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From: Marc S. <stu...@gm...> - 2009-06-12 09:33:52
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Hi all, good news from the example files. I just validated all examples from the website. Only two files contain minor errors: ------- file name: MzMLFile_PDA.mzML file type: mzML Validating mzML file against XML schema version 1.10 Success: the file is valid! Semantically validating mzML file: Error: CV term must have a unit: MS:1000515 - intensity array Error: CV term must have a unit: MS:1000515 - intensity array Failed: errors are listed above! ------- file name: neutral_loss_example_1.1.0.mzML file type: mzML Validating mzML file against XML schema version 1.10 Success: the file is valid! Semantically validating mzML file: Error: Violated mapping rule 'precursor_isolationwindow_must' at element '/mzML/run/spectrumList/spectrum/precursorList/precursor/isolationWindow', 1 should be present, 0 found! Error: Violated mapping rule 'product_isolationwindow_must' at element '/mzML/run/spectrumList/spectrum/productList/product/isolationWindow', 1 should be present, 0 found! Failed: errors are listed above! Best, Marc |
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From: Fredrik L. <Fre...@im...> - 2009-06-12 12:59:11
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Hi, I am afraid that it will not be possible to make the neutral loss spectra valid with a required target mass for precursor and product, since there are none those a spectra (just two moving isolation windows). So I guess these new rules will have to be changed back to MAY again, even if they should be required in most other types of spectra. The other exception is precursor ion spectra, were the precursor isolation window is also moving. Fredrik Marc Sturm wrote: > Hi all, > > good news from the example files. I just validated all examples from the > website. Only two files contain minor errors: > > ------- > > file name: MzMLFile_PDA.mzML > file type: mzML > > Validating mzML file against XML schema version 1.10 > Success: the file is valid! > > Semantically validating mzML file: > Error: CV term must have a unit: MS:1000515 - intensity array > Error: CV term must have a unit: MS:1000515 - intensity array > Failed: errors are listed above! > > ------- > > file name: neutral_loss_example_1.1.0.mzML > file type: mzML > > Validating mzML file against XML schema version 1.10 > Success: the file is valid! > > Semantically validating mzML file: > Error: Violated mapping rule 'precursor_isolationwindow_must' at element > '/mzML/run/spectrumList/spectrum/precursorList/precursor/isolationWindow', > 1 should be present, 0 found! > Error: Violated mapping rule 'product_isolationwindow_must' at element > '/mzML/run/spectrumList/spectrum/productList/product/isolationWindow', 1 > should be present, 0 found! > Failed: errors are listed above! > > Best, > Marc > > > ------------------------------------------------------------------------------ > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensing option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > |
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From: Matt C. <mat...@va...> - 2009-06-12 13:10:20
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Yes, looks like I forgot about neutral change spectra while getting so ambitious with the mapping file changes. Either we need some basic logic in the mapping file (if spectrum is this type, this use this rule, else another rule), or this is another one of those special rules. I'll fix this later today. -Matt Fredrik Levander wrote: > Hi, I am afraid that it will not be possible to make the neutral loss > spectra valid with a required target mass for precursor and product, > since there are none those a spectra (just two moving isolation > windows). So I guess these new rules will have to be changed back to MAY > again, even if they should be required in most other types of spectra. > The other exception is precursor ion spectra, were the precursor > isolation window is also moving. > > Fredrik > > Marc Sturm wrote: > >> Hi all, >> >> good news from the example files. I just validated all examples from the >> website. Only two files contain minor errors: >> >> ------- >> >> file name: MzMLFile_PDA.mzML >> file type: mzML >> >> Validating mzML file against XML schema version 1.10 >> Success: the file is valid! >> >> Semantically validating mzML file: >> Error: CV term must have a unit: MS:1000515 - intensity array >> Error: CV term must have a unit: MS:1000515 - intensity array >> Failed: errors are listed above! >> >> ------- >> >> file name: neutral_loss_example_1.1.0.mzML >> file type: mzML >> >> Validating mzML file against XML schema version 1.10 >> Success: the file is valid! >> >> Semantically validating mzML file: >> Error: Violated mapping rule 'precursor_isolationwindow_must' at element >> '/mzML/run/spectrumList/spectrum/precursorList/precursor/isolationWindow', >> 1 should be present, 0 found! >> Error: Violated mapping rule 'product_isolationwindow_must' at element >> '/mzML/run/spectrumList/spectrum/productList/product/isolationWindow', 1 >> should be present, 0 found! >> Failed: errors are listed above! >> >> Best, >> Marc >> |
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From: Matthew C. <mat...@va...> - 2009-06-12 15:10:00
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Fixed. Matt Chambers wrote: > Yes, looks like I forgot about neutral change spectra while getting so > ambitious with the mapping file changes. Either we need some basic logic > in the mapping file (if spectrum is this type, this use this rule, else > another rule), or this is another one of those special rules. I'll fix > this later today. > > -Matt > > > Fredrik Levander wrote: > >> Hi, I am afraid that it will not be possible to make the neutral loss >> spectra valid with a required target mass for precursor and product, >> since there are none those a spectra (just two moving isolation >> windows). So I guess these new rules will have to be changed back to MAY >> again, even if they should be required in most other types of spectra. >> The other exception is precursor ion spectra, were the precursor >> isolation window is also moving. >> >> Fredrik >> >> Marc Sturm wrote: >> >> >>> Hi all, >>> >>> good news from the example files. I just validated all examples from the >>> website. Only two files contain minor errors: >>> >>> ------- >>> >>> file name: MzMLFile_PDA.mzML >>> file type: mzML >>> >>> Validating mzML file against XML schema version 1.10 >>> Success: the file is valid! >>> >>> Semantically validating mzML file: >>> Error: CV term must have a unit: MS:1000515 - intensity array >>> Error: CV term must have a unit: MS:1000515 - intensity array >>> Failed: errors are listed above! >>> >>> ------- >>> >>> file name: neutral_loss_example_1.1.0.mzML >>> file type: mzML >>> >>> Validating mzML file against XML schema version 1.10 >>> Success: the file is valid! >>> >>> Semantically validating mzML file: >>> Error: Violated mapping rule 'precursor_isolationwindow_must' at element >>> '/mzML/run/spectrumList/spectrum/precursorList/precursor/isolationWindow', >>> 1 should be present, 0 found! >>> Error: Violated mapping rule 'product_isolationwindow_must' at element >>> '/mzML/run/spectrumList/spectrum/productList/product/isolationWindow', 1 >>> should be present, 0 found! >>> Failed: errors are listed above! >>> >>> Best, >>> Marc >>> >>> > > > ------------------------------------------------------------------------------ > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensing option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > Psidev-ms-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-ms-dev > |
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From: Steffen N. <sne...@ip...> - 2009-06-12 14:03:28
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On Fri, 2009-06-12 at 11:34 +0200, Marc Sturm wrote: > Error: CV term must have a unit: MS:1000515 - intensity array > Error: CV term must have a unit: MS:1000515 - intensity array The PDA is measuring absorbance of light by the sample. Our machine software reports "milli-AU". My first guesses do not validate: Semantically validating mzML file: Error: Unit CV term not allowed: UO:0000186 - dimensionless unit of term MS:1000515 - intensity array Error: Unit CV term not allowed: UO:0000157 - light unit of term MS:1000515 - intensity array Error: Unit CV term not allowed: UO:0000187 - percent of term MS:1000515 - intensity array Failed: errors are listed above! So I propose something like: [Term] id: XX:XXXXXXX name: Absorbance Units def: "A dimensionless logarithmic unit to measure the absorbance of light transmitted through a partially absorbing substance." is_a: UO:0000186 ! dimensionless unit maybe is_a: ID: PSI:1000460 Name: Unit where I am unsure whether that should go into MS:XXXXXXX or OU:XXXXXXX. Once I have some CV Term I can use, I'll fix the MzMLFile_PDA.xml Yours, Steffen * http://en.wikipedia.org/wiki/Absorbance Although absorbance does not have true units, it is quite often reported in "Absorbance Units" or AU * http://www.unc.edu/~rowlett/units/dictA.html absorbance unit (AU) a logarithmic unit used to measure optical density, the absorbance of light transmitted through a partially absorbing substance. If T is the percentage of light transmitted, then the absorbance is defined to be -log10 T absorbance units. An increase in absorbance of 1.0 AU corresponds to a reduction in transmittance by a factor of 10. If the absorbance is 1.0 AU then 10% of the light is transmitted; at 2.0 AU only 1% of the light is transmitted, and so on. BTW, there are two different "percent" in the Ontologies: ID: PSI:1000138 Name: Percent and ID: UO:0000187 Name: percent Yours, Steffen -- IPB Halle AG Massenspektrometrie & Bioinformatik Dr. Steffen Neumann http://www.IPB-Halle.DE Weinberg 3 http://msbi.bic-gh.de 06120 Halle Tel. +49 (0) 345 5582 - 1470 +49 (0) 345 5582 - 0 sneumann(at)IPB-Halle.DE Fax. +49 (0) 345 5582 - 1409 |
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