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psidev-ms-cvs
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From: Puneet S. <ps...@us...> - 2007-06-27 16:49:48
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Date: Wednesday June 27, 2007 @ 9:49 Author: psouda http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4717/controlledVocabulary Log Message: Directory /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary added to the repository |
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From: Puneet S. <ps...@us...> - 2007-06-27 16:57:28
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Date: Wednesday June 27, 2007 @ 9:57 Author: psouda http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv7836 Added Files: psi-ms.obo Log Message: Result of the PSI workshop at EBI (Hinxton) from 25-27 June 2007. The controlled vocabulary has been thoroughly revised, reworking most of the term structure in accordance with the mzML schema; pseudo-retired many terms ('purgatory' branch) and added quite a few new terms. Some existing terms were also revised in accordance with IUPAC. |
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From: luisa m. <lui...@us...> - 2007-06-29 14:43:53
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Date: Friday June 29, 2007 @ 7:43 Author: luisa_montecchi http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv3834/psi-ms/mzML/controlledVocabulary Modified Files: psi-ms.obo Log Message: Cv terms capitalization updated to all lower case except for Model names and any term with more than 1 upper case letter in the same word. Also added comments to 'source file type', 'ms level', 'spectrum type', 'methods of combination' and 'compression type' Cv terms that should not be used with the CV param element because they have an XML dedicated attribute. |
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From: Puneet S. <ps...@us...> - 2007-08-13 23:18:51
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Date: Monday August 13, 2007 @ 16:18 Author: psouda http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19029 Modified Files: psi-ms.obo Log Message: Revised definitions and updated synonymns. Majority of definitions are completed now. Additional definitions will be updated after further discussion among the group. Majority of definitions are in compliance with IUPAC. Luisa has briefly reviewed this file. All TO DO items addressed. |
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From: Eric D. <ede...@us...> - 2007-09-25 07:41:36
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Date: Tuesday September 25, 2007 @ 0:41 Author: edeutsch http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv1427 Modified Files: psi-ms.obo Log Message: Recapitalized some proper names |
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From: luisa m. <lui...@us...> - 2007-09-26 15:47:01
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Date: Wednesday September 26, 2007 @ 8:46 Author: luisa_montecchi http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9504/psi-ms/mzML/controlledVocabulary Modified Files: psi-ms.obo Log Message: Added 5 new terms under Eric request for the contact person details description. |
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From: Eric D. <ede...@us...> - 2007-09-26 18:00:54
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Date: Wednesday September 26, 2007 @ 11:00 Author: edeutsch http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv26566 Modified Files: psi-ms.obo Log Message: fixed typo in contact address |
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From: Eric D. <ede...@us...> - 2007-10-02 06:55:58
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Date: Monday October 1, 2007 @ 23:56 Author: edeutsch http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22223 Modified Files: psi-ms.obo Log Message: Moved profile/centroid terms, added MassLynx raw format and 3 new converter softwares |
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From: luisa m. <lui...@us...> - 2007-10-11 14:09:46
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Date: Thursday October 11, 2007 @ 7:09 Author: luisa_montecchi http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19045/psi-ms/mzML/controlledVocabulary Added Files: lastID.txt Log Message: Initinal check in of a file storing the last numeric ID used in the psi-ms.obo file. This file should be manually updated every time a new psi-ms.obo file is checked in. The aim of the file it to allow multiple editors to change the obo file avoiding IDs inconsistencies. |
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From: luisa m. <lui...@us...> - 2007-11-08 17:04:36
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Date: Thursday November 8, 2007 @ 9:04 Author: luisa_montecchi http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv18403/psi-ms/mzML/controlledVocabulary Modified Files: psi-ms.obo Log Message: By Pete Souda -added electron transfer dissociation and pulsed q dissociation - Removed synonym BP for Base Peak m/z (MS:1000504) because it was same synonym for another term base peak (MS:1000210). - Changed definition for: MS:1000585. - Removed DLI as synonym for MS:1000552, maldi spot identifier. It is a synonym of MS:1000249, direct liquid introduction. - Added definition for MS:1000487, ion optics. - Deleted q as synonym from MS:1000487, ion optics. - Definition changed for MS:1000234, mass resolving power. - Cleaned up MS:1000297, paul ion trap. Added synonym: quadrupole ion trap. - Removed BP as synonym for MS:1000499, spectrum attribute. Its already a synonym for MS:1000210, BP. - Added/cleaned definitions for MS:1000593:Baseline Reduction,MS:1000592: Smoothing and MS:1000594:Low Intensity Data Point Removal. - Added definintions for MS:1000441:Scan and MS:1000442:Spectrum. - Added definition for MS:1000138:percent collision energy. By Luisa - obsoleted obsiouly redundant terms and remapped them (MS:1000244 consecutive reaction monitoring, MS:1000241, MS:1000394:Laser Desorption and other children ionisation types) - strutured the children of ionisation type - added remark: When appropriate the definition and synonyms of a term are reported exactly as in the chapter 12 of IUPAC orange book. See http://www.iupac.org/projects/2003/2003-056-2-500.html. |
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From: luisa m. <lui...@us...> - 2007-11-08 17:05:08
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Date: Thursday November 8, 2007 @ 9:05 Author: luisa_montecchi http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19113/psi-ms/mzML/controlledVocabulary Modified Files: lastID.txt Log Message: id update following same date update of the psi-ms.obo file |
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From: Eric D. <ede...@us...> - 2008-02-19 09:19:21
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Date: Tuesday February 19, 2008 @ 1:19 Author: edeutsch http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv16350 Modified Files: psi-ms.obo Log Message: - added Shimadzu instruments from David Sparkman - removed "peak processing" synonyms - remove synonym "Microchannel Plate Detector" - fixed MSn spectrum synonym - removed erroneous syn for Proteios - added terms "dta file", "ProteinLynx Global Server mass spectrum XML file" for Fredrik |
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From: Eric D. <ede...@us...> - 2008-02-19 09:20:08
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Date: Tuesday February 19, 2008 @ 1:20 Author: edeutsch http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv17759 Modified Files: lastID.txt Log Message: updated lastID |
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From: Eric D. <ede...@us...> - 2008-02-21 18:11:09
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Date: Thursday February 21, 2008 @ 10:11 Author: edeutsch http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv14367 Modified Files: psi-ms.obo Log Message: added ProteoWizard software |
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From: Eric D. <ede...@us...> - 2008-02-21 18:42:34
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Date: Thursday February 21, 2008 @ 10:42 Author: edeutsch http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv25629 Modified Files: psi-ms.obo Log Message: added term "preset scan configuration" which represents Thermo's "scan event" |
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From: Lennart M. <mar...@us...> - 2008-04-25 15:59:51
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Date: Friday April 25, 2008 @ 8:59 Author: martlenn http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv18442 Modified Files: psi-ms.obo Log Message: - Changed name of root tag. - Moved to OBO v1.2 - Introduced remark with placeholder for version number ('version: x.y.z') |
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From: luisa m. <lui...@us...> - 2008-05-14 17:10:35
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Date: Wednesday May 14, 2008 @ 10:10 Author: luisa_montecchi http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv26638/psi-ms/mzML/controlledVocabulary Modified Files: lastID.txt psi-ms.obo Log Message: Addition of 16 terms related to ThermoFinningan instruments and software. |
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From: luisa m. <lui...@us...> - 2008-05-14 21:14:14
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Date: Wednesday May 14, 2008 @ 14:14 Author: luisa_montecchi http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv19974/psi-ms/mzML/controlledVocabulary Modified Files: psi-ms.obo Log Message: Addition of 16 terms related to ThermoFinningan instruments and software v2. |
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From: luisa m. <lui...@us...> - 2008-05-22 14:51:46
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Date: Thursday May 22, 2008 @ 7:51 Author: luisa_montecchi http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv25099/psi-ms/mzML/controlledVocabulary Modified Files: lastID.txt psi-ms.obo Log Message: 23 new terms added for AB SCIEX or Applied Biosystems instrument models and softwares. |
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From: luisa m. <lui...@us...> - 2008-05-22 14:59:48
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Date: Thursday May 22, 2008 @ 7:59 Author: luisa_montecchi http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv28165/psi-ms/mzML/controlledVocabulary Modified Files: psi-ms.obo Log Message: 23 new terms added for AB SCIEX or Applied Biosystems instrument models and softwares + hierarchy fixing for existing Voyager-DE instruments. |
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From: Darren K. <dke...@us...> - 2008-05-27 18:53:41
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Date: Tuesday May 27, 2008 @ 11:53 Author: dkessner http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv5276 Modified Files: psi-ms.obo Added Files: unit.obo Log Message: added unit.obo to repository, import, plus example unit and value specification to 'scan time' term as first example |
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From: Darren K. <dke...@us...> - 2008-06-11 18:15:10
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Date: Wednesday June 11, 2008 @ 11:15 Author: dkessner http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv20723 Added Files: oboedit_notes.txt Log Message: added oboedit_notes.txt |
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From: Darren K. <dke...@us...> - 2008-06-22 14:05:36
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Date: Sunday June 22, 2008 @ 7:05 Author: dkessner http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv11859 Modified Files: lastID.txt oboedit_notes.txt psi-ms.obo Log Message: added value type and has_units specifications |
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From: Darren K. <dke...@us...> - 2008-07-07 21:35:46
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Date: Monday July 7, 2008 @ 14:35 Author: dkessner http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv8786 Modified Files: oboedit_notes.txt psi-ms.obo Log Message: added string value types, removed <new synonym>, removed \n |
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From: Lennart M. <mar...@us...> - 2008-07-09 14:29:18
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Date: Wednesday July 9, 2008 @ 7:29 Author: martlenn http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/psidev/psi/psi-ms/mzML/controlledVocabulary Update of /cvsroot/psidev/psi/psi-ms/mzML/controlledVocabulary In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv30154 Modified Files: psi-ms.obo Log Message: Merged some synonyms provided by Matt into the latest file. |
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