PacBioDatasets

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<!-- edited with XMLSpy v2015 rel. 3 sp1 (x64) (http://www.altova.com) by Lakhvir Rai (Pacific Biosciences) -->
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<xs:schema xmlns="http://pacificbiosciences.com/PacBioDatasets.xsd" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" xmlns:pbmeta="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd" xmlns:pbsample="http://pacificbiosciences.com/PacBioSampleInfo.xsd" targetNamespace="http://pacificbiosciences.com/PacBioDatasets.xsd" elementFormDefault="qualified" id="PacBioDatasets">
  <xs:import namespace="http://pacificbiosciences.com/PacBioBaseDataModel.xsd" schemaLocation="PacBioBaseDataModel.xsd"/>
  <xs:import namespace="http://pacificbiosciences.com/PacBioCollectionMetadata.xsd" schemaLocation="PacBioCollectionMetadata.xsd"/>
  <xs:import namespace="http://pacificbiosciences.com/PacBioSampleInfo.xsd" schemaLocation="PacBioSampleInfo.xsd"/>
  <xs:element name="AlignmentSet">
    <xs:annotation>
      <xs:documentation>DataSets for aligned subreads and CCS reads.</xs:documentation>
    </xs:annotation>
    <xs:complexType>
      <xs:complexContent>
        <xs:extension base="AlignmentSetType"/>
      </xs:complexContent>
    </xs:complexType>
  </xs:element>
  <xs:element name="BarcodeSet">
    <xs:annotation>
      <xs:documentation>DataSets of Barcodes. Basically a thin metadata layer on top of the barcode FASTA.</xs:documentation>
    </xs:annotation>
    <xs:complexType>
      <xs:complexContent>
        <xs:extension base="BarcodeSetType"/>
      </xs:complexContent>
    </xs:complexType>
  </xs:element>
  <xs:element name="ConsensusAlignmentSet">
    <xs:annotation>
      <xs:documentation>DataSets of aligned CCS reads.</xs:documentation>
    </xs:annotation>
    <xs:complexType>
      <xs:complexContent>
        <xs:extension base="AlignmentSetType"/>
      </xs:complexContent>
    </xs:complexType>
  </xs:element>
  <xs:element name="TranscriptAlignmentSet">
    <xs:annotation>
      <xs:documentation>DataSets of aligned RNA transcripts.</xs:documentation>
    </xs:annotation>
    <xs:complexType>
      <xs:complexContent>
        <xs:extension base="AlignmentSetType"/>
      </xs:complexContent>
    </xs:complexType>
  </xs:element>
  <xs:element name="ConsensusReadSet">
    <xs:annotation>
      <xs:documentation>DataSets of CCS reads (typically in unaligned BAM format).</xs:documentation>
    </xs:annotation>
    <xs:complexType>
      <xs:complexContent>
        <xs:extension base="ReadSetType"/>
      </xs:complexContent>
    </xs:complexType>
  </xs:element>
  <xs:element name="TranscriptSet">
    <xs:annotation>
      <xs:documentation>DataSet for processed Iso-Seq transcripts.</xs:documentation>
    </xs:annotation>
    <xs:complexType>
      <xs:complexContent>
        <xs:extension base="TranscriptSetType"/>
      </xs:complexContent>
    </xs:complexType>
  </xs:element>
  <xs:element name="Contigs">
    <xs:annotation>
      <xs:documentation>DEPRECATED List of contigs in a ContigSet; optional and will be removed in the future</xs:documentation>
    </xs:annotation>
    <xs:complexType>
      <xs:complexContent>
        <xs:extension base="pbbase:BaseEntityType">
          <xs:sequence>
            <xs:element name="Contig" minOccurs="0" maxOccurs="unbounded">
              <xs:complexType>
                <xs:complexContent>
                  <xs:extension base="pbbase:BaseEntityType">
                    <xs:attribute name="Length" use="required"/>
                    <xs:attribute name="Digest" use="required"/>
                  </xs:extension>
                </xs:complexContent>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
        </xs:extension>
      </xs:complexContent>
    </xs:complexType>
  </xs:element>
  <xs:element name="ContigSet">
    <xs:annotation>
      <xs:documentation>DataSets of contigs sequences. Basically a thin metadata layer on top of a contigs FASTA (e.g. from HGAP).</xs:documentation>
    </xs:annotation>
    <xs:complexType>
      <xs:complexContent>
        <xs:extension base="ContigSetType"/>
      </xs:complexContent>
    </xs:complexType>
  </xs:element>
  <xs:element name="DataSet" type="DataSetType"/>
  <xs:element name="DataSetRoot" type="DataSetRootType"/>
  <xs:element name="HdfSubreadSet">
    <xs:annotation>
      <xs:documentation>DataSets of subreads in bax.h5 or bas.h5 format.</xs:documentation>
    </xs:annotation>
    <xs:complexType>
      <xs:complexContent>
        <xs:extension base="ReadSetType"/>
      </xs:complexContent>
    </xs:complexType>
  </xs:element>
  <xs:element name="ReferenceSet">
    <xs:annotation>
      <xs:documentation>DataSets of reference sequences. Replaces the reference.info.xml.</xs:documentation>
    </xs:annotation>
    <xs:complexType>
      <xs:complexContent>
        <xs:extension base="ContigSetType"/>
      </xs:complexContent>
    </xs:complexType>
  </xs:element>
  <xs:element name="GmapReferenceSet">
    <xs:annotation>
      <xs:documentation>DataSets of reference sequences, with GMAP indices.</xs:documentation>
    </xs:annotation>
    <xs:complexType>
      <xs:complexContent>
        <xs:extension base="ContigSetType"/>
      </xs:complexContent>
    </xs:complexType>
  </xs:element>
  <xs:element name="SubreadSet">
    <xs:complexType>
      <xs:complexContent>
        <xs:extension base="SubreadSetType"/>
      </xs:complexContent>
    </xs:complexType>
  </xs:element>
  <xs:element name="Subsets">
    <xs:complexType>
      <xs:sequence>
        <xs:element name="Subset" type="SubsetType" maxOccurs="unbounded"/>
      </xs:sequence>
    </xs:complexType>
  </xs:element>
  <xs:complexType name="AlignmentSetMetadataType">
    <xs:complexContent>
      <xs:extension base="DataSetMetadataType">
        <xs:sequence>
          <xs:element name="Aligner" minOccurs="0"/>
        </xs:sequence>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>
  <xs:complexType name="AlignmentSetType">
    <xs:annotation>
      <xs:documentation>Type for DataSets consisting of aligned subreads and CCS reads.</xs:documentation>
    </xs:annotation>
    <xs:complexContent>
      <xs:extension base="DataSetType">
        <xs:sequence>
          <xs:element name="DataSetMetadata" type="AlignmentSetMetadataType" minOccurs="0"/>
        </xs:sequence>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>
  <xs:complexType name="TranscriptSetType">
    <xs:annotation>
      <xs:documentation>Type for DataSets containing processed RNA transcripts</xs:documentation>
    </xs:annotation>
    <xs:complexContent>
      <xs:extension base="DataSetType">
        <xs:sequence>
          <xs:element name="DataSetMetadata" type="TranscriptSetMetadataType" minOccurs="0"/>
        </xs:sequence>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>
  <xs:complexType name="TranscriptSetMetadataType">
    <xs:complexContent>
      <xs:extension base="DataSetMetadataType"/>
    </xs:complexContent>
  </xs:complexType>
  <xs:complexType name="BarcodeSetMetadataType">
    <xs:complexContent>
      <xs:extension base="DataSetMetadataType">
        <xs:sequence>
          <xs:element name="BarcodeConstruction" type="xs:string"/>
        </xs:sequence>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>
  <xs:complexType name="BarcodeSetType">
    <xs:annotation>
      <xs:documentation>Type for the Barcode DataSet.</xs:documentation>
    </xs:annotation>
    <xs:complexContent>
      <xs:extension base="DataSetType">
        <xs:sequence>
          <xs:element name="DataSetMetadata" type="BarcodeSetMetadataType"/>
        </xs:sequence>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>
  <xs:complexType name="ContigSetMetadataType">
    <xs:complexContent>
      <xs:extension base="DataSetMetadataType">
        <xs:sequence>
          <xs:element name="Organism" type="xs:string" minOccurs="0"/>
          <xs:element name="Ploidy" type="xs:string" minOccurs="0"/>
          <xs:element ref="Contigs" minOccurs="0"/>
        </xs:sequence>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>
  <xs:complexType name="ContigSetType">
    <xs:annotation>
      <xs:documentation>Type for a Contig DataSet.</xs:documentation>
    </xs:annotation>
    <xs:complexContent>
      <xs:extension base="DataSetType">
        <xs:sequence>
          <xs:element name="DataSetMetadata" type="ContigSetMetadataType"/>
        </xs:sequence>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>
  <xs:complexType name="DataSetMetadataType">
    <xs:annotation>
      <xs:documentation>Extend this type to provide DataSetMetadata element in each DataSet.</xs:documentation>
    </xs:annotation>
    <xs:sequence>
      <xs:element name="TotalLength" type="xs:long"/>
      <xs:element name="NumRecords" type="xs:int"/>
      <xs:element name="Provenance" minOccurs="0">
        <xs:complexType>
          <xs:sequence>
            <xs:element name="CommonServicesInstanceId" type="xs:IDREF" minOccurs="0"/>
            <xs:element name="CreatorUserId" type="xs:IDREF" minOccurs="0"/>
            <xs:element name="ParentJobId" type="xs:IDREF" minOccurs="0"/>
            <xs:element name="ParentTool" type="pbbase:BaseEntityType" minOccurs="0"/>
            <xs:element name="ParentDataSet" type="pbbase:StrictEntityType" minOccurs="0"/>
          </xs:sequence>
          <xs:attribute name="CreatedBy" use="required">
            <xs:simpleType>
              <xs:restriction base="xs:string">
                <xs:enumeration value="Instrument"/>
                <xs:enumeration value="User"/>
                <xs:enumeration value="AnalysisJob"/>
              </xs:restriction>
            </xs:simpleType>
          </xs:attribute>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
  </xs:complexType>
  <xs:complexType name="DataSetRootType">
    <xs:choice>
      <xs:element ref="AlignmentSet" minOccurs="0"/>
      <xs:element ref="BarcodeSet" minOccurs="0"/>
      <xs:element ref="ConsensusAlignmentSet" minOccurs="0"/>
      <xs:element ref="ConsensusReadSet" minOccurs="0"/>
      <xs:element ref="ContigSet" minOccurs="0"/>
      <xs:element ref="HdfSubreadSet" minOccurs="0"/>
      <xs:element ref="ReferenceSet" minOccurs="0"/>
      <xs:element ref="SubreadSet" minOccurs="0"/>
      <xs:element ref="TranscriptSet" minOccurs="0"/>
      <xs:element ref="TranscriptAlignmentSet" minOccurs="0"/>
    </xs:choice>
  </xs:complexType>
  <xs:complexType name="DataSetType">
    <xs:complexContent>
      <xs:extension base="pbbase:StrictEntityType">
        <xs:sequence>
          <xs:element ref="pbbase:ExternalResources"/>
          <xs:element ref="pbbase:SupplementalResources" minOccurs="0"/>
          <xs:element name="Filters" minOccurs="0">
            <xs:annotation>
              <xs:documentation>The set of filters defined here apply to the resident data set.  Should DataSet subsets be created out of this parent DataSet, each sub-DataSet may contain its own filters.</xs:documentation>
            </xs:annotation>
            <xs:complexType>
              <xs:sequence>
                <xs:element name="Filter" type="pbbase:FilterType" maxOccurs="unbounded"/>
              </xs:sequence>
            </xs:complexType>
          </xs:element>
          <xs:element name="DataSets" minOccurs="0">
            <xs:complexType>
              <xs:sequence>
                <xs:element ref="DataSet" minOccurs="0" maxOccurs="unbounded"/>
              </xs:sequence>
            </xs:complexType>
          </xs:element>
        </xs:sequence>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>
  <xs:complexType name="ReadSetMetadataType">
    <xs:complexContent>
      <xs:extension base="DataSetMetadataType">
        <xs:sequence>
          <xs:element ref="pbsample:BioSamples" minOccurs="0"/>
          <xs:element ref="pbmeta:Collections" minOccurs="0"/>
          <xs:element name="SummaryStats" minOccurs="0">
            <xs:complexType>
              <xs:sequence>
                <xs:element name="AdapterDimerFraction" type="xs:float"/>
                <xs:element name="ShortInsertFraction" type="xs:float"/>
                <xs:element name="NumSequencingZmws" type="xs:int"/>
                <xs:element name="ProdDist" type="pbbase:StatsDiscreteDistType"/>
                <xs:element name="ReadTypeDist" type="pbbase:StatsDiscreteDistType"/>
                <xs:element name="ReadLenDist" type="pbbase:StatsContinuousDistType"/>
                <xs:element name="ReadQualDist" type="pbbase:StatsContinuousDistType"/>
                <xs:element name="ControlReadLenDist" type="pbbase:StatsContinuousDistType"/>
                <xs:element name="ControlReadQualDist" type="pbbase:StatsContinuousDistType"/>
                <xs:element name="MedianInsertDist" type="pbbase:StatsContinuousDistType"/>
                <xs:element name="InsertReadLenDist" type="pbbase:StatsContinuousDistType"/>
                <xs:element name="InsertReadQualDist" type="pbbase:StatsContinuousDistType"/>
              </xs:sequence>
            </xs:complexType>
          </xs:element>
        </xs:sequence>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>
  <xs:complexType name="ReadSetType">
    <xs:annotation>
      <xs:documentation>Type for DataSets consisting of unaligned subreads and CCS reads DataSets</xs:documentation>
    </xs:annotation>
    <xs:complexContent>
      <xs:extension base="DataSetType">
        <xs:sequence>
          <xs:element name="DataSetMetadata" type="ReadSetMetadataType" minOccurs="0"/>
        </xs:sequence>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>
  <xs:complexType name="SubreadSetMetadataType">
    <xs:complexContent>
      <xs:extension base="DataSetMetadataType">
        <xs:sequence>
          <xs:element name="AverageSubreadLength" type="xs:int"/>
          <xs:element name="AverageSubreadQuality" type="xs:float"/>
        </xs:sequence>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>
  <xs:complexType name="SubreadSetType">
    <xs:complexContent>
      <xs:extension base="ReadSetType"/>
    </xs:complexContent>
  </xs:complexType>
  <xs:complexType name="SubsetType">
    <xs:complexContent>
      <xs:extension base="pbbase:StrictEntityType">
        <xs:sequence>
          <xs:element name="Filters" minOccurs="0">
            <xs:annotation>
              <xs:documentation>The set of filters defined here apply to the resident data set.  Should DataSet subsets be created out of this parent DataSet, each sub-DataSet may contain its own filters.</xs:documentation>
            </xs:annotation>
            <xs:complexType>
              <xs:sequence>
                <xs:element name="Filter" type="pbbase:FilterType" maxOccurs="unbounded"/>
              </xs:sequence>
            </xs:complexType>
          </xs:element>
          <xs:element ref="pbbase:DataPointers" minOccurs="0"/>
        </xs:sequence>
      </xs:extension>
    </xs:complexContent>
  </xs:complexType>
</xs:schema>