Menu
▾
▴
psidev-pi-dev
|
From: David C. <dc...@ma...> - 2008-11-11 16:38:19
|
Hi everyone, There will be an AnalysisXML working group conference call on WEDNESDAY (instead of Thursday) at: http://www.timeanddate.com/worldclock/fixedtime.html?day=12&month=11&year=2008&hour=16&min=0&sec=0&p1=136 Minutes from last meeting at: http://psidev.info/index.php?q=node/384 Agenda: (strangely identical to last week, although progress has been made!) 1. Review of minutes of last meeting 2. Status of mapping document and CV 3. Issue 30: Enzymes http://code.google.com/p/psi-pi/issues/detail?id=30 Almost complete now? http://code.google.com/p/psi-pi/issues/detail?id=30&can=1#c37 4. Other items on the issues list: http://code.google.com/p/psi-pi/issues/list Dial in details: + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
|
From: David C. <dc...@ma...> - 2008-11-12 12:16:21
|
I've started on the MIAPE conformance doc: http://psidev.info/index.php?q=node/386 Can we discuss whether this is a suitable format on the call later. (Looks as though we may have a couple of things to add to the schema...) Thanks, David David Creasy wrote: > Hi everyone, > > There will be an AnalysisXML working group conference call on WEDNESDAY > (instead of Thursday) at: > http://www.timeanddate.com/worldclock/fixedtime.html?day=12&month=11&year=2008&hour=16&min=0&sec=0&p1=136 > > > Minutes from last meeting at: > http://psidev.info/index.php?q=node/384 > > > Agenda: (strangely identical to last week, although progress has been > made!) > 1. Review of minutes of last meeting > > 2. Status of mapping document and CV > > 3. Issue 30: Enzymes > http://code.google.com/p/psi-pi/issues/detail?id=30 > Almost complete now? > http://code.google.com/p/psi-pi/issues/detail?id=30&can=1#c37 > > 4. Other items on the issues list: > http://code.google.com/p/psi-pi/issues/list > > Dial in details: > > + Germany: 08001012079 > + Switzerland: 0800000860 > + UK: 08081095644 > + USA: 1-866-314-3683 > + Generic international: +44 2083222500 (UK number) > > access code: 297427 > -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
|
From: Pierre-Alain B. <pie...@is...> - 2008-11-12 14:26:26
|
Thanks David. FYI, for mzML, we had generated a excel mapping spreadsheet (if you want to see it...) The format is ok for me. About the notes: the descriptions of what should be the content from a MIAPE point of view are in the MIAPE document, in the Annex table. Note also that for mzML-MIAPE MS mapping, there were a few items not covered by MIAPE, and also not covered by mzML. The latest have either been annotated for a future version of mzML (similar to the quantitation in AnalysisXML), or just left out and annotated as such (for instance flow rates, detector sensitivity). Either they are independant or an estimation that looks more like an interpretation. We there need to decide whether those should be taken out of MIAPE or not. I have commented two of the notes. If there are unclear items, just put a note in and I can clarify One more: for mzML, we have two (at least) levels of stringency for the validators: basic semantic and MIAPE compliance. Therefore we can deal with legacy being compliant woth the format, even if it does not comply with MIAPE Cheers Pierre-Alain David Creasy wrote: > I've started on the MIAPE conformance doc: > > http://psidev.info/index.php?q=node/386 > > Can we discuss whether this is a suitable format on the call later. > (Looks as though we may have a couple of things to add to the schema...) > > Thanks, > David > > David Creasy wrote: > >> Hi everyone, >> >> There will be an AnalysisXML working group conference call on WEDNESDAY >> (instead of Thursday) at: >> http://www.timeanddate.com/worldclock/fixedtime.html?day=12&month=11&year=2008&hour=16&min=0&sec=0&p1=136 >> >> >> Minutes from last meeting at: >> http://psidev.info/index.php?q=node/384 >> >> >> Agenda: (strangely identical to last week, although progress has been >> made!) >> 1. Review of minutes of last meeting >> >> 2. Status of mapping document and CV >> >> 3. Issue 30: Enzymes >> http://code.google.com/p/psi-pi/issues/detail?id=30 >> Almost complete now? >> http://code.google.com/p/psi-pi/issues/detail?id=30&can=1#c37 >> >> 4. Other items on the issues list: >> http://code.google.com/p/psi-pi/issues/list >> >> Dial in details: >> >> + Germany: 08001012079 >> + Switzerland: 0800000860 >> + UK: 08081095644 >> + USA: 1-866-314-3683 >> + Generic international: +44 2083222500 (UK number) >> >> access code: 297427 >> >> > > |
|
From: David C. <dc...@ma...> - 2008-11-12 15:05:51
|
Hi Pierre-Alain, Pierre-Alain Binz wrote: > Thanks David. > FYI, for mzML, we had generated a excel mapping spreadsheet (if you want > to see it...) Yes please. (I can't see it on psidev.info). > > The format is ok for me. About the notes: the descriptions of what > should be the content from a MIAPE point of view are in the MIAPE > document, in the Annex table. Oh yes... > > Note also that for mzML-MIAPE MS mapping, there were a few items not > covered by MIAPE, and also not covered by mzML. The latest have either > been annotated for a future version of mzML (similar to the quantitation > in AnalysisXML), or just left out and annotated as such (for instance > flow rates, detector sensitivity). Either they are independant or an > estimation that looks more like an interpretation. We there need to > decide whether those should be taken out of MIAPE or not. We will aim to add anything missing (apart from quantitation) before submission to the document process. > > I have commented two of the notes. If there are unclear items, just put > a note in and I can clarify Yes please! I can't remember what we intended from "Location of the files generated". The definition is: "The location of the data generated. If made available in a public repository, describe the URI (for instance an url, or the url of the repository and the information on how to retrieve the data). If not made available for public access, describe the contact person reference or source and the internal coordinates of the data." But _what_ data does this refer to? The peak list, the analysisXML document, intermediate files like Sequest .out files or any/all of these? If it's the analysisXML file, you presumably have it and you must know where you got it from ;) > > One more: for mzML, we have two (at least) levels of stringency for the > validators: basic semantic and MIAPE compliance. Therefore we can deal > with legacy being compliant woth the format, even if it does not comply > with MIAPE Sounds good, David > > > Cheers > Pierre-Alain > > David Creasy wrote: >> I've started on the MIAPE conformance doc: >> >> http://psidev.info/index.php?q=node/386 >> >> Can we discuss whether this is a suitable format on the call later. >> (Looks as though we may have a couple of things to add to the schema...) >> >> Thanks, >> David >> >> David Creasy wrote: >> >>> Hi everyone, >>> >>> There will be an AnalysisXML working group conference call on WEDNESDAY >>> (instead of Thursday) at: >>> http://www.timeanddate.com/worldclock/fixedtime.html?day=12&month=11&year=2008&hour=16&min=0&sec=0&p1=136 >>> >>> >>> Minutes from last meeting at: >>> http://psidev.info/index.php?q=node/384 >>> >>> >>> Agenda: (strangely identical to last week, although progress has been >>> made!) >>> 1. Review of minutes of last meeting >>> >>> 2. Status of mapping document and CV >>> >>> 3. Issue 30: Enzymes >>> http://code.google.com/p/psi-pi/issues/detail?id=30 >>> Almost complete now? >>> http://code.google.com/p/psi-pi/issues/detail?id=30&can=1#c37 >>> >>> 4. Other items on the issues list: >>> http://code.google.com/p/psi-pi/issues/list >>> >>> Dial in details: >>> >>> + Germany: 08001012079 >>> + Switzerland: 0800000860 >>> + UK: 08081095644 >>> + USA: 1-866-314-3683 >>> + Generic international: +44 2083222500 (UK number) >>> >>> access code: 297427 >>> >>> >> >> -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
|
From: Pierre-Alain B. <pie...@is...> - 2008-11-12 16:25:45
|
Hi, David Creasy wrote: > Hi Pierre-Alain, > > Pierre-Alain Binz wrote: >> Thanks David. >> FYI, for mzML, we had generated a excel mapping spreadsheet (if you >> want to see it...) > Yes please. (I can't see it on psidev.info). you can find a temp version at ftp://ftp.genebio.com/div/MIAPE-mzML-mapping.01.xls > >> >> The format is ok for me. About the notes: the descriptions of what >> should be the content from a MIAPE point of view are in the MIAPE >> document, in the Annex table. > Oh yes... > >> >> Note also that for mzML-MIAPE MS mapping, there were a few items not >> covered by MIAPE, and also not covered by mzML. The latest have >> either been annotated for a future version of mzML (similar to the >> quantitation in AnalysisXML), or just left out and annotated as such >> (for instance flow rates, detector sensitivity). Either they are >> independant or an estimation that looks more like an interpretation. >> We there need to decide whether those should be taken out of MIAPE or >> not. > We will aim to add anything missing (apart from quantitation) before > submission to the document process. > >> >> I have commented two of the notes. If there are unclear items, just >> put a note in and I can clarify > Yes please! I can't remember what we intended from "Location of the > files generated". The definition is: > "The location of the data generated. If made available in a public > repository, describe the URI (for instance an url, or the url of the > repository and the information on how to retrieve the data). If not > made available for public access, describe the contact person > reference or source and the internal coordinates of the data." > > But _what_ data does this refer to? The peak list, the analysisXML > document, intermediate files like Sequest .out files or any/all of > these? If it's the analysisXML file, you presumably have it and you > must know where you got it from ;) the files used to generate the AnalysisXML file... > >> >> One more: for mzML, we have two (at least) levels of stringency for >> the validators: basic semantic and MIAPE compliance. Therefore we can >> deal with legacy being compliant woth the format, even if it does not >> comply with MIAPE > Sounds good, > > David voila, Pierre-Alain >> >> >> Cheers >> Pierre-Alain >> >> David Creasy wrote: >>> I've started on the MIAPE conformance doc: >>> >>> http://psidev.info/index.php?q=node/386 >>> >>> Can we discuss whether this is a suitable format on the call later. >>> (Looks as though we may have a couple of things to add to the >>> schema...) >>> >>> Thanks, >>> David >>> >>> David Creasy wrote: >>> >>>> Hi everyone, >>>> >>>> There will be an AnalysisXML working group conference call on >>>> WEDNESDAY >>>> (instead of Thursday) at: >>>> http://www.timeanddate.com/worldclock/fixedtime.html?day=12&month=11&year=2008&hour=16&min=0&sec=0&p1=136 >>>> >>>> >>>> Minutes from last meeting at: >>>> http://psidev.info/index.php?q=node/384 >>>> >>>> >>>> Agenda: (strangely identical to last week, although progress has >>>> been made!) >>>> 1. Review of minutes of last meeting >>>> >>>> 2. Status of mapping document and CV >>>> >>>> 3. Issue 30: Enzymes >>>> http://code.google.com/p/psi-pi/issues/detail?id=30 >>>> Almost complete now? >>>> http://code.google.com/p/psi-pi/issues/detail?id=30&can=1#c37 >>>> >>>> 4. Other items on the issues list: >>>> http://code.google.com/p/psi-pi/issues/list >>>> >>>> Dial in details: >>>> >>>> + Germany: 08001012079 >>>> + Switzerland: 0800000860 >>>> + UK: 08081095644 >>>> + USA: 1-866-314-3683 >>>> + Generic international: +44 2083222500 (UK number) >>>> >>>> access code: 297427 >>>> >>>> >>> >>> > |
|
From: David C. <dc...@ma...> - 2008-11-12 17:56:06
|
Minutes available here: http://psidev.info/index.php?q=node/388 (Please let me know of any corrections) Next meeting: http://www.timeanddate.com/worldclock/fixedtime.html?day=20&month=11&year=2008&hour=16&min=0&sec=0&p1=136 David Creasy wrote: > Hi everyone, > > There will be an AnalysisXML working group conference call on WEDNESDAY > (instead of Thursday) at: > http://www.timeanddate.com/worldclock/fixedtime.html?day=12&month=11&year=2008&hour=16&min=0&sec=0&p1=136 > > > Minutes from last meeting at: > http://psidev.info/index.php?q=node/384 > > > Agenda: (strangely identical to last week, although progress has been > made!) > 1. Review of minutes of last meeting > > 2. Status of mapping document and CV > > 3. Issue 30: Enzymes > http://code.google.com/p/psi-pi/issues/detail?id=30 > Almost complete now? > http://code.google.com/p/psi-pi/issues/detail?id=30&can=1#c37 > > 4. Other items on the issues list: > http://code.google.com/p/psi-pi/issues/list > > Dial in details: > > + Germany: 08001012079 > + Switzerland: 0800000860 > + UK: 08081095644 > + USA: 1-866-314-3683 > + Generic international: +44 2083222500 (UK number) > > access code: 297427 > -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
|
From: Jones, A. <And...@li...> - 2008-11-14 16:32:54
|
Hi all, New schema uploaded: - Removed runtimeParams and analysisParams from SpectrumIdentificatino and ProteinDetection - Added creationDate to AnalysisXML root node Cheers Andy > -----Original Message----- > From: David Creasy [mailto:dc...@ma...] > Sent: 12 November 2008 17:56 > To: psi...@li... > Subject: Re: [Psidev-pi-dev] PSI-PI Working group conference call on Wednesday > 12th November at 4:00pm UK time > > Minutes available here: > > http://psidev.info/index.php?q=node/388 > (Please let me know of any corrections) > > Next meeting: > http://www.timeanddate.com/worldclock/fixedtime.html?day=20&month=11&year=2 > 008&hour=16&min=0&sec=0&p1=136 > > > David Creasy wrote: > > Hi everyone, > > > > There will be an AnalysisXML working group conference call on WEDNESDAY > > (instead of Thursday) at: > > > http://www.timeanddate.com/worldclock/fixedtime.html?day=12&month=11&year=2 > 008&hour=16&min=0&sec=0&p1=136 > > > > > > Minutes from last meeting at: > > http://psidev.info/index.php?q=node/384 > > > > > > Agenda: (strangely identical to last week, although progress has been > > made!) > > 1. Review of minutes of last meeting > > > > 2. Status of mapping document and CV > > > > 3. Issue 30: Enzymes > > http://code.google.com/p/psi-pi/issues/detail?id=30 > > Almost complete now? > > http://code.google.com/p/psi-pi/issues/detail?id=30&can=1#c37 > > > > 4. Other items on the issues list: > > http://code.google.com/p/psi-pi/issues/list > > > > Dial in details: > > > > + Germany: 08001012079 > > + Switzerland: 0800000860 > > + UK: 08081095644 > > + USA: 1-866-314-3683 > > + Generic international: +44 2083222500 (UK number) > > > > access code: 297427 > > > > -- > David Creasy > Matrix Science > 64 Baker Street > London W1U 7GB, UK > Tel: +44 (0)20 7486 1050 > Fax: +44 (0)20 7224 1344 > > dc...@ma... > http://www.matrixscience.com > > Matrix Science Ltd. is registered in England and Wales > Company number 3533898 > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
|
From: David C. <dc...@ma...> - 2008-11-17 14:23:01
|
I've updated: http://psidev.info/index.php?q=node/386 There are quite a few missing 'ticks' for the examples. (Less for the ones that I'm responsible for because I made the changes as I filled in the table!). If you make changes to the examples to fill in more gaps, either let me know or edit the table as described at the top of that page. There are still a few TODOs in the table, and I've not completed the 3 items for section 4 because I'm not clear how we are describing this in AnalysisXML. Perhaps we can discuss at the next telecon David Jones, Andy wrote: > Hi all, > > New schema uploaded: > > - Removed runtimeParams and analysisParams from SpectrumIdentificatino and > ProteinDetection > > - Added creationDate to AnalysisXML root node > > > Cheers > Andy > >> -----Original Message----- >> From: David Creasy [mailto:dc...@ma...] >> Sent: 12 November 2008 17:56 >> To: psi...@li... >> Subject: Re: [Psidev-pi-dev] PSI-PI Working group conference call on Wednesday >> 12th November at 4:00pm UK time >> >> Minutes available here: >> >> http://psidev.info/index.php?q=node/388 >> (Please let me know of any corrections) >> >> Next meeting: >> http://www.timeanddate.com/worldclock/fixedtime.html?day=20&month=11&year=2 >> 008&hour=16&min=0&sec=0&p1=136 >> >> >> David Creasy wrote: >>> Hi everyone, >>> >>> There will be an AnalysisXML working group conference call on WEDNESDAY >>> (instead of Thursday) at: >>> >> http://www.timeanddate.com/worldclock/fixedtime.html?day=12&month=11&year=2 >> 008&hour=16&min=0&sec=0&p1=136 >>> >>> Minutes from last meeting at: >>> http://psidev.info/index.php?q=node/384 >>> >>> >>> Agenda: (strangely identical to last week, although progress has been >>> made!) >>> 1. Review of minutes of last meeting >>> >>> 2. Status of mapping document and CV >>> >>> 3. Issue 30: Enzymes >>> http://code.google.com/p/psi-pi/issues/detail?id=30 >>> Almost complete now? >>> http://code.google.com/p/psi-pi/issues/detail?id=30&can=1#c37 >>> >>> 4. Other items on the issues list: >>> http://code.google.com/p/psi-pi/issues/list >>> >>> Dial in details: >>> >>> + Germany: 08001012079 >>> + Switzerland: 0800000860 >>> + UK: 08081095644 >>> + USA: 1-866-314-3683 >>> + Generic international: +44 2083222500 (UK number) >>> >>> access code: 297427 >>> >> -- >> David Creasy >> Matrix Science >> 64 Baker Street >> London W1U 7GB, UK >> Tel: +44 (0)20 7486 1050 >> Fax: +44 (0)20 7224 1344 >> >> dc...@ma... >> http://www.matrixscience.com >> >> Matrix Science Ltd. is registered in England and Wales >> Company number 3533898 >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >> Build the coolest Linux based applications with Moblin SDK & win great prizes >> Grand prize is a trip for two to an Open Source event anywhere in the world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> Psidev-pi-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
×
Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.
Thanks for helping keep SourceForge clean.
X