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psidev-ms-cvs
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From: Gerhard M. <ger...@us...> - 2013-01-22 08:01:54
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Date: Tuesday January 22, 2013 @ 8:01 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv7697 Modified Files: psi-ms.obo Log Message: def: "A putative identified peptide issued from a decoy sequence database." [PSI:PI] |
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From: Gerhard M. <ger...@us...> - 2013-02-22 07:50:10
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Date: Friday February 22, 2013 @ 7:50 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv18018 Modified Files: lastID.txt psi-ms.obo Log Message: New version 3.46.0: - New terms for SRM transitions - New terms for ProteomeDiscoverer input parameters |
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From: Gerhard M. <ger...@us...> - 2013-04-05 14:43:38
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Date: Friday April 5, 2013 @ 14:43 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv6181 Modified Files: lastID.txt psi-ms.obo Log Message: New version 3.47.0 |
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From: Gerhard M. <ger...@us...> - 2013-04-29 07:04:13
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Date: Monday April 29, 2013 @ 7:04 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv23596 Modified Files: lastID.txt psi-ms.obo Log Message: New version 3.49.0: - LC / GC separation - detector potential - SRM quantitation analysis - new terms for Waters / LECO / Bruker instruments |
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From: Gerhard M. <ger...@us...> - 2013-05-16 11:06:43
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Date: Thursday May 16, 2013 @ 11:06 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv25416 Modified Files: lastID.txt psi-ms.obo Log Message: New version 3.49.0: - new terms for Bruker instruments - definition of domain ranges for use in p-value and E-value terms - fragment ions have the new parent term MS:1002307 (fragmentation ion type). |
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From: Gerhard M. <ger...@us...> - 2013-05-31 07:06:07
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Date: Friday May 31, 2013 @ 7:06 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv8274 Modified Files: lastID.txt psi-ms.obo Log Message: New version 3.50.0: - Issues 74: Retention time changes - Improved definitions for Waters instrument terms - 3 new terms for the Byonic search engine |
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From: Gerhard M. <ger...@us...> - 2013-07-01 07:49:04
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Date: Monday July 1, 2013 @ 7:49 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv13714 Modified Files: lastID.txt psi-ms.obo Log Message: New version 3.51.0 - some new terms for MS-Numpress - new term for consensus results in mzIdentML |
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From: Gerhard M. <ger...@us...> - 2013-08-20 15:08:25
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Date: Tuesday August 20, 2013 @ 15:08 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv20382 Modified Files: lastID.txt psi-ms.obo Log Message: New version 3.52.0 of psi-ms.obo: - some new ProteomeDiscoverer 1.4 input parameters - scores for MS Amanda and Andromeda - some new terms for conversion and analysis software |
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From: Gerhard M. <ger...@us...> - 2013-09-02 06:52:59
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Date: Monday September 2, 2013 @ 6:52 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv30676 Modified Files: lastID.txt psi-ms.obo Log Message: New version 3.53.0: - added ProteomeXchange project tag - added Added 'higher score better' for Andromeda:score |
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From: Gerhard M. <ger...@us...> - 2013-09-11 15:00:04
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Date: Wednesday September 11, 2013 @ 15:00 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv28153 Modified Files: lastID.txt psi-ms.obo Log Message: New version 3.54.0 of psi-ms.obo: - The term 'translation frame' was de-obsoleted - A new term for second-pass peptide identifications was added - the definitions for the 'retention time' terms were changed |
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From: Gerhard M. <ger...@us...> - 2013-10-22 08:03:04
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Date: Tuesday October 22, 2013 @ 8:03 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv27324 Modified Files: lastID.txt psi-ms.obo Log Message: New version 3.55.0: ============ - added terms for the MZmine and Maltcms frameworks - obsoleted unused purgatory terms |
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From: Gerhard M. <ger...@us...> - 2013-11-14 15:15:13
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Date: Thursday November 14, 2013 @ 15:15 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv30717 Modified Files: lastID.txt psi-ms.obo Log Message: - new terms for FDR etc. - term for FLR added - new PD input parameters - new Shimadzu terms |
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From: Gerhard M. <ger...@us...> - 2013-11-15 09:32:38
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Date: Friday November 15, 2013 @ 9:32 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv8392 Added Files: 2007_Montecchi-Palazzi_etal_Guidelines_for_the_development_of_controlled_vocabularies.pdf 2013_Murray_etal_Definitions of terms relating to MS (IUPAC recommendations 2013).pdf GO_xrefs.xrf_abbs PSI_Ten_minutes_guide_for_requesting_new_CV_terms.pdf Log Message: Added some documentation files |
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From: Gerhard M. <ger...@us...> - 2013-12-12 08:42:55
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Date: Thursday December 12, 2013 @ 8:42 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv5143 Modified Files: lastID.txt psi-ms.obo Log Message: Version 3.57.0: - New terms for SCiLS and PIA |
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From: Gerhard M. <ger...@us...> - 2013-12-20 09:54:31
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Date: Friday December 20, 2013 @ 9:54 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv31164 Modified Files: lastID.txt oboedit_notes.txt psi-ms.obo Added Files: 2013_Mayer_etal_Database_Virtual_Issue_The_HUPO_Proteomics_Standards_Initiative-Mass_Spectrometry_Controlled_Vocabulary.pdf Log Message: New version 3.58.0: ============ - protein grouping terms - encoding of SRM in mzQuantML - some new Thermo Scientific instrument models |
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From: Gerhard M. <ger...@us...> - 2014-01-22 13:00:50
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Date: Wednesday January 22, 2014 @ 13:00 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv9404 Modified Files: psi-ms.obo Log Message: New version 3.59.0: ============ - put it under a licences - changed has_order and has_domain to relationships - added two relationships to the PIA term |
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From: Gerhard M. <ger...@us...> - 2014-01-22 13:09:18
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Date: Wednesday January 22, 2014 @ 13:09 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv10649 Added Files: Licence.txt Log Message: Check-in of the Licence.txt file |
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From: Gerhard M. <ger...@us...> - 2014-02-18 07:40:25
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Date: Tuesday February 18, 2014 @ 7:40 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv10467 Modified Files: lastID.txt psi-ms.obo Log Message: Version 3.60.0: ========= Added new CV terms for the ProteinPilot / Paragon algorithm. |
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From: Gerhard M. <ger...@us...> - 2014-03-05 08:06:16
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Date: Wednesday March 5, 2014 @ 8:06 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv13075 Modified Files: lastID.txt psi-ms.obo Log Message: Version 3.61.0: ========== - flags for the SpectrumIdentificationLists in mzIdentML version 1.2 - netCDF ANDI file formats |
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From: Gerhard M. <ger...@us...> - 2014-03-19 08:16:03
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Date: Wednesday March 19, 2014 @ 8:16 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv22194 Modified Files: lastID.txt psi-ms.obo Log Message: Version 3.62.0: ========= - new terms for Agilent instruments |
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From: Gerhard M. <ger...@us...> - 2014-04-10 13:32:32
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Date: Thursday April 10, 2014 @ 13:32 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv11228 Modified Files: lastID.txt psi-ms.obo Log Message: New version 3.63.0: ============ - new terms for Paragon, PEAKS and ion series |
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From: Gerhard M. <ger...@us...> - 2014-05-21 06:38:58
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Date: Wednesday May 21, 2014 @ 6:38 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv12209 Modified Files: lastID.txt psi-ms.obo Added Files: 2013_Schober_Mayer_etal_ODLS2013_Ontological analysis of controlled vocabularies used in PSIMSI supported XML standards.pdf MS_Abbreviations.txt Log Message: New version 3.64.0 of psi-ms.obo: ===================== - New terms for mzTab, for specifying the neutral losses, for collision-induced dissociation, for ion mobility MS, for PeptideShaker and for ProteoAnnotator. - The neutral losses are now defined as terms independently from the ions in order to decouple the two concepts ion and neutral loss from each other. - The old neutral loss terms have now the suffix " DEPRECATED" in their name, but are not obsoleted. The new parent term "ion series considered in search" (MS:1002473) now contains all the ions and neutral loss terms. - some terms from the purgatory branch are now obsolete. - corrected some spelling errors in definitions. |
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From: Gerhard M. <ger...@us...> - 2014-06-18 06:45:17
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Date: Wednesday June 18, 2014 @ 6:45 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv10945 Modified Files: psi-ms.obo Log Message: Corrected parsing problems: ================= - trailing tab in line 12526 - escaping { and } characters as \{ and \} |
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From: Gerhard M. <ger...@us...> - 2014-07-02 06:59:01
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Date: Wednesday July 2, 2014 @ 6:59 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv28840 Modified Files: lastID.txt psi-ms.obo Log Message: Version 3.65.0 containing a new "statistical threshold" term as parent of the different thresholding mechanisms, two new terms for MassIVE and a bunch of new terms for use in the coming mzIdentML version 1.2 (for peptide-level scoring, modification localization re-scoring and cross-linking) and for absolute quantitation. |
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From: Gerhard M. <ger...@us...> - 2014-07-04 13:49:30
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Date: Friday July 4, 2014 @ 13:49 Author: gerhard64mayer 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 sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv21763 Modified Files: psi-ms.obo Log Message: Removed a blank |
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