then post as a single tiny1 - example files + Jim has an example that he will send out + Jim will send out examples of the nativeIDs for Thermo ________________________________ From: Eric Deutsch Sent: Monday, May 05, 2008 12:12 AM To: 'Mass spectrometry standard development'; Juan Antonio Vizcaíno González Cc: Eric Deutsch Subject: RE: PSI-MSS WG call Tuesday Hi everyone, as previously mentioned, the PSI Mass Spectrometry Standards Working Group call is Tuesday May 6 at 9am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=6&month=5&year=2008&hour=17&min=0&sec=0&p1=136 + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 The agenda will be to review and discuss what remains to be done to finish up mzML, including the latest release and some recent issues discovered while making examples. Thanks, Eric |
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From: Eric D. <ede...@sy...> - 2008-05-20 16:37:17
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Hi everyone, there are the minutes for the telecon of 2008-05-20. Present: Matt, Darren, Eric, Jim, Pierre-Alain Thank you to Phil for setting up the call. - schema + Discussed Fredrik's suggested changes of 2008-05-20 + Add unitCvRef attribute to cvParam + apply same exact attributes to precursor as there is now for acquisition + Matt will make the changes and release 0.99.12 - MIAPE example document? + Darren and Pierre-Alain will get together and finish this - CV status + Darren has sent a proposal for of datatype and has_units + Eric will with Luisa 5/15 9:52am + Then Darren will go ahead and implemented - CV template updates to vendors + Eric has sent out and will follow up + Thermo and Waters have returned results - documentation + Eric will generate a HTML and .doc spec document for 0.99.12 and post - website + Eric will update web site for 0.99.12 - validator + Eric will contact Lennart and Fredrik and see how to proceed + Does the validator check that if there is a acquisition list, then there would be a combination type (like sum of spectra) provided - example files + Darren added examples of small with and without compression. Will be released in a few days. + Matt will take a stab at MALDI example + Remove tiny4 and point to "small" which includes LTQ-FT demo usage + Fredrik sent out a nice example of dta -> mzML + Matt will generate an example MGF -> mzML using pwiz and post + Jim will send Eric some example RAW files and converted files (including PDA, SRM) - ASMS + Eric will have a draft of a poster for the next call and send out for folks to look at + Eric will follow up with Randy about ASMS "Computer applications interest group" + or try mark.sanders@therm + Everyone present at the call will be at ASMS + Try to plan for one night going out to dinner as a group Mon, Tue, Wed. Jim can't due Tue. + Or a lunch - Amsterdam + Poster in Eric's name was submitted. No word on acceptance, but Eric cannot attend. + PSI session during the congress at Sunday 17th 9:30a-12 + Tentative presenter at PSI session is Jim Shofstahl with backups of Randy and Pierre-Alain - Open schema issue: where to put "centroided" and "deisotoped" + We will allow spectrum representation (like centroid/profile) in the fileContent section - Next call + Same time next week ________________________________ From: Eric Deutsch Sent: Tuesday, May 13, 2008 10:12 AM To: 'Mass spectrometry standard development' Cc: Eric Deutsch Subject: PSI-MSS WG call minutes Hi everyone, there are the minutes for the telecon of 2008-05-13. Present: Matt, Darren, Eric, Jim, Pierre-Alain Thank you to Juan Antonio for setting up the call. - Schema updated to 0.99.11 + Eric will update web site for that + Darren has updated the codebase and will check if the latest output validates - MIAPE example document? + A few small items left. + A final example document will be finished in the next week for inspection - CV status + Fredrik volunteers to help with the CV, too + Eric has updated the CV a couple times + Darren will send around a few examples of datatype and unittype - CV template updates to vendors + Eric has sent out and will follow up + Thermo and Waters have returned results - documentation + Check whether instrumentConfiguration is well defined in xsd + Eric will generate a HTML and .doc spec document for 0.99.11 and post - website + Eric will update web site for 0.99.11 - validator + Eric will contact Lennart and Fredrik and see how to proceed + Does the validator check that if there is a acquisition list, then there would be a combination type (like sum of spectra) provided - example files + Remove tiny4 and point to "small" which includes LTQ-FT demo usage + Fredrik sent out a nice example of dta -> mzML + Matt will generate an example MGF -> mzML using pwiz and post + Jim will send Eric some example RAW files and converted files (including PDA, SRM) - ASMS + Eric will follow up with Randy about ASMS "Computer applications interest group" + or try mark.sanders@therm - Amsterdam + Poster in Eric's name was submitted. No word on acceptance, but Eric cannot attend. + PSI session during the congress at Sunday 17th 9:30a-12 + Tentative presenter at PSI session is Jim Shofstahl with backups of Randy and Pierre-Alain - Open schema issue: where to put "centroided" and "deisotoped" + We will allow spectrum representation (like centroid/profile) in the fileContent section - Next call + Same time next week. Eric will figure how to start the call ________________________________ From: Eric Deutsch Sent: Tuesday, May 06, 2008 10:04 AM To: 'Mass spectrometry standard development' Cc: Eric Deutsch Subject: RE: RE: PSI-MSS WG call Tuesday Hi everyone, here are the minutes for the telecon of 2008-05-06. Please see action items for you. Anyone not on the call willing to help out is welcome. Present: Darren, Matt, Eric, Jim, Pierre-Alain Thank you to Juan Antonio for setting up the call. Agenda: - What is the purpose of <mzML> id and accession attributes? + Make the id= attribute optional in schema + Recommend in the documentation that you use LSID or local identifiers + Make all sample instance documents use a psidev LSID + Leave accession= optional as is, perhaps with better documentation - Make <run> instrumentConfigurationRef optional or remove it: - if remove, then this attribute can be required in <scan> - if optional, semval must insure that it is provide either in <run> or <scan> + OR consensus opinion: rename <run> instrumentConfigurationRef to defaultInstrumentConfigurationRef and keep it required + Document the intrumentConfiguration a bit better. Applies to LTQ-FT but not LTQ, for example. For different modes, use ParamGroups + Discussion of issue of how to use ParamGroups without having to do two passes through the file. - Issue of exactly how other spectra are referenced in <acquisition> + We agree to move forward with Matt suggestion: spectrumRef (infer reference as current file and spectrumRef is IDREF pointing to an existing spectrum's id) sourceFileRef + externalNativeID (original file is native) sourceFileRef + externalSpectrumID (original file is mzML) For example external mzXML files, the externalNativeID would refer to mzXML scanNumber In fact, anything that's not mzML would have externNativeID Matt says that XML schema can enforce these various options - MIAPE spreadsheet? + Pierre-Alain has spreadsheet. Darren added some comments trying to implement it + Rename Darren's tiny2 to tiny5 or some other name since "tiny2" is used by another document + Get miape-ms.pwiz.mzML posted + Pierre-Alain will continue to work on the spreadsheet + Before next call, send out or post miape-ms.pwiz.mzML and spreadsheet of issues to discuss - CV? + Randy has pink teddy bear, but haven't heard from him + Eric will take it and work on some changes to the CV + Eric will create the CV spreadsheets and start sending to vendors + Some contacts: Bruker :Herbert Thiele? Waters: Ronan O'Malley? - documentation? + latest is posted without figures - schema? + Eric will add Darren & Matt as a developers (dkessner) (chambm) + Darren will update 0.99.10 to 0.99.11 with changes above + Matt can help with multiple accession configs in <acquisition> - website + Eric post 0.99.10 schemas + Darren verify that tiny.pwiz encodes all ideas of tiny1 and then post as a single tiny1 - example files + Jim has an example that he will send out + Jim will send out examples of the nativeIDs for Thermo ________________________________ From: Eric Deutsch Sent: Monday, May 05, 2008 12:12 AM To: 'Mass spectrometry standard development'; Juan Antonio Vizcaíno González Cc: Eric Deutsch Subject: RE: PSI-MSS WG call Tuesday Hi everyone, as previously mentioned, the PSI Mass Spectrometry Standards Working Group call is Tuesday May 6 at 9am PDT: http://www.timeanddate.com/worldclock/fixedtime.html?day=6&month=5&year=2008&hour=17&min=0&sec=0&p1=136 + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 The agenda will be to review and discuss what remains to be done to finish up mzML, including the latest release and some recent issues discovered while making examples. Thanks, Eric |
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