<?xml version="1.0"?>
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The Original Code is PharmGen.

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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 haplotype related entities.
      For complete documentation, see http://preview.pharmgkb.org/schema/.
    </xsd:documentation>
  </xsd:annotation>


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


  <!-- haplotypeSet -->
  <xsd:element name="haplotypeSet">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a set of inferred haplotypes.
        See http://preview.pharmgkb.org/schema/docs/haplotypeSet.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="experimentXref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
            <xsd:element name="studyGroupXref" type="XrefClass" minOccurs="1" maxOccurs="unbounded" />
            <xsd:element name="analyzer" type="AnalyzerClass" minOccurs="1" maxOccurs="unbounded" />
            <xsd:element name="selectionProcess" type="xsd:string" minOccurs="1" maxOccurs="1" />
            <xsd:element name="haplotype" type="HaplotypeClass" minOccurs="1" maxOccurs="unbounded" />
            <xsd:element name="xref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
          </xsd:sequence>
        </xsd:extension>
      </xsd:complexContent>
    </xsd:complexType>
  </xsd:element>


  <!-- AnalyzerClass -->
  <xsd:complexType name="AnalyzerClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines an analyzer used to infer haplotypes.
        See http://preview.pharmgkb.org/schema/docs/analyzer.html for details.
      </xsd:documentation>
    </xsd:annotation>
    <!-- subelements -->
    <xsd:sequence>
      <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
      <xsd:element name="program">
        <xsd:simpleType>
          <xsd:restriction base="xsd:token">
            <xsd:enumeration value="Arlequin" />
            <xsd:enumeration value="EH" />
            <xsd:enumeration value="Hapgen" />
            <xsd:enumeration value="HAPLEA" />
            <xsd:enumeration value="HAPLO" />
            <xsd:enumeration value="Haplotyper" />
            <xsd:enumeration value="PHASE" />
            <xsd:enumeration value="SNPEM" />
          </xsd:restriction>
        </xsd:simpleType>
      </xsd:element>
      <xsd:element name="version" type="xsd:token" />
      <xsd:element name="parameters" type="xsd:string" />
    </xsd:sequence>
  </xsd:complexType>


  <!-- HaplotypeClass -->
  <xsd:complexType name="HaplotypeClass">
    <xsd:annotation>
      <xsd:documentation>
        This class defines a haplotype.
        See http://preview.pharmgkb.org/schema/docs/haplotype.html for details.
      </xsd:documentation>
      <xsd:appinfo>
        <sch:pattern name="Required elements for HaplotypeClass">
          <sch:rule context="pgkb:haplotype">
            <sch:report test="not(@pharmgkbId) and
                              not(pgkb:numberObserved) and
                              not(pgkb:subjectDetail)">Missing element:  either numberObserved or subjectDetail</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="polymorphismXref" type="XrefClass" minOccurs="1" maxOccurs="unbounded" />
          <xsd:element name="numberObserved" type="xsd:nonNegativeInteger" minOccurs="0" maxOccurs="1" />
          <xsd:element name="subjectDetail" minOccurs="0" maxOccurs="unbounded">
            <xsd:complexType>
              <xsd:sequence>
                <xsd:element name="subjectXref" type="XrefClass" />
                <xsd:element name="reliability" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
              </xsd:sequence>
            </xsd:complexType>
          </xsd:element>
        </xsd:sequence>
      </xsd:extension>
    </xsd:complexContent>
  </xsd:complexType>


</xsd:schema>