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psidev-ms-cvs
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From: Lennart M. <mar...@us...> - 2008-08-13 08:53:53
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Date: Wednesday August 13, 2008 @ 1:54 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-serv30838 Modified Files: psi-ms.obo Log Message: Changes done together with Fredrik Levander. 1. Added the term 'parameter file' as a child of 'Source File Type' (MS:1000560). This allows annotation of the (currently completely unannotated) 'parameter.par' file listed in our pwiz example. 2. Moved 'Precursor activation attribute' (MS:1000510) one level up (to 'Spectrum' (MS:1000442)), so it will no longer be a child of precursor activation (MS:1000456) itself (only one child of precursor activation is allowed, which is sensible, whereas there should be several attributes allowed, which is also sensible). 3. Added Term 'conversion to dta' as a file format conversion parameter. 4. Added term for BioWorks SRF file (as suggested by Jim Shofstahl). 5. Removed superfluous comment to 'ms level' 6. Updated version of CV to 1.3.1. |
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From: Lennart M. <mar...@us...> - 2008-10-20 15:52:06
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Date: Monday October 20, 2008 @ 15:51 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv25782 Modified Files: psi-ms.obo Log Message: unit.obo is now referenced through the CVS checkout URL. |
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From: Darren K. <dke...@us...> - 2008-11-10 19:06:12
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Date: Monday November 10, 2008 @ 19:06 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv24281 Modified Files: psi-ms.obo Log Message: added term for TSQ Quantum Ultra AM, and changed wolf->massWolf (with exact synonym wolf) |
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From: Marc S. <mar...@us...> - 2008-11-13 06:10:23
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Date: Thursday November 13, 2008 @ 6:10 Author: marc_sturm 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv16615 Modified Files: lastID.txt psi-ms.obo Log Message: Added changes just as discussed on the mailing list |
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From: chambm <ch...@us...> - 2008-11-13 23:21:32
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Date: Thursday November 13, 2008 @ 23:21 Author: chambm 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv19561/psi-ms/mzML/controlledVocabulary Modified Files: psi-ms.obo Log Message: - moved apparently redundant ELEMENT2 term to purgatory - added Thermo instruments: TSQ, TSQ 7000, SSQ 7000, TSQ Quantum Ultra |
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From: Marc S. <mar...@us...> - 2008-11-14 12:34:20
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Date: Friday November 14, 2008 @ 12:34 Author: marc_sturm 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv18407 Modified Files: psi-ms.obo Log Message: Changed several term relations. This was necessary for the new mapping rules |
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From: Marc S. <mar...@us...> - 2008-11-14 13:44:32
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Date: Friday November 14, 2008 @ 13:44 Author: marc_sturm 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv23364 Modified Files: lastID.txt psi-ms.obo Log Message: added TOPP software section with tools (as discussed on the mailing list in July 2008) |
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From: Fredrik L. <fle...@us...> - 2008-11-21 10:20:09
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Date: Friday November 21, 2008 @ 10:20 Author: flevander 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv2213 Modified Files: psi-ms.obo Log Message: Added native ID terms and version of unit CV |
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From: Fredrik L. <fle...@us...> - 2008-11-21 10:38:42
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Date: Friday November 21, 2008 @ 10:38 Author: flevander 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv4051 Modified Files: psi-ms.obo Log Message: Added native ID terms and version of unit CV |
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From: Marc S. <mar...@us...> - 2008-11-25 14:37:17
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Date: Tuesday November 25, 2008 @ 14:37 Author: marc_sturm 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv10618 Modified Files: psi-ms.obo Log Message: fixed is_a relation of native ID format terms |
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From: chambm <ch...@us...> - 2008-11-25 21:16:58
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Date: Tuesday November 25, 2008 @ 21:16 Author: chambm 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv4755/psi-ms/mzML/controlledVocabulary Modified Files: psi-ms.obo Log Message: - redefined "smoothing" to be algorithm-agnostic; added child terms for specific algorithms: Savitzky-Golay, Gaussian/binomial, moving-average/box/boxcar - removed "TOPP Tool -" prefix from TOPP definitions (redundant prefixes aren't consistent with the style used elsewhere in the CV) - added "charge state calculation" and "precursor recalculation" as |
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From: Marc S. <mar...@us...> - 2008-12-04 08:51:36
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Date: Thursday December 4, 2008 @ 8:51 Author: marc_sturm 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv12409 Modified Files: lastID.txt psi-ms.obo Log Message: - make 'sample state' a 'sample attribute' - added 'non-standard data array' - added 'inclusive low intensity threshold' and 'inclusive high intensity threshold' |
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From: Marc S. <mar...@us...> - 2008-12-04 09:00:00
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Date: Thursday December 4, 2008 @ 8:59 Author: marc_sturm 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv12706 Modified Files: psi-ms.obo Log Message: fixed last commit - term stanzas were missing |
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From: Marc S. <mar...@us...> - 2008-12-05 09:35:37
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Date: Friday December 5, 2008 @ 9:35 Author: marc_sturm 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv7362/controlledVocabulary Modified Files: psi-ms.obo Log Message: updated non-standard data array term (now has a string value) |
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From: Marc S. <mar...@us...> - 2008-12-08 12:45:14
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Date: Monday December 8, 2008 @ 12:45 Author: marc_sturm 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv2921 Modified Files: lastID.txt psi-ms.obo Log Message: Added the changes (by Wilfred) to 'spectrum type' and 'scanning method' we agreed on; fixed intensity unit accessions |
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From: chambm <ch...@us...> - 2008-12-08 15:56:28
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Date: Monday December 8, 2008 @ 15:56 Author: chambm 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv1446/psi-ms/mzML/controlledVocabulary Modified Files: psi-ms.obo Log Message: - added isolation window lower and upper limits and "isolation window attribute" - put "isolation width" in purgatory |
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From: Marc S. <mar...@us...> - 2008-12-10 12:42:37
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Date: Wednesday December 10, 2008 @ 12:42 Author: marc_sturm 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv15871 Modified Files: psi-ms.obo Log Message: Added new term for scan combination (no combination) |
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From: Fredrik L. <fle...@us...> - 2008-12-17 13:52:50
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Date: Wednesday December 17, 2008 @ 13:52 Author: flevander 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv12670 Modified Files: psi-ms.obo Log Message: Added terms for mass resolving power, unknown software and MGF attributes. Updated mass resolution definition |
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From: Marc S. <mar...@us...> - 2008-12-18 14:53:00
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Date: Thursday December 18, 2008 @ 14:52 Author: marc_sturm 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv27782 Modified Files: psi-ms.obo Log Message: sent 'scanning method' to purgatory; made 'zoom scan' a 'spectrum attribute' |
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From: RCote <rg...@us...> - 2009-01-21 16:08:34
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Date: Wednesday January 21, 2009 @ 16:08 Author: rglcote 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv1699 Modified Files: psi-ms.obo Log Message: there was an extra linebreak at line 90 that caused the OBO parser to fail to load the ontology properly. the offending linebreak has been deleted and the ontology can be loaded into OBOEdit and the OLS |
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From: Marc S. <mar...@us...> - 2009-01-28 10:33:28
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Date: Wednesday January 28, 2009 @ 10:33 Author: marc_sturm 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv31538/controlledVocabulary Modified Files: psi-ms.obo Log Message: Added new peak picking types |
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From: Marc S. <mar...@us...> - 2009-01-28 15:02:23
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Date: Wednesday January 28, 2009 @ 15:02 Author: marc_sturm 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv24153 Modified Files: lastID.txt psi-ms.obo Log Message: fixed typo in term name |
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From: Matt C. <ch...@us...> - 2009-02-03 22:29:49
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Date: Tuesday February 3, 2009 @ 22:29 Author: chambm 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv14442/psi-ms/mzML/controlledVocabulary Modified Files: psi-ms.obo Log Message: - fixed Thermo native id format - fixed spectrum type hierarchy - obsoleted merged "enhanced resolution spectrum" term - obsoleted merged "product ion spectrum" term - obsoleted merged "nth generation product ion spectrum" term |
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From: Matt C. <ch...@us...> - 2009-02-04 17:44:39
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Date: Wednesday February 4, 2009 @ 17:44 Author: chambm 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv16588/psi-ms/mzML/controlledVocabulary Modified Files: psi-ms.obo Log Message: - fixed obsolete terms |
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From: Matt C. <ch...@us...> - 2009-02-04 18:01:55
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Date: Wednesday February 4, 2009 @ 18:01 Author: chambm 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 ddv4jf1.ch3.sourceforge.com:/tmp/cvs-serv18384/psi-ms/mzML/controlledVocabulary Modified Files: psi-ms.obo Log Message: - updated revision to reflect previous changes |
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