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Added relaxed semantic validation file for xcms
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examples/2_0-Metabolomics_Release/mzTab_2_0-M_mapping-xcms.xml
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<?xml version="1.0" encoding="UTF-8"?> | ||
<?xml-stylesheet href="https://raw.githubusercontent.com/HUPO-PSI/psi-tools/master/xml-schemas/xsl/cv-mapping/CvMappingRules.xsl" type="text/xsl"?> | ||
<!-- | ||
The mapping file for mzTab refers to attribute and object names in the Java-typical CamelCase notation. | ||
The mzTab specification uses a dialect of snake_case-for_attributes to name objects and associated attributes. | ||
To select certain axis in xpath for example metadata/snake_case-for_attribute in mzTab, this would be written as /metadata/snakeCase/@forAttributes | ||
Note that the JXPath library does not include the MzTab object as an explicit root in selections, but rather implies it as the anonymous root '/'. | ||
Special considerations: a rule with AND as cvTermsCombinationLogic can have at most one term child with allowChildren = true to avoid nonsensical term expansion and combination. | ||
Alternative term roots should either be expressed as OR (for choose any, even from the expanded term roots when allowChildren = true) or XOR to require EXACTLY one of the term roots' children to be present. | ||
Changelog: | ||
- September 10th, 2020 - Added CHMO ontology for chemistry related terms, e.g. chromatography, modified sample_processing_may | ||
- March 28th, 2019 - Initial Version | ||
--> | ||
<CvMapping xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.psidev.info/files/validator/CvMapping.xsd" modelName="mzTab_m_swagger.yml" modelURI="https://raw.githubusercontent.com/nilshoffmann/jmzTab-m/master/api/src/main/resources/mzTab_m_swagger.yml" modelVersion="2.0.0"> | ||
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<CvReferenceList> | ||
<CvReference cvName="PSI-MS" cvIdentifier="MS"/> | ||
<CvReference cvName="DOID" cvIdentifier="DOID"/> | ||
<CvReference cvName="CL" cvIdentifier="CL"/> | ||
<CvReference cvName="BTO" cvIdentifier="BTO"/> | ||
<CvReference cvName="NCBITaxon" cvIdentifier="NCBITaxon"/> | ||
<CvReference cvName="UO" cvIdentifier="UO"/> | ||
<CvReference cvName="PRIDE" cvIdentifier="PRIDE"/> | ||
<CvReference cvName="MSIO" cvIdentifier="MSIO"/> | ||
<CvReference cvName="CHEBI" cvIdentifier="CHEBI"/> | ||
<CvReference cvName="CHMO" cvIdentifier="CHMO"/> | ||
</CvReferenceList> | ||
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<CvMappingRuleList> | ||
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<!-- run --> | ||
<CvMappingRule id="msrun_format_may" cvElementPath="/metadata/msRun/@format" requirementLevel="MAY" scopePath="/metadata/msRun" cvTermsCombinationLogic="AND"> | ||
<CvTerm termAccession="MS:1000560" useTerm="false" termName="mass spectrometer file format" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<CvMappingRule id="msrun_id_format_may" cvElementPath="/metadata/msRun/@idFormat" requirementLevel="MAY" scopePath="/metadata/msRun" cvTermsCombinationLogic="AND"> | ||
<CvTerm termAccession="MS:1000767" useTerm="false" termName="native spectrum identifier format" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<CvMappingRule id="msrun_fragmentation_method_may" cvElementPath="/metadata/msRun/@fragmentationMethod" requirementLevel="MAY" scopePath="/metadata/msRun" cvTermsCombinationLogic="OR"> | ||
<CvTerm termAccession="MS:1000044" useTerm="false" termName="dissociation method" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<CvMappingRule id="msrun_scan_polarity_must" cvElementPath="/metadata/msRun/@scanPolarity" requirementLevel="MUST" scopePath="/metadata/msRun" cvTermsCombinationLogic="OR"> | ||
<CvTerm termAccession="MS:1000129" useTerm="true" termName="negative scan" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm> | ||
<CvTerm termAccession="MS:1000130" useTerm="true" termName="positive scan" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<CvMappingRule id="msrun_hash_method_may" cvElementPath="/metadata/msRun/@hashMethod" requirementLevel="MAY" scopePath="/metadata/msRun" cvTermsCombinationLogic="AND"> | ||
<CvTerm termAccession="MS:1000561" useTerm="false" termName="data file checksum type" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<!-- sample processing --> | ||
<CvMappingRule id="sample_processing_may" cvElementPath="/metadata/sampleProcessing/@sampleProcessing" requirementLevel="MAY" scopePath="/metadata/sampleprocessing" cvTermsCombinationLogic="OR"> | ||
<CvTerm termAccession="OBI:0000094" useTerm="false" termName="material processing" isRepeatable="true" allowChildren="true" cvIdentifierRef="MSIO"></CvTerm> | ||
<CvTerm termAccession="OBI:0000094" useTerm="false" termName="material processing" isRepeatable="true" allowChildren="true" cvIdentifierRef="CHMO"></CvTerm> | ||
</CvMappingRule> | ||
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<!-- instrument --> | ||
<CvMappingRule id="instrument_name_may" cvElementPath="/metadata/instrument/@name" requirementLevel="MAY" scopePath="/metadata/instrument" cvTermsCombinationLogic="AND"> | ||
<CvTerm termAccession="MS:1000031" useTerm="false" termName="instrument model" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<CvMappingRule id="instrument_source_may" cvElementPath="/metadata/instrument/@source" requirementLevel="MAY" scopePath="/metadata/instrument" cvTermsCombinationLogic="AND"> | ||
<CvTerm termAccession="MS:1000458" useTerm="false" termName="source" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<CvMappingRule id="instrument_analyzer_may" cvElementPath="/metadata/instrument/@analyzer" requirementLevel="MAY" scopePath="/metadata/instrument" cvTermsCombinationLogic="AND"> | ||
<CvTerm termAccession="MS:1000451" useTerm="false" termName="mass analyzer" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<CvMappingRule id="instrument_detector_may" cvElementPath="/metadata/instrument/@detector" requirementLevel="MAY" scopePath="/metadata/instrument" cvTermsCombinationLogic="AND"> | ||
<CvTerm termAccession="MS:1000026" useTerm="false" termName="detector type" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<!-- software --> | ||
<CvMappingRule id="software_must" cvElementPath="/metadata/software/@parameter" requirementLevel="MUST" scopePath="/metadata/software" cvTermsCombinationLogic="AND"> | ||
<!--<CvTerm termAccession="MS:1002878" useTerm="false" termName="small molecule analysis software" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm>--> | ||
<CvTerm termAccession="MS:1000531" useTerm="false" termName="software" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<!-- quantification method --> | ||
<CvMappingRule id="quantification_method_must" cvElementPath="/metadata/@quantificationMethod" requirementLevel="MUST" scopePath="/metadata" cvTermsCombinationLogic="OR"> | ||
<CvTerm termAccession="PRIDE:0000307" useTerm="false" termName="Quantification method" isRepeatable="false" allowChildren="true" cvIdentifierRef="PRIDE"></CvTerm> | ||
<CvTerm termAccession="MS:1001833" useTerm="false" termName="quantitation analysis summary" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<!-- sample --> | ||
<CvMappingRule id="sample_species_may" cvElementPath="/metadata/sample/@species" requirementLevel="MAY" scopePath="/metadata/sample" cvTermsCombinationLogic="OR"> | ||
<CvTerm termAccession="PRIDE:0000033" useTerm="false" termName="NEWT" isRepeatable="false" allowChildren="true" cvIdentifierRef="PRIDE"></CvTerm> | ||
<CvTerm termAccession="NCBITaxon:1" useTerm="false" termName="root" isRepeatable="false" allowChildren="true" cvIdentifierRef="NCBITaxon"></CvTerm> | ||
</CvMappingRule> | ||
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<CvMappingRule id="sample_tissue_may" cvElementPath="/metadata/sample/@tissue" requirementLevel="MAY" scopePath="/metadata/sample" cvTermsCombinationLogic="OR"> | ||
<CvTerm termAccession="BTO:0000000" useTerm="false" termName="tissues, cell types and enzyme sources" isRepeatable="false" allowChildren="true" cvIdentifierRef="BTO"></CvTerm> | ||
<CvTerm termAccession="PRIDE:0000442" useTerm="false" termName="Tissue not applicable to dataset" isRepeatable="false" allowChildren="true" cvIdentifierRef="PRIDE"></CvTerm> | ||
</CvMappingRule> | ||
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<CvMappingRule id="sample_cell_type_may" cvElementPath="/metadata/sample/@cellType" requirementLevel="MAY" scopePath="/metadata/sample" cvTermsCombinationLogic="AND"> | ||
<CvTerm termAccession="CL:0000000" useTerm="false" termName="cell" isRepeatable="false" allowChildren="true" cvIdentifierRef="CL"></CvTerm> | ||
</CvMappingRule> | ||
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<CvMappingRule id="sample_disease_may" cvElementPath="/metadata/sample/@disease" requirementLevel="MAY" scopePath="/metadata/sample" cvTermsCombinationLogic="OR"> | ||
<CvTerm termAccession="DOID:4" useTerm="false" termName="disease" isRepeatable="false" allowChildren="true" cvIdentifierRef="DOID"></CvTerm> | ||
<CvTerm termAccession="PRIDE:0000018" useTerm="true" termName="Disease free" isRepeatable="false" allowChildren="true" cvIdentifierRef="PRIDE"></CvTerm> | ||
</CvMappingRule> | ||
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<!-- database --> | ||
<CvMappingRule id="database_must" cvElementPath="/metadata/database/@param" requirementLevel="MUST" scopePath="/metadata/database" cvTermsCombinationLogic="XOR"> | ||
<CvTerm termAccession="MS:1001013" useTerm="false" termName="database name" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
<CvTerm termAccession="MS:1001347" useTerm="false" termName="database file formats" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
<CvTerm termAccession="MS:1001011" useTerm="false" termName="search database details" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<!-- study variable --> | ||
<CvMappingRule id="study_variable_average_function_may" cvElementPath="/metadata/studyVariable/@averageFunction" requirementLevel="MAY" scopePath="/metadata/studyvariable" cvTermsCombinationLogic="AND"> | ||
<CvTerm termAccession="MS:1002882" useTerm="false" termName="study variable average function" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<CvMappingRule id="study_variable_variation_function_may" cvElementPath="/metadata/studyVariable/@variationFunction" requirementLevel="MAY" scopePath="/metadata/studyvariable" cvTermsCombinationLogic="AND"> | ||
<CvTerm termAccession="MS:1002884" useTerm="false" termName="study variable variation function" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<!-- derivatization agent --> | ||
<CvMappingRule id="derivatization_agent_may" cvElementPath="/metadata/@derivatizationAgent" requirementLevel="MAY" scopePath="/metadata" cvTermsCombinationLogic="AND"> | ||
<CvTerm termAccession="CHEBI:23367" useTerm="false" termName="molecular entity" isRepeatable="false" allowChildren="true" cvIdentifierRef="CHEBI"></CvTerm> | ||
</CvMappingRule> | ||
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<!-- small molecule quantification unit --> | ||
<CvMappingRule id="small_molecule_quantification_unit_must" cvElementPath="/metadata/@smallMoleculeQuantificationUnit" requirementLevel="MUST" scopePath="/metadata" cvTermsCombinationLogic="XOR"> | ||
<CvTerm termAccession="PRIDE:0000392" useTerm="false" termName="Quantification unit" isRepeatable="false" allowChildren="true" cvIdentifierRef="PRIDE"></CvTerm> | ||
<CvTerm termAccession="UO:0000051" useTerm="false" termName="concentration unit" isRepeatable="false" allowChildren="true" cvIdentifierRef="UO"></CvTerm> | ||
<CvTerm termAccession="MS:1000043" useTerm="false" termName="intensity unit" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
<CvTerm termAccession="UO:0000006" useTerm="false" termName="substance unit" isRepeatable="false" allowChildren="true" cvIdentifierRef="UO"></CvTerm> | ||
</CvMappingRule> | ||
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<!-- small molecule feature quantification unit --> | ||
<CvMappingRule id="small_molecule_feature_quantification_unit_must" cvElementPath="/metadata/@smallMoleculeFeatureQuantificationUnit" requirementLevel="MUST" scopePath="/metadata" cvTermsCombinationLogic="XOR"> | ||
<CvTerm termAccession="PRIDE:0000392" useTerm="false" termName="Quantification unit" isRepeatable="false" allowChildren="true" cvIdentifierRef="PRIDE"></CvTerm> | ||
<CvTerm termAccession="UO:0000051" useTerm="false" termName="concentration unit" isRepeatable="false" allowChildren="true" cvIdentifierRef="UO"></CvTerm> | ||
<CvTerm termAccession="MS:1000043" useTerm="false" termName="intensity unit" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
<CvTerm termAccession="UO:0000006" useTerm="false" termName="substance unit" isRepeatable="false" allowChildren="true" cvIdentifierRef="UO"></CvTerm> | ||
</CvMappingRule> | ||
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<!-- small_molecule-identification_reliability --> | ||
<CvMappingRule id="small_molecule_identification_reliability_may" cvElementPath="/metadata/@smallMoleculeIdentificationReliability" requirementLevel="MAY" scopePath="/metadata" cvTermsCombinationLogic="AND"> | ||
<CvTerm termAccession="MS:1002895" useTerm="false" termName="small molecule identification attribute" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<!-- id confidence measure --> | ||
<CvMappingRule id="id_confidence_measure_may" cvElementPath="/metadata/@idConfidenceMeasure" requirementLevel="MAY" scopePath="/metadata" cvTermsCombinationLogic="OR"> | ||
<CvTerm termAccession="MS:1002888" useTerm="false" termName="small molecule confidence measure" isRepeatable="true" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<!-- best id confidence measure --> | ||
<CvMappingRule id="best_id_confidence_measure_may" cvElementPath="/smallMoleculeSummary/@bestIdConfidenceMeasure" requirementLevel="MAY" scopePath="/smallMoleculeSummary" cvTermsCombinationLogic="AND"> | ||
<CvTerm termAccession="MS:1002888" useTerm="false" termName="small molecule confidence measure" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<!-- derivatized form --> | ||
<CvMappingRule id="derivatized_form_may" cvElementPath="/smallMoleculeEvidence/@derivatizedForm" requirementLevel="MAY" scopePath="/smallMoleculeEvidence" cvTermsCombinationLogic="AND"> | ||
<CvTerm termAccession="CHEBI:24433" useTerm="false" termName="group" isRepeatable="false" allowChildren="true" cvIdentifierRef="CHEBI"></CvTerm> | ||
</CvMappingRule> | ||
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<!-- ms level --> | ||
<CvMappingRule id="ms_level_may" cvElementPath="/smallMoleculeEvidence/@msLevel" requirementLevel="MAY" scopePath="/smallMoleculeSummary" cvTermsCombinationLogic="AND"> | ||
<CvTerm termAccession="MS:1000511" useTerm="false" termName="ms level" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<!-- identification method --> | ||
<CvMappingRule id="identification_method_may" cvElementPath="/smallMoleculeEvidence/@identificationMethod" requirementLevel="MAY" scopePath="/smallMoleculeEvidence" cvTermsCombinationLogic="XOR"> | ||
<CvTerm termAccession="MS:1001058" useTerm="true" termName="quality estimation by manual validation" isRepeatable="false" allowChildren="false" cvIdentifierRef="MS"></CvTerm> | ||
<CvTerm termAccession="MS:1001060" useTerm="false" termName="search type" isRepeatable="false" allowChildren="true" cvIdentifierRef="MS"></CvTerm> | ||
</CvMappingRule> | ||
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<!-- TODO: isotopomer --> | ||
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</CvMappingRuleList> | ||
</CvMapping> | ||
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