-
Notifications
You must be signed in to change notification settings - Fork 17
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Added relaxed semantic validation file for xcms
- Loading branch information
1 parent
5efb314
commit cd5df63
Showing
1 changed file
with
183 additions
and
0 deletions.
There are no files selected for viewing
183 changes: 183 additions & 0 deletions
183
examples/2_0-Metabolomics_Release/mzTab_2_0-M_mapping-xcms.xml
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,183 @@ | ||
| <?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"> | ||
|
|
||
| <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> | ||
|
|
||
| <CvMappingRuleList> | ||
|
|
||
| <!-- 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> | ||
|
|
||
| <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> | ||
|
|
||
| <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> | ||
|
|
||
| <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> | ||
|
|
||
| <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> | ||
|
|
||
| <!-- 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> | ||
|
|
||
| <!-- 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> | ||
|
|
||
| <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> | ||
|
|
||
| <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> | ||
|
|
||
| <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> | ||
|
|
||
| <!-- 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> | ||
|
|
||
| <!-- 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> | ||
|
|
||
| <!-- 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> | ||
|
|
||
| <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> | ||
|
|
||
| <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> | ||
|
|
||
| <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> | ||
|
|
||
| <!-- 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> | ||
|
|
||
| <!-- 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> | ||
|
|
||
| <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> | ||
|
|
||
| <!-- 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> | ||
|
|
||
| <!-- 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> | ||
|
|
||
| <!-- 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> | ||
|
|
||
| <!-- 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> | ||
|
|
||
| <!-- 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> | ||
|
|
||
| <!-- 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> | ||
|
|
||
| <!-- 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> | ||
|
|
||
| <!-- 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> | ||
|
|
||
| <!-- 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> | ||
|
|
||
| <!-- TODO: isotopomer --> | ||
|
|
||
| </CvMappingRuleList> | ||
| </CvMapping> | ||
|
|