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Re: [Psidev-pi-dev] FW: Spec doc
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From: Andreas B. <be...@in...> - 2008-12-04 13:33:56
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Hi David, > I've updated the Mascot_MSMS_example.axml, > <FragmentTolerance> > <pf:cvParam accession="PI:00404" name="absolut mass unit" > value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton" > unitCvRef="UO" /> <pf:cvParam accession="PI:00404" name="absolut mass unit" > value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton" > unitCvRef="UO" /> </FragmentTolerance> > <ParentTolerance> > <pf:cvParam accession="PI:00403" name="relative mass unit" > value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187" unitName="percent" > unitCvRef="UO" /> <pf:cvParam accession="PI:00403" name="relative mass > unit" value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187" > unitName="percent" unitCvRef="UO" /> </ParentTolerance> Is there a reason to repeat the unit lines? I've added term UO:0000187 percent to the allowed ones, this is a synonym of parts per hundred, however separately listed in unit.obo... > but this doesn't validate: The file still does not validate with some new errors, as you suggested ;) Error: Name of CVTerm not correct: 'PI:00404 - absolut mass unit' should be 'absolute mass unit' Error: Violated mapping rule 'R17a' number of term repeats at element '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ParentTolerance' Error: Violated mapping rule 'R17b' number of term repeats at element '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/FragmentTolerance' Blame me, if you experience other unexpected results. > I'm also slightly concerned about PSI-PI group getting the wrong(?) > reputation. Martin, could you change PI:00404 from being a brand of vodka > to "absolute". Thanks. (I've still not installed OboEdit.) (Maybe the CV and mapping file look much clearer with enough absolut) @Martin: I've changed terms 403 and 404, added value-types and added percentage unit. Hopefully this merges with your local changes (if any). Thanks, A. -- Div. for Simulation of Biological Systems, WSI, University of Tuebingen Room C322, Sand 14, 72076 Tuebingen, Germany phone: +49-7071-29-70461 fax: +49-7071-29-5152 http://www-bs.informatik.uni-tuebingen.de |
