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Re: [Psidev-ms-dev] CV param readability
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From: Kessner, D. E. <Dar...@cs...> - 2008-02-07 16:56:43
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Thank you to everyone for clearing up the issue for me! Darren -----Original Message----- From: psi...@li... [mailto:psi...@li...] On Behalf Of jtasman Sent: Thursday, February 07, 2008 7:51 AM To: len...@eb...; Mass spectrometry standard development Subject: Re: [Psidev-ms-dev] CV param readability Great, thanks for clearing that up. I must have been remembering a previous version of the validator. Josh Lennart Martens wrote: > Hi Josh, > > > >> Yes, but the official validator will complain if the 'name' string doesn't exactly match the CV, capitalization included. >> > > This is incorrect (I actually tested it with version 0.99.1 of the > semantic mzML validator we wrote and distributed in the kit). > > The tool validates solely on the CV accession numbers, because this is > the only 'fixed quantity' (names have exact synonyms for instance), and > the 'name' attribute is mainly in the standard format for readability > reasons. > > So I think it's acceptable if people use acronyms instead of full > versions, especially if they are present as exact synonyms in the CV. > If the correct CV accession number is used for a term, there should > never be a problem, since it has been decided throughout the PSI a long > time ago (and I think we can all agree on this as well) that the > accession number takes precedence over the name at all times. > > > >> Kessner, Darren E. wrote: >> >>> I wasn't thinking about validation, since I'm ignoring the 'name' >>> attribute. >>> >>> This is solely a readability issue, for the mzML and for MSData client >>> code. >>> >>> >>> Darren >>> >>> >>> -----Original Message----- >>> From: psi...@li... >>> [mailto:psi...@li...] On Behalf Of Joshua >>> Tasman >>> Sent: Wednesday, February 06, 2008 12:00 PM >>> To: Mass spectrometry standard development >>> Subject: Re: [Psidev-ms-dev] CV param readability >>> >>> Hi Darren, >>> >>> Speaking only for myself, I think that the "name" attribute should be >>> optional in the file and not interfere with validation. I've never >>> understood why the text string needs to exactly match the CV for >>> validation; someone one the list had brought up other languages, etc. >>> But I think it came up on the list before, and requiring strict mapping >>> between accession numbers and text string seemed to be important for the >>> format. >>> >>> At the least, acronyms would require additional 'mapping files' or >>> something similar to be added to the specification, and the validator to >>> be updated. Maybe someone more familiar with these tasks could step in. >>> Maybe the CV could be expanded so that every entry had an additional >>> "acronym" field. This brings up other questions, like would uniqueness >>> be enforced, etc? >>> >>> Josh >>> >>> >>> Kessner, Darren E. wrote: >>> >>>> I would like to propose using standard acronyms in the CV term names >>>> when it is clear what they mean. >>>> >>>> >>>> >>>> We currently have: >>>> >>>> <cvParam cvLabel="MS" accession="MS:1000075" name="matrix assisted >>>> >>> laser >>> >>>> desorption ionization" value=""/> >>>> >>>> <cvParam cvLabel="MS" accession="MS:1000079" name="fourier transform >>>> >>> ion >>> >>>> cyclotron resonance mass spectrometer" value=""/> >>>> >>>> >>>> >>>> I think this is more readable: >>>> >>>> <cvParam cvLabel="MS" accession="MS:1000075" name="MALDI" value=""/> >>>> >>>> <cvParam cvLabel="MS" accession="MS:1000079" name="FT-ICR MS" >>>> >>> value=""/> >>> >>>> >>>> >>>> The full name can still be available in the term description field. >>>> >>>> >>>> >>>> I have an ulterior motive for this -- in the code generation of the >>>> MSData library, the above terms become constants: >>>> >>>> MS_matrix_assisted_laser_desorption_ionization = 1000075, >>>> >>>> MS_fourier_transform_ion_cyclotron_resonance_mass_spectrometer = >>>> 1000079, >>>> >>>> >>>> >>>> But I think the following is more programmer-friendly: >>>> >>>> MS_MALDI = 1000075, >>>> >>>> MS_FT_ICR_MS = 1000079, >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Darren >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Darren Kessner >>>> >>>> Scientific Programmer >>>> >>>> Dar...@cs... <mailto:Dar...@cs...> >>>> >>>> 310-423-9538 >>>> >>>> >>>> >>>> Spielberg Family Center for Applied Proteomics >>>> >>>> Cedars-Sinai Medical Center >>>> >>>> http://www.sfcap.cshs.org/ >>>> >>>> >>>> >>>> >>>> >>>> IMPORTANT WARNING: This message is intended for the use of the person >>>> >>> or >>> >>>> entity to which it is addressed and may contain information that is >>>> privileged and confidential, the disclosure of which is governed by >>>> applicable law. If the reader of this message is not the intended >>>> recipient, or the employee or agent responsible for delivering it to >>>> >>> the >>> >>>> intended recipient, you are hereby notified that any dissemination, >>>> distribution or copying of this information is STRICTLY PROHIBITED. >>>> >>>> If you have received this message in error, please notify us >>>> >>> immediately >>> >>>> by calling (310) 423-6428 and destroy the related message. Thank You >>>> >>> for >>> >>>> your cooperation. >>>> >>>> >>>> >>>> >>> ------------------------------------------------------------------------ >>> ------------------------------------------------------------------------ >>> - >>> >>>> This SF.net email is sponsored by: Microsoft >>>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>>> >>>> >>>> >>>> >>> ------------------------------------------------------------------------ >>> >>>> _______________________________________________ >>>> Psidev-ms-dev mailing list >>>> Psi...@li... >>>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >>>> >>> ------------------------------------------------------------------------ >>> - >>> This SF.net email is sponsored by: Microsoft >>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>> _______________________________________________ >>> Psidev-ms-dev mailing list >>> Psi...@li... >>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >>> IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by >>> applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is STRICTLY PROHIBITED. >>> >>> If you have received this message in error, please notify us immediately >>> by calling (310) 423-6428 and destroy the related message. Thank You for your cooperation. >>> >>> ------------------------------------------------------------------------ - >>> This SF.net email is sponsored by: Microsoft >>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>> _______________________________________________ >>> Psidev-ms-dev mailing list >>> Psi...@li... >>> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >>> >> ------------------------------------------------------------------------ - >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2008. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> _______________________________________________ >> Psidev-ms-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev >> >> > > ------------------------------------------------------------------------ - > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > ------------------------------------------------------------------------ - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Psidev-ms-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is STRICTLY PROHIBITED. If you have received this message in error, please notify us immediately by calling (310) 423-6428 and destroy the related message. Thank You for your cooperation. |
