<?xml version="1.0"?>
<!--
***** BEGIN LICENSE BLOCK *****
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The contents of this file are subject to the Mozilla Public License Version
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Software distributed under the License is distributed on an "AS IS" basis,
WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
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The Original Code is PharmGen.

The Initial Developer of the Original Code is
PharmGKB (The Pharmacogenetics and Pharmacogenetics Knowledge Base,
supported by NIH U01GM61374).
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the Initial Developer. All Rights Reserved.

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-->

<xsd:schema version="4.0"
  targetNamespace="http://www.pharmgkb.org/schema/"
  xmlns="http://www.pharmgkb.org/schema/"
  xmlns:xsd="http://www.w3.org/2001/XMLSchema"
  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xmlns:sch="http://www.ascc.net/xml/schematron"
  elementFormDefault="qualified">

  <xsd:annotation>
    <xsd:documentation>
      This XML schema defines all experiment related elements.
      For complete documentation, see http://www.pharmgkb.org/schema/.
    </xsd:documentation>
    <xsd:appinfo>
      <sch:pattern name="Constraints for assayXref">
        <sch:rule context="pgkb:assayXref">
          <sch:report test="not(@resource='PharmGKB') and not(@resource='local')">Resource attribute must be 'PharmGKB' or 'local'</sch:report>
          <sch:report test="@resource='PharmGKB' and
                            not((starts-with(., 'PA') and floor(substring(., 3))=number(substring(., 3))) or
                            floor(.)=number(.))">Cross-reference resource from PharmGKB does not appear to have a valid PharmGKB Accession ID</sch:report>
        </sch:rule>
      </sch:pattern>
    </xsd:appinfo>
  </xsd:annotation>


  <!-- Included XML Schema Files -->
  <xsd:include schemaLocation="http://www.pharmgkb.org/schema/types.xsd" />
  <xsd:include schemaLocation="http://www.pharmgkb.org/schema/types-sequence.xsd" />
  <xsd:include schemaLocation="http://www.pharmgkb.org/schema/sampleset.xsd" />



  <!-- ExperimentClass -->
  <xsd:complexType name="ExperimentClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines an experiment performed against a reference sequence.
        See http://www.pharmgkb.org/schema/docs/experiment.html for details.
      </xsd:documentation>
      <xsd:appinfo>
        <sch:pattern name="Required elements for ExperimentClass">
          <sch:rule context="pgkb:genotypesInSample/pgkb:sampleXref">
            <sch:report test="count(../../pgkb:genotypesInSample/pgkb:sampleXref[normalize-space() = normalize-space(current())]) > 1">genotypesInSample must point to unique samples within an experiment.  Duplicate sample referenced</sch:report>
          </sch:rule>
        </sch:pattern>
        <sch:pattern name="Constraints for experimentXref">
          <sch:rule context="pgkb:experimentXref">
            <sch:report test="not(@resource='PharmGKB') and not(@resource='local')">Resource attribute must be 'PharmGKB' or 'local'</sch:report>
            <sch:report test="@resource='PharmGKB' and
                              not((starts-with(., 'PA') and floor(substring(., 3))=number(substring(., 3))) or
                              floor(.)=number(.))">Cross-reference resource from PharmGKB does not appear to have a valid PharmGKB Accession ID</sch:report>
          </sch:rule>
        </sch:pattern>
      </xsd:appinfo>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
          <xsd:element name="coordinateSystem" type="CoordinateSystemClass" minOccurs="0" maxOccurs="1" />
          <xsd:choice minOccurs="1" maxOccurs="unbounded">
            <xsd:element name="dhplcAssay" type="DhplcAssayClass" />
            <xsd:element name="pcrSizingAssay" type="PcrSizingAssayClass" />
            <!-- sequencing assays -->
            <xsd:element name="sequencingAssay" type="SequencingAssayClass" />
            <xsd:element name="pcrAssay" type="PcrAssayClass" />
            <!-- genotyping assays -->
            <xsd:element name="genotypingAssay" type="GenotypingAssayClass" />
            <xsd:element name="pyrosequencingAssay" type="PyrosequencingAssayClass" />
            <xsd:element name="rflpAssay" type="RflpAssayClass" />
            <xsd:element name="taqmanAssay" type="TaqmanAssayClass" />
          </xsd:choice>
          <xsd:element name="sampleSetXref" type="XrefClass" minOccurs="1" maxOccurs="unbounded" />
          <xsd:choice minOccurs="1" maxOccurs="unbounded">
            <xsd:element name="genotypesInSample" type="GenotypesInSampleClass" minOccurs="0" maxOccurs="unbounded" />
            <xsd:element name="aggregatedGenotypes" type="AggregatedGenotypesClass" minOccurs="0" maxOccurs="unbounded" />
            <xsd:element name="pooledGenotypes" type="PooledGenotypesClass" minOccurs="0" maxOccurs="unbounded" />
          </xsd:choice>
          <xsd:element name="xref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- SequencingAssayClass -->
  <xsd:complexType name="SequencingAssayClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a sequencing assay.
        See http://www.pharmgkb.org/schema/docs/sequencingAssay.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="name" type="NonEmptyTokenType" minOccurs="1" maxOccurs="1" />
          <xsd:element name="analyzedRegion" type="RegionClass" minOccurs="1" maxOccurs="1" />
          <xsd:element name="referenceSequenceIsDefault" type="xsd:boolean" minOccurs="0" maxOccurs="1" default="true" />
          <xsd:element name="method" type="DbSnpMethodClass" minOccurs="1" maxOccurs="1" />
          <xsd:element name="xref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- GenotypingAssayClass -->
  <xsd:complexType name="GenotypingAssayClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a genotyping assay.
        See http://www.pharmgkb.org/schema/docs/genotypingAssay.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="name" type="NonEmptyTokenType" minOccurs="1" maxOccurs="1" />
          <xsd:element name="interrogatedPosition" type="xsd:integer" minOccurs="1" maxOccurs="1" />
          <xsd:element name="method" type="DbSnpMethodClass" minOccurs="1" maxOccurs="1" />
          <xsd:element name="xref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- PcrAssayClass -->
  <xsd:complexType name="PcrAssayClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a PCR assay.
        See http://www.pharmgkb.org/schema/docs/pcrAssay.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
          <xsd:element name="amplicon" type="RegionClass" minOccurs="1" maxOccurs="1" />
          <xsd:element name="forwardPrimer" type="PcrPrimerClass" minOccurs="0" maxOccurs="1" />
          <xsd:element name="reversePrimer" type="PcrPrimerClass" minOccurs="0" maxOccurs="1" />
          <xsd:element name="method" type="DbSnpMethodClass" minOccurs="1" maxOccurs="1" />
          <xsd:element name="xref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- PcrSizingAssayClass -->
  <xsd:complexType name="PcrSizingAssayClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a PCR sizing assay.
        See http://www.pharmgkb.org/schema/docs/pcrSizingAssay.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
          <xsd:element name="repeatedDnaSequence" type="DnaSequenceType" minOccurs="1" maxOccurs="1" />
          <xsd:element name="analyzedRegion" type="RegionClass" minOccurs="1" maxOccurs="1" />
          <xsd:element name="forwardPrimer" type="PcrPrimerClass" minOccurs="0" maxOccurs="1" />
          <xsd:element name="reversePrimer" type="PcrPrimerClass" minOccurs="0" maxOccurs="1" />
          <xsd:element name="method" type="DbSnpMethodClass" minOccurs="1" maxOccurs="1" />
          <xsd:element name="xref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- PcrPrimerClass -->
  <xsd:complexType name="PcrPrimerClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a PCR Primer.
        See http://www.pharmgkb.org/schema/docs/pcrPrimer.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <!-- subelements -->
    <xsd:sequence>
      <xsd:element name="dnaSequence" type="DnaSequenceType" minOccurs="1" maxOccurs="1" />
      <xsd:element name="annealingRegionInPrimer" type="RegionClass" minOccurs="1" maxOccurs="1"/>
      <xsd:element name="annealingRegionInReferenceSequence" type="RegionClass" minOccurs="1" maxOccurs="1" />
    </xsd:sequence>
  </xsd:complexType>


  <!-- PyrosequencingAssayClass -->
  <xsd:complexType name="PyrosequencingAssayClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a pyrosequencing assay.
        See http://www.pharmgkb.org/schema/docs/pyrosequencingAssay.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
          <xsd:element name="interrogatedPosition" type="xsd:integer" minOccurs="1" maxOccurs="1" />
          <xsd:element name="analyzedRegion" type="RegionClass" minOccurs="0" maxOccurs="1" />
          <xsd:element name="forwardPrimer" type="PcrPrimerClass" minOccurs="0" maxOccurs="1" />
          <xsd:element name="reversePrimer" type="PcrPrimerClass" minOccurs="0" maxOccurs="1" />
          <xsd:element name="pyrosequencingPrimer" minOccurs="1" maxOccurs="1">
            <xsd:complexType>
              <xsd:sequence>
                <xsd:element name="dnaSequence" type="DnaSequenceType" minOccurs="1" maxOccurs="1" />
                <xsd:element name="orientation" minOccurs="1" maxOccurs="1">
                  <xsd:simpleType>
                    <xsd:restriction base="xsd:token">
                      <xsd:enumeration value="forward" />
                      <xsd:enumeration value="reverse" />
                    </xsd:restriction>
                  </xsd:simpleType>
                </xsd:element>
              </xsd:sequence>
            </xsd:complexType>
          </xsd:element>
          <xsd:element name="method" type="DbSnpMethodClass" minOccurs="1" maxOccurs="1" />
          <xsd:element name="xref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- TaqmanAssayClass -->
  <xsd:complexType name="TaqmanAssayClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a TaqMan assay.
        See http://www.pharmgkb.org/schema/docs/taqmanAssay.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
          <xsd:element name="interrogatedPosition" type="xsd:integer" minOccurs="1" maxOccurs="1" />
          <xsd:element name="forwardPrimer" type="PcrPrimerClass" minOccurs="0" maxOccurs="1" />
          <xsd:element name="reversePrimer" type="PcrPrimerClass" minOccurs="0" maxOccurs="1" />
          <xsd:element name="referenceProbe" type="TaqmanProbeClass" minOccurs="0" maxOccurs="1" />
          <xsd:element name="variantProbe" type="TaqmanProbeClass" minOccurs="0" maxOccurs="1" />
          <xsd:element name="method" type="DbSnpMethodClass" minOccurs="1" maxOccurs="1" />
          <xsd:element name="xref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- TaqmanProbeClass -->
  <xsd:complexType name="TaqmanProbeClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a probe used in a TaqMan assay.
        See http://www.pharmgkb.org/schema/docs/taqmanProbe.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <!-- subelements -->
    <xsd:sequence>
      <xsd:element name="dye" type="xsd:token" minOccurs="1" maxOccurs="1" />
      <xsd:element name="dnaSequence" type="DnaSequenceType" minOccurs="1" maxOccurs="1" />
      <xsd:element name="targetGenotype" type="DnaSequenceType" minOccurs="1" maxOccurs="1" />
    </xsd:sequence>
  </xsd:complexType>


  <!-- RflpAssayClass -->
  <xsd:complexType name="RflpAssayClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines an RFLP assay.
        See http://www.pharmgkb.org/schema/docs/rflpAssay.html for details.
      </xsd:documentation>
      <xsd:appinfo>
        <sch:pattern name="Required elements for RflpAssayClass">
          <sch:rule context="pgkb:rflpAssay">
            <sch:report test="pgkb:targetGenotype and
                              string-length(normalize-space(pgkb:targetGenotype)) != 1">targetGenotype must be a single base</sch:report>
          </sch:rule>
        </sch:pattern>
      </xsd:appinfo>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
          <xsd:element name="interrogatedPosition" type="xsd:integer" minOccurs="1" maxOccurs="1" />
          <xsd:element name="targetGenotype" type="DnaSequenceType" minOccurs="1" maxOccurs="1" />
          <xsd:element name="method" type="DbSnpMethodClass" minOccurs="1" maxOccurs="1" />
          <xsd:element name="xref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- DhplcAssayClass -->
  <xsd:complexType name="DhplcAssayClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a DHPLC assay.
        See http://www.pharmgkb.org/schema/docs/dhplcAssay.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
          <xsd:element name="analyzedRegion" type="RegionClass" minOccurs="1" maxOccurs="1" />
          <xsd:element name="poolSize" type="xsd:positiveInteger" minOccurs="1" maxOccurs="1" />
          <xsd:element name="baselineSampleSize" type="xsd:positiveInteger" minOccurs="1" maxOccurs="1" />
          <xsd:element name="method" type="DbSnpMethodClass" minOccurs="1" maxOccurs="1" />
          <xsd:element name="xref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- DbSnpMethodClass -->
  <xsd:complexType name="DbSnpMethodClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines an experimental method.
        See http://www.pharmgkb.org/schema/docs/method.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <!-- subelements -->
    <xsd:sequence>
      <xsd:element name="name" type="NonEmptyTokenType" minOccurs="1" maxOccurs="1" />
      <xsd:element name="type" minOccurs="1" maxOccurs="1">
        <xsd:simpleType>
          <xsd:restriction base="xsd:token">
            <xsd:enumeration value="Computation" />
            <xsd:enumeration value="DHPLC" />
            <xsd:enumeration value="Hybridization" />
            <xsd:enumeration value="Sequence" />
            <xsd:enumeration value="SSCP" />
            <xsd:enumeration value="Other" />
            <xsd:enumeration value="Unknown" />
          </xsd:restriction>
        </xsd:simpleType>
      </xsd:element>
      <xsd:element name="templateType" minOccurs="1" maxOccurs="1">
        <xsd:simpleType>
          <xsd:restriction base="xsd:token">
            <xsd:enumeration value="Diploid" />
            <xsd:enumeration value="Clone" />
            <xsd:enumeration value="Other" />
            <xsd:enumeration value="Unknown" />
          </xsd:restriction>
        </xsd:simpleType>
      </xsd:element>
      <xsd:element name="multPcrAmplificationTested" type="BooleanUnknownNaType" minOccurs="1" maxOccurs="1" />
      <xsd:element name="multClonesTested" type="BooleanUnknownNaType" minOccurs="1" maxOccurs="1" />
      <xsd:element name="description" type="xsd:string" minOccurs="1" maxOccurs="1"/>
      <xsd:element name="parameters" type="xsd:string" minOccurs="1" maxOccurs="1" />
      <xsd:element name="protocol" type="ProtocolClass" minOccurs="0" maxOccurs="1" />
      <xsd:element name="buffer" type="BufferClass" minOccurs="0" maxOccurs="1" />
    </xsd:sequence>
  </xsd:complexType>


  <!-- MethodClass -->
  <xsd:complexType name="MethodClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines an experimental method.
        See http://www.pharmgkb.org/schema/docs/method.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <!-- subelements -->
    <xsd:sequence>
      <xsd:element name="name" type="NonEmptyTokenType" minOccurs="1" maxOccurs="1" />
      <xsd:element name="description" type="xsd:string" minOccurs="0" maxOccurs="1"/>
      <xsd:element name="parameters" type="xsd:string" minOccurs="0" maxOccurs="1" />
      <xsd:element name="protocol" type="ProtocolClass" minOccurs="0" maxOccurs="1" />
      <xsd:element name="buffer" type="BufferClass" minOccurs="0" maxOccurs="1" />
    </xsd:sequence>
  </xsd:complexType>


  <!-- ProtocolClass -->
  <xsd:complexType name="ProtocolClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a protocol.
        See http://www.pharmgkb.org/schema/docs/protocol.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <!-- subelements -->
    <xsd:sequence>
      <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
      <xsd:element name="description" type="xsd:string" minOccurs="0" maxOccurs="1" />
    </xsd:sequence>
  </xsd:complexType>


  <!-- BufferClass -->
  <xsd:complexType name="BufferClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a buffer.
        See http://www.pharmgkb.org/schema/docs/buffer.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <!-- subelements -->
    <xsd:sequence>
      <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
      <xsd:element name="description" type="xsd:string" minOccurs="0" maxOccurs="1" />
    </xsd:sequence>
  </xsd:complexType>


  <!-- VariantClass -->
  <xsd:complexType name="VariantClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a variant.
        See http://www.pharmgkb.org/schema/docs/variant.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="position" type="xsd:integer" minOccurs="1" maxOccurs="1" />
          <xsd:element name="allele" type="VariantDnaSequenceType" minOccurs="1" maxOccurs="unbounded" />
          <xsd:element name="xref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- DhplcResultClass -->
  <xsd:complexType name="DhplcResultClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines the results of a DHPLC assay.
        See http://www.pharmgkb.org/schema/docs/dhplcResult.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- elemenets -->
        <xsd:sequence>
          <xsd:element name="assayXref" type="XrefClass" minOccurs="1" maxOccurs="1" />
          <xsd:choice minOccurs="1" maxOccurs="1">
            <xsd:element name="noResult" />
            <xsd:element name="sameAsMajority" type="xsd:boolean" />
          </xsd:choice>
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- SequencingResultClass -->
  <xsd:complexType name="SequencingResultClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines the results of a sequencing assay.
        See http://www.pharmgkb.org/schema/docs/sequencingResult.html for details.
      </xsd:documentation>
      <xsd:appinfo>
        <sch:pattern name="Required elements for SequencingResultClass">
          <sch:rule context="pgkb:sequencingResult">
            <sch:report test="not(@pharmgkbId) and
                              pgkb:interrogatedRange and
                              not(pgkb:interrogatedRange/pgkb:forwardRead) and
                              not(pgkb:interrogatedRange/pgkb:reverseRead)">Missing element:  at least one forwardRead or reverseRead in interrogatedRange</sch:report>
          </sch:rule>
        </sch:pattern>
      </xsd:appinfo>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="assayXref" type="XrefClass" minOccurs="1" maxOccurs="1" />
          <xsd:element name="interrogatedRange" minOccurs="0" maxOccurs="unbounded">
            <xsd:complexType>
              <xsd:sequence>
                <xsd:element name="forwardRead" type="RegionClass" minOccurs="0" maxOccurs="1" />
                <xsd:element name="reverseRead" type="RegionClass" minOccurs="0" maxOccurs="1" />
              </xsd:sequence>
            </xsd:complexType>
          </xsd:element>
          <xsd:element name="sequencedBothStrands" type="xsd:boolean" minOccurs="0" maxOccurs="1" default="false" />
          <xsd:choice minOccurs="1" maxOccurs="1">
            <xsd:element name="noResult" />
            <xsd:element name="variant" type="VariantClass" minOccurs="0" maxOccurs="unbounded" />
          </xsd:choice>
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- GenotypingResultClass -->
  <xsd:complexType name="GenotypingResultClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines the result of a genotyping assay.
        See http://www.pharmgkb.org/schema/docs/genotypingResult.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="assayXref" type="XrefClass" minOccurs="1" maxOccurs="1" />
          <xsd:choice minOccurs="1" maxOccurs="1">
            <xsd:element name="noResult" />
            <xsd:element name="variant" type="VariantClass" />
          </xsd:choice>
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- GenotypesInSampleClass -->
  <xsd:complexType name="GenotypesInSampleClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines the genotypes discovered in a sample.
        See http://www.pharmgkb.org/schema/docs/genotypesInSample.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="sampleXref" type="XrefClass" minOccurs="1" maxOccurs="1" />
          <xsd:choice minOccurs="1" maxOccurs="unbounded">
            <xsd:element name="dhplcResult" type="DhplcResultClass" />
            <xsd:element name="sequencingResult" type="SequencingResultClass" />
            <xsd:element name="genotypingResult" type="GenotypingResultClass" />
          </xsd:choice>
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>

  </xsd:complexType>


  <!-- AggregatedGenotypesClass -->
  <xsd:complexType name="AggregatedGenotypesClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a aggregated genotyping result.
        See http://www.pharmgkb.org/schema/docs/aggregatedGenotypes.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
          <xsd:element name="assayXref" type="XrefClass" minOccurs="1" maxOccurs="unbounded" />
          <xsd:element name="sampleXref" type="XrefClass" minOccurs="1" maxOccurs="unbounded" />
          <xsd:element name="observedVariant" type="ObservedVariantClass" minOccurs="1" maxOccurs="unbounded" />
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- ObservedVariantClass -->
  <xsd:complexType name="ObservedVariantClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a variant observed in a aggregated genotyping result.
        See http://www.pharmgkb.org/schema/docs/observedVariant.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="VariantClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="numberObserved" type="xsd:nonNegativeInteger" minOccurs="1" maxOccurs="1" />
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- PooledGenotypesClass -->
  <xsd:complexType name="PooledGenotypesClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a pooled genotyping result.
        See http://www.pharmgkb.org/schema/docs/pooledGenotypes.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
          <xsd:element name="assayXref" type="XrefClass" minOccurs="1" maxOccurs="1" />
          <xsd:element name="sampleXref" type="XrefClass" minOccurs="1" maxOccurs="unbounded" />
          <xsd:element name="variant" type="VariantClass" minOccurs="1" maxOccurs="unbounded" />
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- regionCopyAssay -->
  <xsd:element name="regionCopyAssay">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a region copy assay.
        See http://www.pharmgkb.org/schema/docs/regionCopyAssay.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexType>
      <xsd:complexContent>
        <xsd:extension base="AccessionObjectClass">
          <!-- subelements -->
          <xsd:sequence>
            <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
            <xsd:element name="method" type="MethodClass" minOccurs="1" maxOccurs="1" />
            <xsd:element name="isQuantitative" type="xsd:boolean" default="true" minOccurs="0" maxOccurs="1" />
            <xsd:element name="organism" type="OrganismClass" minOccurs="1" maxOccurs="1" />
            <xsd:element name="chromosome" type="ChromosomeType" minOccurs="1" maxOccurs="1"/>
            <xsd:element name="sampleSetXref" type="XrefClass" minOccurs="1" maxOccurs="unbounded" />
            <xsd:element name="regionCopyResult" type="RegionCopyResultClass" minOccurs="1" maxOccurs="unbounded" />
            <xsd:element name="xref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
          </xsd:sequence>
        </xsd:extension>
      </xsd:complexContent>
    </xsd:complexType>
  </xsd:element>

  <!-- RegionCopyResultClass -->
  <xsd:complexType name="RegionCopyResultClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a region copy assay result.
        See http://www.pharmgkb.org/schema/docs/regionCopyResult.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="sampleXref" type="XrefClass" minOccurs="1" maxOccurs="1" />
          <xsd:choice minOccurs="1" maxOccurs="1">
            <xsd:element name="noResult" />
            <xsd:sequence>
              <xsd:element name="totalCopies" type="NonNegativeIntegerOrNType" minOccurs="1" maxOccurs="1" />
              <xsd:element name="region" minOccurs="1" maxOccurs="unbounded">
                <xsd:simpleType>
                  <xsd:restriction base="xsd:token">
                    <xsd:minLength value="1" />
                    <xsd:maxLength value="3" />
                    <xsd:pattern value="([pq][0-9]+\-?)|([pq][0-9]+\-[pq][0-9]+)" />
                  </xsd:restriction>
                </xsd:simpleType>
              </xsd:element>
            </xsd:sequence>
          </xsd:choice>
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- translocationAssay -->
  <xsd:element name="translocationAssay">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a translocation assay.
        See http://www.pharmgkb.org/schema/docs/translocationAssay.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexType>
      <xsd:complexContent>
        <xsd:extension base="AccessionObjectClass">
          <!-- subelements -->
          <xsd:sequence>
            <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
            <xsd:element name="method" type="MethodClass" minOccurs="1" maxOccurs="1" />
            <xsd:element name="sampleSetXref" type="XrefClass" minOccurs="1" maxOccurs="unbounded" />
            <xsd:element name="translocationResult" type="TranslocationResultClass" minOccurs="1" maxOccurs="unbounded" />
            <xsd:element name="xref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
          </xsd:sequence>
        </xsd:extension>
      </xsd:complexContent>
    </xsd:complexType>
  </xsd:element>

  <!-- TranslocationResultClass -->
  <xsd:complexType name="TranslocationResultClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a translocation assay result.
        See http://www.pharmgkb.org/schema/docs/translocationResult.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="sampleXref" type="XrefClass" minOccurs="1" maxOccurs="1" />
          <xsd:choice minOccurs="1" maxOccurs="1">
            <xsd:element name="noResult" />
            <xsd:element name="translocation" minOccurs="0" maxOccurs="1">
              <xsd:simpleType>
                <xsd:restriction base="xsd:token">
                  <xsd:minLength value="13" />
                  <xsd:pattern value="t\(([0-9]+)|([XY]);([0-9]+)|([XY])\)\([pq][0-9]+;[pq][0-9]+\)" />
                </xsd:restriction>
              </xsd:simpleType>
            </xsd:element>
          </xsd:choice>
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- CopiesPerSourceClass -->
  <xsd:complexType name="CopiesPerSourceClass">
    <xsd:sequence>
      <xsd:element name="numCopies" type="xsd:nonNegativeInteger" minOccurs="1" maxOccurs="1" />
      <xsd:element name="source">
        <xsd:simpleType>
          <xsd:restriction base="xsd:token">
            <xsd:enumeration value="maternal"/>
            <xsd:enumeration value="paternal"/>
            <xsd:enumeration value="A"/>
            <xsd:enumeration value="B"/>
          </xsd:restriction>
        </xsd:simpleType>
      </xsd:element>
    </xsd:sequence>
  </xsd:complexType>


  <!-- geneCopyAssay -->
  <xsd:element name="geneCopyAssay">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a gene copy assay.
        See http://www.pharmgkb.org/schema/docs/geneCopyAssay.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexType>
      <xsd:complexContent>
        <xsd:extension base="AccessionObjectClass">
          <!-- subelements -->
          <xsd:sequence>
            <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
            <xsd:element name="method" type="MethodClass" minOccurs="1" maxOccurs="1" />
            <xsd:element name="isQuantitative" type="xsd:boolean" default="true" minOccurs="0" maxOccurs="1" />
            <xsd:element name="geneXref" type="XrefClass" minOccurs="1" maxOccurs="1" />
            <xsd:element name="sampleSetXref" type="XrefClass" minOccurs="1" maxOccurs="unbounded" />
            <xsd:element name="geneCopyResult" type="GeneCopyResultClass" minOccurs="1" maxOccurs="unbounded" />
            <xsd:element name="xref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
          </xsd:sequence>
        </xsd:extension>
      </xsd:complexContent>
    </xsd:complexType>
  </xsd:element>

  <!-- GeneCopyResultClass -->
  <xsd:complexType name="GeneCopyResultClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a gene copy assay result.
        See http://www.pharmgkb.org/schema/docs/geneCopyResult.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="sampleXref" type="XrefClass" minOccurs="1" maxOccurs="1" />
          <xsd:choice minOccurs="1" maxOccurs="1">
            <xsd:element name="noResult" />
            <xsd:sequence>
              <xsd:element name="totalCopies" type="NonNegativeIntegerOrNType" minOccurs="1" maxOccurs="1" />
              <xsd:element name="geneCopy" type="GeneCopyClass" minOccurs="0" maxOccurs="unbounded" />
            </xsd:sequence>
          </xsd:choice>
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>

  <!-- GeneCopyClass -->
  <xsd:complexType name="GeneCopyClass">
    <xsd:sequence>
      <xsd:element name="copyNumber" minOccurs="1" maxOccurs="1"/>
      <xsd:element name="source" type="CopiesPerSourceClass" minOccurs="0" maxOccurs="4" />
      <xsd:element name="referenceSequenceXref" type="XrefClass" minOccurs="0" maxOccurs="1" />
    </xsd:sequence>
  </xsd:complexType>


  <!-- chromosomeCopyAssay -->
  <xsd:element name="chromosomeCopyAssay">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a chromosome copy assay.
        See http://www.pharmgkb.org/schema/docs/chromosomeCopyAssay.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexType>
      <xsd:complexContent>
        <xsd:extension base="AccessionObjectClass">
          <!-- subelements -->
          <xsd:sequence>
            <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
            <xsd:element name="method" type="MethodClass" minOccurs="1" maxOccurs="1" />
            <xsd:element name="isQuantitative" type="xsd:boolean" default="true" minOccurs="0" maxOccurs="1" />
            <xsd:element name="organism" type="OrganismClass" minOccurs="1" maxOccurs="1" />
            <xsd:element name="chromosome" type="ChromosomeType" minOccurs="1" maxOccurs="1"/>
            <xsd:element name="sampleSetXref" type="XrefClass" minOccurs="1" maxOccurs="unbounded" />
            <xsd:element name="chromosomeCopyResult" type="ChromosomeCopyResultClass" minOccurs="1" maxOccurs="unbounded" />
            <xsd:element name="xref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
          </xsd:sequence>
        </xsd:extension>
      </xsd:complexContent>
    </xsd:complexType>
  </xsd:element>

  <!-- ChromosomeCopyResultClass -->
  <xsd:complexType name="ChromosomeCopyResultClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a chromosome copy assay result.
        See http://www.pharmgkb.org/schema/docs/chromosomeCopyResult.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexContent>
      <xsd:extension base="AccessionObjectClass">
        <!-- subelements -->
        <xsd:sequence>
          <xsd:element name="sampleXref" type="XrefClass" minOccurs="1" maxOccurs="1" />
          <xsd:choice minOccurs="1" maxOccurs="1">
            <xsd:element name="noResult" />
            <xsd:sequence>
              <xsd:element name="totalCopies" type="NonNegativeIntegerOrNType" minOccurs="1" maxOccurs="1" />
              <xsd:element name="source" type="CopiesPerSourceClass" minOccurs="0" maxOccurs="4" />
            </xsd:sequence>
          </xsd:choice>
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


  <!-- SnpArrayExperiment -->
  <xsd:element name="snpArrayExperiment">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a SNP array assay run.
        See http://www.pharmgkb.org/schema/docs/snpArrayExperiment.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <xsd:complexType>
      <xsd:complexContent>
        <xsd:extension base="AccessionObjectClass">
          <!-- subelements -->
          <xsd:sequence>
            <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
            <xsd:element name="platform" minOccurs="1" maxOccurs="1">
              <xsd:simpleType>
                <xsd:restriction base="xsd:token">
                  <xsd:enumeration value="Affymetrix" />
                  <xsd:enumeration value="Illumina" />
                </xsd:restriction>
              </xsd:simpleType>
            </xsd:element>
            <xsd:element name="platformType" type="NonEmptyTokenType" minOccurs="1" maxOccurs="1" />
            <xsd:element name="isCustomType" type="NonEmptyTokenType" minOccurs="1" maxOccurs="1" />
            <xsd:element name="numberOfPositions" type="NonEmptyStringType" minOccurs="1" maxOccurs="1" />
            <xsd:element name="rsIds" type="NonEmptyTokenType" minOccurs="1" maxOccurs="1" />
            <xsd:element name="method" type="MethodClass" minOccurs="1" maxOccurs="1" />
            <xsd:element name="description" type="NonEmptyStringType" minOccurs="0" maxOccurs="1" />
            <xsd:element name="category" type="NonEmptyStringType" minOccurs="0" maxOccurs="1" />
            <xsd:element name="subcategory" type="NonEmptyStringType" minOccurs="0" maxOccurs="1" />
            <xsd:element name="drugXref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
            <xsd:element name="diseaseXref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
            <xsd:element name="knowledgeCategory" type="PharmacogeneticKnowledgeCategoryEnum" minOccurs="0" maxOccurs="5" />
            <xsd:element name="sampleXref" type="XrefClass" minOccurs="1" maxOccurs="unbounded" />
            <xsd:element name="xref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
          </xsd:sequence>
        </xsd:extension>
      </xsd:complexContent>
    </xsd:complexType>
  </xsd:element>

</xsd:schema>