mzIdentML-mapping_1.1.0.xml

1) I added such a file to the svn repository and changed element names and 
upper / lower case of the existing rules according to the schema update.

2) Also I added new rules for PeptideEvidence sub-elements (see below), because 
they have cvParams; but I had no idea, which terms from the psi-ms.obo should 
be used in these rules, so they are commented out.

3) In the 1.0.0 mapping file there were also some rules commented out, where we 
did not know, which terms to use (see also below). At least the 
ProteinAmbiguityRule should be possible, as there will be terms about 
"grouping".

4) Completeness of the rules has to be checked (all cvParams of the schema 
covered?), maybe thats easier in the validator implementation?

5) The sense of rules has to be checked (have "child-terms-allowed=yes" rule 
terms really child terms? (If I remember correctly someone found such non-sense 
rules.)

        <!--CvMappingRule id="PeptideSubstitutionModification_rule" cvElementPath="/MzIdentML/SequenceCollection/Peptide/SubstitutionModification/cvParam/@accession" requirementLevel="MUST"  scopePath="" cvTermsCombinationLogic="OR">
            <CvTerm termAccession="UNIMOD:0" useTermName="false" useTerm="false" termName="UNIMOD root" isRepeatable="true" allowChildren="true" cvIdentifierRef="UNIMOD" />
            <CvTerm termAccession="MOD:00000" useTermName="false" useTerm="false" termName="protein modification" isRepeatable="true" allowChildren="true" cvIdentifierRef="MOD" />
            <CvTerm termAccession="MS:1001471" useTermName="false" useTerm="false" termName="peptide modification details" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
        </CvMappingRule-->

        <!--CvMappingRule id="R30" cvElementPath="/MzIdentML/SequenceCollection/PeptideEvidenceList/PeptideEvidence/cvParam/@accession" requirementLevel="MAY"  scopePath="" cvTermsCombinationLogic="OR">
            <CvTerm termAccession="" useTermName="false" useTerm="false" termName="" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
        </CvMappingRule-->

        <!--CvMappingRule id="R30a" cvElementPath="/MzIdentML/SequenceCollection/PeptideEvidenceList/EnzymeRef/cvParam/@accession" requirementLevel="MAY"  scopePath="" cvTermsCombinationLogic="OR">
            <CvTerm termAccession="" useTermName="false" useTerm="false" termName="" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
        </CvMappingRule-->

        <!--CvMappingRule id="R30b" cvElementPath="/MzIdentML/SequenceCollection/PeptideEvidenceList/AdditionalParams/cvParam/@accession" requirementLevel="MAY"  scopePath="" cvTermsCombinationLogic="OR">
            <CvTerm termAccession="" useTermName="false" useTerm="false" termName="" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
        </CvMappingRule-->

        <!--CvMappingRule id="R37" cvElementPath="/MzIdentML/DataCollection/AnalysisData/ProteinDetectionList/ProteinAmbiguityGroup/cvParam/@accession" requirementLevel="MAY"  scopePath="" cvTermsCombinationLogic="OR">
            <CvTerm termAccession="" useTermName="false" useTerm="false" termName="" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS" />
        </CvMappingRule-->
Original issue reported on code.google.com by eisena...@googlemail.com on 5 May 2011 at 8:12
vogelwk / psi-pi

mzIdentML-mapping_1.1.0.xml #65
