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Re: [Psidev-ms-dev] Data analysis description
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From: Race, A. <Ala...@un...> - 2017-03-21 09:52:08
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Hi Mathias, I thought that seemed most sensible too - the confusion just came from the fact that the softwareRef is defined on the processingMethod rather than the dataProcessing tag, which seems the wrong way around to me. Thanks again, Alan -----Original Message----- From: Mathias Walzer [mailto:wa...@in...] Sent: 21 March 2017 10:36 To: Mass spectrometry standard development <psi...@li...> Subject: Re: [Psidev-ms-dev] Data analysis description Hi Alan, I'd roll with the name of the tag. One software with multiple methods/steps, multiple method tags. best, mths ----- Original Message ----- From: "Alan Race" <Ala...@un...> To: "Mass spectrometry standard development" <psi...@li...> Sent: Monday, 20 March, 2017 3:41:14 PM Subject: Re: [Psidev-ms-dev] Data analysis description Hi Mathias, Thank you for your reply. Okay that sounds good, I'll put together a list and submit it to the vocab mailing list. With regards to the one software application per processingMethod tag - if one software applied multiple methods that have the same parameter names (e.g. Gaussian smoothing with a window size, and TopHat baseline correction with a window size) would you recommend putting these in the same processingMethod tag because they are the same software? Or separate them out into two processingMethod tags to avoid confusion with the window size CVParams? Thanks, Alan -----Original Message----- From: Mathias Walzer [mailto:wa...@in...] Sent: 20 March 2017 10:53 To: Mass spectrometry standard development <psi...@li...> Subject: Re: [Psidev-ms-dev] Data analysis description Hi, Alan! yes, you can reflect all parameters of a workflow, one software application per processionmethod tag. If there is no adequate cvParam for one used parameter, then you have the choice of using a userParam (http://www.peptideatlas.org/tmp/mzML1.1.0.html#userParam) for the short term and suggest a new cv term - best at psi...@li.... Or stick with userParam representation if that param won't be any good for any other software. For the latter, you should probably also consider if there is the chance of misinterpretation if the userParam cannot be read or interpreted (e.g. submission software). best, mths ----- Original Message ----- From: "Alan Race" <Ala...@un...> To: psi...@li... Sent: Friday, 17 March, 2017 8:56:25 AM Subject: [Psidev-ms-dev] Data analysis description Hello, I have a question regarding recommended implementation of a full description of data analysis steps, for example. Say that I wanted to include a description of a full preprocessing workflow – how would you suggest to include the parameters related to each method? I assumed that it would be through the inclusion of additional cvParam tags, but I couldn’t see anything obvious in the obo. Perhaps I am missing something? Assuming that there are tags, then should each processingMethod tag only describe (fully) a single method and it’s corresponding parameters (as below)? the example on the mzML website ( http://www.peptideatlas.org/tmp/mzML1.1.0.html#processingMethod ) suggests that the processingMethod tag can include a whole preprocessing workflow including multiple methods, and, the way that I see it, including parameters for each method in this situation may result in them being attributed incorrectly to a given method. <dataProcessingList count="2"> <dataProcessing id="preprocessing"> <processingMethod order="1" softwareRef="test"> <cvParam cvRef="MS" accession="MS:1000782" name="Savitzky-Golay smoothing" value=""/> <cvParam cvRef="MS" accession="MS:???????" name="Polynomial order" value="2"/> <cvParam cvRef="MS" accession="MS:???????" name="Window size" value=""/> </processingMethod> … </dataProcessing> … Thanks for your help, Alan ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Psidev-ms-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Psidev-ms-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Psidev-ms-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Psidev-ms-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev |
