<?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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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 sequence 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/feature.xsd" />
  <xsd:include schemaLocation="http://preview.pharmgkb.org/schema/experiment.xsd" />



  <!-- referenceSequence -->
  <xsd:element name="referenceSequence">
    <xsd:annotation>
      <xsd:documentation>
      This class defines a reference sequence.
      See http://preview.pharmgkb.org/schema/docs/referenceSequence.html for details.
      </xsd:documentation>
      <xsd:appinfo>
        <sch:pattern name="Required elements for referenceSequence">
          <sch:rule context="pgkb:referenceSequence">
            <sch:report test="not(@pharmgkbId) and
            not(pgkb:dnaSequence)">Missing element:  dnaSequence</sch:report>
            <sch:report test="not(@pharmgkbId) and
            not(pgkb:dnaSequenceSource)">Missing element:  dnaSequenceSource</sch:report>
            <sch:report test="pgkb:dnaSequence and
            string-length(translate(pgkb:dnaSequence, 'AaBbCcDdGgHhKkMmNnTtUuRrSsVvWwYy ', '')) != 0">Invalid format:  dnaSequence must comply with the IUPAC codes</sch:report>
          </sch:rule>
        </sch:pattern>
        <sch:pattern name="Constraints for referenceSequenceXref">
          <sch:rule context="pgkb:referenceSequenceXref">
            <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:complexType>
      <xsd:complexContent>
        <xsd:extension base="AccessionObjectClass">
          <!-- subelements -->
          <xsd:sequence>
            <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
            <xsd:element name="organism" type="OrganismClass" minOccurs="0" maxOccurs="1" />
            <xsd:element name="geneXref" type="XrefClass" minOccurs="0" maxOccurs="1" />
            <!--
            XXX: this should use the IupacDnaSequenceType, but a bug in Xerces prevents us from doing so
            XXX: until the bug is fixed, we'll check for this using Schematron
            -->
            <xsd:element name="dnaSequence" minOccurs="0" maxOccurs="1">
              <xsd:simpleType>
                <xsd:restriction base="xsd:string">
                  <xsd:minLength value="100"/>
                </xsd:restriction>
              </xsd:simpleType>
            </xsd:element>
            <xsd:element name="dnaSequenceSource" minOccurs="0" maxOccurs="1">
              <xsd:simpleType>
                <xsd:restriction base="xsd:token">
                  <xsd:enumeration value="genomic" />
                  <xsd:enumeration value="cDNA" />
                  <xsd:enumeration value="mitochondria" />
                  <xsd:enumeration value="chloroplast" />
                </xsd:restriction>
              </xsd:simpleType>
            </xsd:element>
            <xsd:element name="xref" type="XrefClass" minOccurs="0" maxOccurs="unbounded" />
            <xsd:element name="featureSet" type="FeatureSetClass" minOccurs="0" maxOccurs="unbounded"/>
            <xsd:element name="experiment" type="ExperimentClass" minOccurs="0" maxOccurs="unbounded" />
          </xsd:sequence>
        </xsd:extension>
      </xsd:complexContent>
    </xsd:complexType>
  </xsd:element>

  <!-- polymorphism -->
  <xsd:element name="polymorphism">
    <xsd:annotation>
      <xsd:documentation>
      This class defines a polymorphism.
      See http://preview.pharmgkb.org/schema/docs/polymorphism.html for details.
      </xsd:documentation>
      <xsd:appinfo>
        <sch:pattern name="Required elements for polymorphism">
          <sch:rule context="pgkb:polymorphism">
            <!-- XXX: disable temporarily
            <sch:report test="not(@pharmgkbId) and
            not(pgkb:referenceSequenceXref)">Missing element:  referenceSequenceXref</sch:report>
            -->
          </sch:rule>
        </sch:pattern>
      </xsd:appinfo>
    </xsd:annotation>
    <xsd:complexType>
      <xsd:complexContent>
        <xsd:extension base="AccessionObjectClass">
          <xsd:sequence>
            <!-- subelements -->
            <xsd:element name="name" type="NonEmptyTokenType" minOccurs="0" maxOccurs="1" />
            <xsd:element name="geneXref" type="XrefClass" minOccurs="0" maxOccurs="1" />
            <xsd:element name="geneStructureXref" type="XrefClass" minOccurs="0" maxOccurs="1" />
            <xsd:element name="referenceSequenceXref" type="XrefClass" minOccurs="0" maxOccurs="1" />
            <xsd:element name="coordinateSystem" type="CoordinateSystemClass" minOccurs="0" maxOccurs="1" />
            <xsd:element name="allelePosition" type="xsd:integer" minOccurs="1" maxOccurs="1" />
            <xsd:element name="referenceAllele" type="DnaSequenceType" minOccurs="1" maxOccurs="1" />
            <xsd:element name="variantAllele" type="VariantDnaSequenceType" minOccurs="1" maxOccurs="1" />
            <xsd:element name="cDnaChange" minOccurs="0" maxOccurs="unbounded">
              <xsd:complexType>
                <xsd:sequence>
                  <xsd:element name="allelePosition" type="xsd:integer" minOccurs="1" maxOccurs="1" />
                  <xsd:element name="referenceAllele" type="VariantDnaSequenceType" minOccurs="1" maxOccurs="1" />
                  <xsd:element name="variantAllele" type="VariantDnaSequenceType" minOccurs="1" maxOccurs="1" />
                  <xsd:element name="isDerived" type="xsd:boolean" default="false" minOccurs="0" maxOccurs="1" />
                </xsd:sequence>
              </xsd:complexType>
            </xsd:element>
            <xsd:element name="proteinChange" type="ProteinChangeClass" minOccurs="0" maxOccurs="unbounded" />
            <xsd:element name="publishedAssayXref" type="XrefClass"  minOccurs="0" maxOccurs="unbounded" />
            <xsd:element name="xref" type="XrefClass"  minOccurs="0" maxOccurs="unbounded" />
          </xsd:sequence>
        </xsd:extension>
      </xsd:complexContent>
    </xsd:complexType>
  </xsd:element>


</xsd:schema>