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From: David O. <do...@eb...> - 2011-08-16 14:13:46
Attachments:
quant_obo_3_7_3_new_and_edited_terms.txt
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Dear all, Related to the development of the mzQuantML standard, the team working on it has a proposal to change and add several terms in the PSI-MS cv. There's more than 70 terms to be added or changed (the changes are mainly about re-location). Martin Eisenacher has made a very complete documentation about where the changes are in the controlled voc. and why the need them. I was waiting for some information from Martin but, in order to make things faster, I'm sending you this message now. I'll attach the changes that Martin has compiled in one small obo file. A complete obo file (to be used with diff purposes) is located at http://code.google.com/p/mzquantml/source/browse/trunk/cv/quant_obo_3_7_3_new_and_edited_terms.txt The explanation of why and where can be found in this document in two formats: http://mzquantml.googlecode.com/svn/trunk/cv/quant_obo_diff_description.pdf http://mzquantml.googlecode.com/svn/trunk/cv/quant_obo_diff_description.pptx Please, take a look into the changes proposed and make your comments and suggestions. After everybody is OK with this, I'll submitt the changes in the PSI-MS cv. Best, -- David Ovelleiro Bioinformatician PRIDE Group Proteomics Services Team, PANDA Group EMBL European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge, UK CB10 1SD |
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From: David O. <do...@eb...> - 2011-08-16 14:18:45
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Sorry, The link to the complete obo (with mzQuantML added) is really in: http://mzquantml.googlecode.com/svn/trunk/cv/psi-ms_3_7_3_with_quant.obo All the documents under: http://code.google.com/p/mzquantml/source/browse/trunk/cv/ David |
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From: David O. <do...@eb...> - 2011-08-18 13:06:45
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Dear all, After reviewing the new 76 term additions modification, I'm absolutely OK with the changes. Only a couple of things: - the 8 "TODOs" comments inside the new proposal should be removed; maybe the TODOs should be done before submitting the new terms, but I understand the need of integrating these terms ASAP: the complete description of the terms could be added in a next release - in addition, the term MS:1001140 should actually be made obsolete after removing the OBSOLETE tag in the definition (adding the line "is_obsolete: true") A part from this (quite trivial), everything fine to me. I'm going to wait a couple of working days and if nobody has anything to say, I'll submit the changes. Best regards, David -- David Ovelleiro Bioinformatician PRIDE Group Proteomics Services Team, PANDA Group EMBL European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge, UK CB10 1SD |
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From: Eric D. <Eri...@sy...> - 2011-08-18 15:36:25
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I believe the SOP states that for an obsoleted term, both the "is_obsolete: true" should be set and the definition should begin with the word OBSOLETE (in case some software does not handle "is_obsolete: true" appropriately, and the definition should also include a sentence on why the term was obsoleted. Thanks, Eric > -----Original Message----- > From: David Ovelleiro [mailto:do...@eb...] > Sent: Thursday, August 18, 2011 6:07 AM > To: 'psi...@li...'; Mass spectrometry standard > development > Subject: Re: [Psidev-ms-dev] List of new c.v. terms and some changes > proposed by the team working in mzQuantML > > Dear all, > > After reviewing the new 76 term additions modification, I'm absolutely > OK with the changes. > Only a couple of things: > - the 8 "TODOs" comments inside the new proposal should be removed; > maybe the TODOs should be done before submitting the new terms, but I > understand the need of integrating these terms ASAP: the complete > description of the terms could be added in a next release > - in addition, the term MS:1001140 should actually be made obsolete > after removing the OBSOLETE tag in the definition (adding the line > "is_obsolete: true") > > A part from this (quite trivial), everything fine to me. I'm going to > wait a couple of working days and if nobody has anything to say, I'll > submit the changes. > > Best regards, > David > > > -- > David Ovelleiro > Bioinformatician > PRIDE Group > Proteomics Services Team, PANDA Group > EMBL European Bioinformatics Institute > Wellcome Trust Genome Campus > Hinxton, Cambridge, UK > CB10 1SD > > > > > > ----------------------------------------------------------------------- > ------- > Get a FREE DOWNLOAD! and learn more about uberSVN rich system, > user administration capabilities and model configuration. Take > the hassle out of deploying and managing Subversion and the > tools developers use with it. http://p.sf.net/sfu/wandisco-d2d-2 > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev |
