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qcML_0.0.8.xsd
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qcML_0.0.8.xsd
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<!-- edited with XMLSpy v2014 sp1 (x64) (http://www.altova.com) by Dr. Peter Bauer (Universitätsklinikum Tübingen) -->
<!-- qcML version 0.0.8
Distributed under the Creative Commons license http://creativecommons.org/licenses/by/2.0/.
-->
<xsd:schema xmlns="http://www.prime-xs.eu/ms/qcml" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsl="http://www.w3.org/1999/XSL/Transform" targetNamespace="http://www.prime-xs.eu/ms/qcml" elementFormDefault="qualified" version="0.0.7">
<xsd:element name="qcML">
<xsd:annotation>
<xsd:documentation>The qcML file XML root element containing several QualityAssessments to runs and an optional QualityAssessment to the whole set</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:complexContent>
<xsd:extension base="qcMLType">
<xsd:attribute name="version" use="required">
<xsd:annotation>
<xsd:documentation>Version number of qcML document.</xsd:documentation>
</xsd:annotation>
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:pattern value="\d+\.\d+\.\d+"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:attribute>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
</xsd:element>
<xsd:complexType name="qcMLType">
<xsd:annotation>
<xsd:documentation>The type of the root element</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element name="runQuality" maxOccurs="unbounded">
<xsd:annotation>
<xsd:documentation>Contains a QualityAssessment to a run as sequence of qualityParameters and attachments</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:complexContent>
<xsd:extension base="runQualityAssessmentType">
<xsd:attribute name="ID" type="xsd:ID" use="required">
<xsd:annotation>
<xsd:documentation>A file unique identifier for this runQuality element</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
</xsd:element>
<xsd:element name="setQuality" minOccurs="0" maxOccurs="unbounded">
<xsd:annotation>
<xsd:documentation>Contains a QualityAssassment to a set of runs referenced from this file as a sequence of qualityParameters or attachments</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:complexContent>
<xsd:extension base="setQualityAssessmentType">
<xsd:attribute name="ID" type="xsd:ID" use="required">
<xsd:annotation>
<xsd:documentation>A file unique identifier for this runQuality element</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
</xsd:element>
<xsd:element name="cvList" type="cvListType">
<xsd:annotation>
<xsd:documentation>the list of source CV referenced in this file</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:any processContents="skip" minOccurs="0" maxOccurs="1">
<xsd:annotation>
<xsd:documentation>Blank element to allow embedding a stylesheet into the document (Needed to make Qt XML validation work).</xsd:documentation>
</xsd:annotation>
</xsd:any>
</xsd:sequence>
</xsd:complexType>
<xsd:complexType name="cvListType">
<xsd:annotation>
<xsd:documentation>The list of controlled vocabularies used in the file.</xsd:documentation>
</xsd:annotation>
<xsd:sequence>
<xsd:element name="cv" type="cvType" maxOccurs="unbounded">
<xsd:annotation>
<xsd:documentation>these are describing the controlled vocabularies containing the used parameters</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
</xsd:complexType>
<xsd:complexType name="qualityAssessmentType" abstract="true">
<xsd:annotation>
<xsd:documentation>The abstract base type for qualityParameter and attachment container</xsd:documentation>
</xsd:annotation>
<xsd:choice maxOccurs="unbounded">
<xsd:sequence>
<xsd:element name="metaDataParameter" minOccurs="0" maxOccurs="unbounded">
<xsd:annotation>
<xsd:documentation>Meta data about the quality parameters, e.g. description of tool(s) the quality parameters were created with, version of the tool(s), creation data, source files the quality parameters were extracted from, etc.</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:complexContent>
<xsd:extension base="metaDataType"/>
</xsd:complexContent>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:sequence>
<xsd:element name="qualityParameter" type="qualityParameterType" maxOccurs="unbounded">
<xsd:annotation>
<xsd:documentation>Describes the @value of a certain quality parameter by reference to a cvType (and unitCvType)</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
<xsd:sequence>
<xsd:element name="attachment" maxOccurs="unbounded">
<xsd:annotation>
<xsd:documentation>Describes the binary data or tabular data of a referenced qualityParameter with a cvTerm describing the attached data and the MIME type as additional unitCvType</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:complexContent>
<xsd:extension base="attachmentType"/>
</xsd:complexContent>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
</xsd:choice>
</xsd:complexType>
<xsd:complexType name="runQualityAssessmentType">
<xsd:annotation>
<xsd:documentation>The derived Type for QualityParameter container of a run</xsd:documentation>
</xsd:annotation>
<xsd:complexContent>
<xsd:extension base="qualityAssessmentType"/>
</xsd:complexContent>
</xsd:complexType>
<xsd:complexType name="setQualityAssessmentType">
<xsd:annotation>
<xsd:documentation>The derived Type for QualityParameter container of a Set</xsd:documentation>
</xsd:annotation>
<xsd:complexContent>
<xsd:extension base="qualityAssessmentType"/>
</xsd:complexContent>
</xsd:complexType>
<xsd:simpleType name="listOfStrings">
<xsd:list itemType="xsd:string"/>
</xsd:simpleType>
<xsd:simpleType name="listOfDoubles">
<xsd:list itemType="xsd:double"/>
</xsd:simpleType>
<xsd:simpleType name="listOfDoublesOrNulls">
<xsd:list itemType="doubleOrNullType"/>
</xsd:simpleType>
<xsd:simpleType name="doubleOrNullType">
<xsd:union memberTypes="xsd:double">
<xsd:simpleType>
<xsd:restriction base="xsd:token">
<xsd:enumeration value="null"/>
</xsd:restriction>
</xsd:simpleType>
</xsd:union>
</xsd:simpleType>
<xsd:simpleType name="versionRegex">
<xsd:restriction base="xsd:string">
<xsd:pattern value="(1\.1\.\d+)"/>
</xsd:restriction>
</xsd:simpleType>
<xsd:complexType name="abstractParamType" abstract="true">
<xsd:annotation>
<xsd:documentation>Abstract entity allowing either cvParam or userParam to be referenced in other schemas. </xsd:documentation>
</xsd:annotation>
<xsd:attribute name="name" type="xsd:string" use="required">
<xsd:annotation>
<xsd:documentation>The name of the cvTerm describing the parameter</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="description" type="xsd:string">
<xsd:annotation>
<xsd:documentation>Description of the parameter, containing information to allow the user interpreting the QC value.</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="value" type="xsd:string">
<xsd:annotation>
<xsd:documentation>The user-entered value of the parameter, e.g. ppm value of accuracy or the file name</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="unitAccession" type="xsd:string">
<xsd:annotation>
<xsd:documentation>The accession number identifying the unit within the OBO foundry Unit CV</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="unitName" type="xsd:string">
<xsd:annotation>
<xsd:documentation>The name of the unit corresponding to the value</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="unitCvRef" type="xsd:IDREF">
<xsd:annotation>
<xsd:documentation>If a unit term is used, this attribute must refer to the corresponding CV 'id' attribute defined in the cvList in this file</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:complexType>
<xsd:complexType name="attachmentType">
<xsd:annotation>
<xsd:documentation>A single attachment containing binary data or a table. The cvParam contains the description fitting to rhe referenced quality parameter. The MIME type is given in unit of the cv.</xsd:documentation>
</xsd:annotation>
<xsd:complexContent>
<xsd:extension base="cvParamType">
<xsd:choice>
<xsd:element name="binary" type="xsd:base64Binary">
<xsd:annotation>
<xsd:documentation>Contains the base64 binary for attached PNG plots</xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="table" type="tableType">
<xsd:annotation>
<xsd:documentation>Describes a table of values to be attached</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:choice>
<xsd:attribute name="ID" type="xsd:ID" use="required">
<xsd:annotation>
<xsd:documentation>A file unique identifier for this attachment element</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="qualityParameterRef" type="xsd:IDREF">
<xsd:annotation>
<xsd:documentation>This attribute should refer to the qualityParameter this attachment belongs to (if any)</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
<xsd:complexType name="tableType">
<xsd:sequence>
<xsd:element name="tableColumnTypes" type="listOfStrings">
<xsd:annotation>
<xsd:documentation>Containes either the names or accessions of cvTerms following in that order in each tableRowValues (space separated) </xsd:documentation>
</xsd:annotation>
</xsd:element>
<xsd:element name="tableRowValues" type="listOfStrings" maxOccurs="unbounded">
<xsd:annotation>
<xsd:documentation>Containes the values in the order given in tableColumnTypes (space separated)</xsd:documentation>
</xsd:annotation>
</xsd:element>
</xsd:sequence>
</xsd:complexType>
<xsd:complexType name="qualityParameterType">
<xsd:annotation>
<xsd:documentation>A quality parameter contains a value and a cv, as well as a optional threshold element</xsd:documentation>
</xsd:annotation>
<xsd:complexContent>
<xsd:extension base="cvParamType">
<xsd:sequence minOccurs="0">
<xsd:element name="threshold" maxOccurs="unbounded">
<xsd:annotation>
<xsd:documentation>Can be used (suggested in an separate file) to define thresholds to certain qualityParameters</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:complexContent>
<xsd:extension base="cvParamType">
<xsd:attribute name="thresholdFilename" type="xsd:string"/>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
</xsd:element>
</xsd:sequence>
<xsd:attribute name="ID" type="xsd:ID" use="required">
<xsd:annotation>
<xsd:documentation>A file unique identifier for this qualityParameter element</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="flag" type="xsd:boolean">
<xsd:annotation>
<xsd:documentation>Indicates if this qualityParameter has passed a given threshold</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
<xsd:complexType name="cvParamType">
<xsd:annotation>
<xsd:documentation>A single entry from an ontology or a controlled vocabulary.</xsd:documentation>
</xsd:annotation>
<xsd:complexContent>
<xsd:extension base="abstractParamType">
<xsd:attribute name="cvRef" type="xsd:IDREF" use="required">
<xsd:annotation>
<xsd:documentation>This attribute must refer to the corresponding CV 'id' attribute defined in the cvList in this file</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="accession" type="xsd:string" use="required">
<xsd:annotation>
<xsd:documentation>The accession number identifying the used cvTterm in the source CV</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:extension>
</xsd:complexContent>
</xsd:complexType>
<xsd:complexType name="cvType">
<xsd:annotation>
<xsd:documentation>A source controlled vocabulary from which cvParams will be obtained.</xsd:documentation>
</xsd:annotation>
<xsd:attribute name="fullName" type="xsd:string" use="required">
<xsd:annotation>
<xsd:documentation>The full name of the CV.</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="version" type="xsd:string">
<xsd:annotation>
<xsd:documentation>The version of the CV.</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="uri" type="xsd:anyURI" use="required">
<xsd:annotation>
<xsd:documentation>The URI of the source CV.</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="ID" type="xsd:ID" use="required">
<xsd:annotation>
<xsd:documentation>The unique identifier of this cv within the document to be referenced by cvParam elements. </xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:complexType>
<xsd:complexType name="metaDataType">
<xsd:annotation>
<xsd:documentation>A meta data annotation CV element.</xsd:documentation>
</xsd:annotation>
<xsd:attribute name="name" type="xsd:string" use="required">
<xsd:annotation>
<xsd:documentation>The name of the cvTerm describing the parameter</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="uri" type="xsd:anyURI">
<xsd:annotation>
<xsd:documentation>The URI of the source CV.</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="description" type="xsd:string">
<xsd:annotation>
<xsd:documentation>Description of the parameter, containing information to allow the user interpreting the QC value.</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="value" type="xsd:string">
<xsd:annotation>
<xsd:documentation>The user-entered value of the parameter if applicable.</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="cvRef" type="xsd:IDREF" use="required">
<xsd:annotation>
<xsd:documentation>This attribute must refer to the corresponding CV 'id' attribute defined in the cvList in this file</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="accession" type="xsd:string" use="required">
<xsd:annotation>
<xsd:documentation>The accession number identifying the used cvTterm in the source CV</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
<xsd:attribute name="ID" type="xsd:ID" use="required">
<xsd:annotation>
<xsd:documentation>A file unique identifier for this meta data element</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
</xsd:complexType>
</xsd:schema>