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Resource "Sequence" Version "1" (StructureDefinition)

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XML or JSON representation. Try out the Profile as a questionnaire based web form . Edit this as XML or JSON. provenance for this resource

Generated Narrative with Details

id: Sequence

meta:

url: http://hl7.org/fhir/StructureDefinition/Sequence

name: Sequence

status: draft

date: 10/24/2019 11:53:00 AM

publisher: Health Level Seven International (Clinical Genomics)

contact: ,

description: Base StructureDefinition for Sequence Resource

fhirVersion: 3.0.2

kind: resource

abstract: false

type: Sequence

baseDefinition: http://hl7.org/fhir/StructureDefinition/DomainResource

derivation: specialization


<?xml version="1.0" encoding="UTF-8"?>
<StructureDefinition xmlns="http://hl7.org/fhir">
  <id value="Sequence"/>
  <meta>
    <versionId value="1"/>
    <lastUpdated value="2020-11-06T21:33:44.486Z"/>
  </meta>
  <text>
    <status value="generated"/>
    <div xmlns="http://www.w3.org/1999/xhtml">
      <p>
        <b>Generated Narrative with Details</b>
      </p>
      <p>
        <b>id</b>: Sequence</p>
      <p>
        <b>meta</b>: </p>
      <p>
        <b>url</b>:
        <a href="http://hl7.org/fhir/StructureDefinition/Sequence">http://hl7.org/fhir/StructureDefinition/Sequence</a>
      </p>
      <p>
        <b>name</b>: Sequence</p>
      <p>
        <b>status</b>: draft</p>
      <p>
        <b>date</b>: 10/24/2019 11:53:00 AM</p>
      <p>
        <b>publisher</b>: Health Level Seven International (Clinical Genomics)</p>
      <p>
        <b>contact</b>: , </p>
      <p>
        <b>description</b>: Base StructureDefinition for Sequence Resource</p>
      <p>
        <b>fhirVersion</b>: 3.0.2</p>
      <p>
        <b>kind</b>: resource</p>
      <p>
        <b>abstract</b>: false</p>
      <p>
        <b>type</b>: Sequence</p>
      <p>
        <b>baseDefinition</b>:
        <a href="http://hl7.org/fhir/StructureDefinition/DomainResource">http://hl7.org/fhir/StructureDefinition/DomainResource</a>
      </p>
      <p>
        <b>derivation</b>: specialization</p>
    </div>
  </text>
  <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm">
    <valueInteger value="1"/>
  </extension>
  <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
    <valueCode value="cg"/>
  </extension>
  <url value="http://hl7.org/fhir/StructureDefinition/Sequence"/>
  <name value="Sequence"/>
  <status value="draft"/>
  <date value="2019-10-24T11:53:00+11:00"/>
  <publisher value="Health Level Seven International (Clinical Genomics)"/>
  <contact>
    <telecom>
      <system value="url"/>
      <value value="http://hl7.org/fhir"/>
    </telecom>
  </contact>
  <contact>
    <telecom>
      <system value="url"/>
      <value value="http://www.hl7.org/Special/committees/clingenomics/index.cfm"/>
    </telecom>
  </contact>
  <description value="Base StructureDefinition for Sequence Resource"/>
  <fhirVersion value="3.0.2"/>
  <mapping>
    <identity value="w5"/>
    <uri value="http://hl7.org/fhir/w5"/>
    <name value="W5 Mapping"/>
  </mapping>
  <mapping>
    <identity value="rim"/>
    <uri value="http://hl7.org/v3"/>
    <name value="RIM Mapping"/>
  </mapping>
  <kind value="resource"/>
  <abstract value="false"/>
  <type value="Sequence"/>
  <baseDefinition value="http://hl7.org/fhir/StructureDefinition/DomainResource"/>
  <derivation value="specialization"/>
  <snapshot>
    <element id="Sequence">
      <path value="Sequence"/>
      <short value="Information about a biological sequence"/>
      <definition value="Raw data describing a biological sequence."/>
      <min value="0"/>
      <max value="*"/>
      <constraint>
        <key value="dom-2"/>
        <severity value="error"/>
        <human value="If the resource is contained in another resource, it SHALL NOT contain nested Resources"/>
        <expression value="contained.contained.empty()"/>
        <xpath value="not(parent::f:contained and f:contained)"/>
        <source value="DomainResource"/>
      </constraint>
      <constraint>
        <key value="dom-1"/>
        <severity value="error"/>
        <human value="If the resource is contained in another resource, it SHALL NOT contain any narrative"/>
        <expression value="contained.text.empty()"/>
        <xpath value="not(parent::f:contained and f:text)"/>
        <source value="DomainResource"/>
      </constraint>
      <constraint>
        <key value="dom-4"/>
        <severity value="error"/>
        <human value="If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated"/>
        <expression value="contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()"/>
        <xpath value="not(exists(f:contained/*/f:meta/f:versionId)) and not(exists(f:contained/*/f:meta/f:lastUpdated))"/>
        <source value="DomainResource"/>
      </constraint>
      <constraint>
        <key value="dom-3"/>
        <severity value="error"/>
        <human value="If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource"/>
        <expression value="contained.where((&apos;#&apos;+id in %resource.descendants().reference).not()).empty()"/>
        <xpath value="not(exists(for $id in f:contained/*/@id return $id[not(ancestor::f:contained/parent::*/descendant::f:reference/@value=concat(&apos;#&apos;, $id))]))"/>
        <source value="DomainResource"/>
      </constraint>
      <constraint>
        <key value="seq-3"/>
        <severity value="error"/>
        <human value="Only 0 and 1 are valid for coordinateSystem"/>
        <expression value="coordinateSystem = 1 or coordinateSystem = 0"/>
        <xpath value="count(f:coordinateSystem[@value=0 and @value=1]) = 1"/>
      </constraint>
      <mapping>
        <identity value="rim"/>
        <map value="Entity. Role, or Act"/>
      </mapping>
      <mapping>
        <identity value="w5"/>
        <map value="clinical.diagnostics"/>
      </mapping>
    </element>
    <element id="Sequence.id">
      <path value="Sequence.id"/>
      <short value="Logical id of this artifact"/>
      <definition value="The logical id of the resource, as used in the URL for the resource. Once assigned, this value never changes."/>
      <comment value="The only time that a resource does not have an id is when it is being submitted to the server using a create operation."/>
      <min value="0"/>
      <max value="1"/>
      <base>
        <path value="Resource.id"/>
        <min value="0"/>
        <max value="1"/>
      </base>
      <type>
        <code value="id"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.meta">
      <path value="Sequence.meta"/>
      <short value="Metadata about the resource"/>
      <definition value="The metadata about the resource. This is content that is maintained by the infrastructure. Changes to the content may not always be associated with version changes to the resource."/>
      <min value="0"/>
      <max value="1"/>
      <base>
        <path value="Resource.meta"/>
        <min value="0"/>
        <max value="1"/>
      </base>
      <type>
        <code value="Meta"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.implicitRules">
      <path value="Sequence.implicitRules"/>
      <short value="A set of rules under which this content was created"/>
      <definition value="A reference to a set of rules that were followed when the resource was constructed, and which must be understood when processing the content."/>
      <comment value="Asserting this rule set restricts the content to be only understood by a limited set of trading partners. This inherently limits the usefulness of the data in the long term. However, the existing health eco-system is highly fractured, and not yet ready to define, collect, and exchange data in a generally computable sense. Wherever possible, implementers and/or specification writers should avoid using this element. &#10;&#10;This element is labelled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it&apos;s meaning or interpretation."/>
      <min value="0"/>
      <max value="1"/>
      <base>
        <path value="Resource.implicitRules"/>
        <min value="0"/>
        <max value="1"/>
      </base>
      <type>
        <code value="uri"/>
      </type>
      <isModifier value="true"/>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.language">
      <path value="Sequence.language"/>
      <short value="Language of the resource content"/>
      <definition value="The base language in which the resource is written."/>
      <comment value="Language is provided to support indexing and accessibility (typically, services such as text to speech use the language tag). The html language tag in the narrative applies to the narrative. The language tag on the resource may be used to specify the language of other presentations generated from the data in the resource Not all the content has to be in the base language. The Resource.language should not be assumed to apply to the narrative automatically. If a language is specified, it should it also be specified on the div element in the html (see rules in HTML5 for information about the relationship between xml:lang and the html lang attribute)."/>
      <min value="0"/>
      <max value="1"/>
      <base>
        <path value="Resource.language"/>
        <min value="0"/>
        <max value="1"/>
      </base>
      <type>
        <code value="code"/>
      </type>
      <binding>
        <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet">
          <valueReference>
            <reference value="http://hl7.org/fhir/ValueSet/all-languages"/>
          </valueReference>
        </extension>
        <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
          <valueString value="Language"/>
        </extension>
        <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-isCommonBinding">
          <valueBoolean value="true"/>
        </extension>
        <strength value="extensible"/>
        <description value="A human language."/>
        <valueSetReference>
          <reference value="http://hl7.org/fhir/ValueSet/languages"/>
        </valueSetReference>
      </binding>
    </element>
    <element id="Sequence.text">
      <path value="Sequence.text"/>
      <short value="Text summary of the resource, for human interpretation"/>
      <definition value="A human-readable narrative that contains a summary of the resource, and may be used to represent the content of the resource to a human. The narrative need not encode all the structured data, but is required to contain sufficient detail to make it &quot;clinically safe&quot; for a human to just read the narrative. Resource definitions may define what content should be represented in the narrative to ensure clinical safety."/>
      <comment value="Contained resources do not have narrative. Resources that are not contained SHOULD have a narrative. In some cases, a resource may only have text with little or no additional discrete data (as long as all minOccurs=1 elements are satisfied). This may be necessary for data from legacy systems where information is captured as a &quot;text blob&quot; or where text is additionally entered raw or narrated and encoded in formation is added later."/>
      <alias value="narrative"/>
      <alias value="html"/>
      <alias value="xhtml"/>
      <alias value="display"/>
      <min value="0"/>
      <max value="1"/>
      <base>
        <path value="DomainResource.text"/>
        <min value="0"/>
        <max value="1"/>
      </base>
      <type>
        <code value="Narrative"/>
      </type>
      <condition value="dom-1"/>
      <mapping>
        <identity value="rim"/>
        <map value="Act.text?"/>
      </mapping>
    </element>
    <element id="Sequence.contained">
      <path value="Sequence.contained"/>
      <short value="Contained, inline Resources"/>
      <definition value="These resources do not have an independent existence apart from the resource that contains them - they cannot be identified independently, and nor can they have their own independent transaction scope."/>
      <comment value="This should never be done when the content can be identified properly, as once identification is lost, it is extremely difficult (and context dependent) to restore it again."/>
      <alias value="inline resources"/>
      <alias value="anonymous resources"/>
      <alias value="contained resources"/>
      <min value="0"/>
      <max value="*"/>
      <base>
        <path value="DomainResource.contained"/>
        <min value="0"/>
        <max value="*"/>
      </base>
      <type>
        <code value="Resource"/>
      </type>
      <mapping>
        <identity value="rim"/>
        <map value="N/A"/>
      </mapping>
    </element>
    <element id="Sequence.extension">
      <path value="Sequence.extension"/>
      <short value="Additional Content defined by implementations"/>
      <definition value="May be used to represent additional information that is not part of the basic definition of the resource. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension."/>
      <comment value="There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone."/>
      <alias value="extensions"/>
      <alias value="user content"/>
      <min value="0"/>
      <max value="*"/>
      <base>
        <path value="DomainResource.extension"/>
        <min value="0"/>
        <max value="*"/>
      </base>
      <type>
        <code value="Extension"/>
      </type>
      <mapping>
        <identity value="rim"/>
        <map value="N/A"/>
      </mapping>
    </element>
    <element id="Sequence.modifierExtension">
      <path value="Sequence.modifierExtension"/>
      <short value="Extensions that cannot be ignored"/>
      <definition value="May be used to represent additional information that is not part of the basic definition of the resource, and that modifies the understanding of the element that contains it. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions."/>
      <comment value="There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone."/>
      <alias value="extensions"/>
      <alias value="user content"/>
      <min value="0"/>
      <max value="*"/>
      <base>
        <path value="DomainResource.modifierExtension"/>
        <min value="0"/>
        <max value="*"/>
      </base>
      <type>
        <code value="Extension"/>
      </type>
      <isModifier value="true"/>
      <mapping>
        <identity value="rim"/>
        <map value="N/A"/>
      </mapping>
    </element>
    <element id="Sequence.identifier">
      <path value="Sequence.identifier"/>
      <short value="Unique ID for this particular sequence. This is a FHIR-defined id"/>
      <definition value="A unique identifier for this particular sequence instance. This is a FHIR-defined id."/>
      <requirements value="Allows sequences to be distinguished and referenced."/>
      <min value="0"/>
      <max value="*"/>
      <type>
        <code value="Identifier"/>
      </type>
      <isSummary value="true"/>
      <mapping>
        <identity value="w5"/>
        <map value="id"/>
      </mapping>
    </element>
    <element id="Sequence.type">
      <path value="Sequence.type"/>
      <short value="aa | dna | rna"/>
      <definition value="Amino Acid Sequence/ DNA Sequence / RNA Sequence."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="code"/>
      </type>
      <isSummary value="true"/>
      <binding>
        <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
          <valueString value="sequenceType"/>
        </extension>
        <strength value="example"/>
        <description value="Type if a sequence -- DNA, RNA, or amino acid sequence"/>
        <valueSetReference>
          <reference value="http://hl7.org/fhir/ValueSet/sequence-type"/>
        </valueSetReference>
      </binding>
    </element>
    <element id="Sequence.coordinateSystem">
      <path value="Sequence.coordinateSystem"/>
      <short value="Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)"/>
      <definition value="Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end)."/>
      <min value="1"/>
      <max value="1"/>
      <type>
        <code value="integer"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.patient">
      <path value="Sequence.patient"/>
      <short value="Who and/or what this is about"/>
      <definition value="The patient whose sequencing results are described by this resource."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="Reference"/>
        <targetProfile value="http://hl7.org/fhir/StructureDefinition/Patient"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.specimen">
      <path value="Sequence.specimen"/>
      <short value="Specimen used for sequencing"/>
      <definition value="Specimen used for sequencing."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="Reference"/>
        <targetProfile value="http://hl7.org/fhir/StructureDefinition/Specimen"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.device">
      <path value="Sequence.device"/>
      <short value="The method for sequencing"/>
      <definition value="The method for sequencing, for example, chip information."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="Reference"/>
        <targetProfile value="http://hl7.org/fhir/StructureDefinition/Device"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.performer">
      <path value="Sequence.performer"/>
      <short value="Who should be responsible for test result"/>
      <definition value="The organization or lab that should be responsible for this result."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="Reference"/>
        <targetProfile value="http://hl7.org/fhir/StructureDefinition/Organization"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quantity">
      <path value="Sequence.quantity"/>
      <short value="The number of copies of the seqeunce of interest. (RNASeq)"/>
      <definition value="The number of copies of the seqeunce of interest. (RNASeq)."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="Quantity"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.referenceSeq">
      <path value="Sequence.referenceSeq"/>
      <short value="A sequence used as reference"/>
      <definition value="A sequence that is used as a reference to describe variants that are present in a sequence analyzed."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="BackboneElement"/>
      </type>
      <constraint>
        <key value="ele-1"/>
        <severity value="error"/>
        <human value="All FHIR elements must have a @value or children"/>
        <expression value="hasValue() | (children().count() &gt; id.count())"/>
        <xpath value="@value|f:*|h:div"/>
        <source value="Element"/>
      </constraint>
      <constraint>
        <key value="seq-4"/>
        <severity value="error"/>
        <human value="Only +1 and -1 are valid for strand"/>
        <expression value="strand.empty() or strand = 1 or strand = -1"/>
        <xpath value="not(exists(f:strand)) or count(f:strand[@value=-1 and @value=1]) = 1"/>
      </constraint>
      <constraint>
        <key value="seq-5"/>
        <severity value="error"/>
        <human value="GenomeBuild and chromosome must be both contained if either one of them is contained"/>
        <expression value="(chromosome.empty() and genomeBuild.empty()) or (chromosome.exists() and genomeBuild.exists())"/>
        <xpath value="(exists(f:chromosome) and exists(f:genomeBuild)) or (not(exists(f:chromosome)) and not(exists(f:genomeBuild)))"/>
      </constraint>
      <constraint>
        <key value="seq-6"/>
        <severity value="error"/>
        <human value="Have and only have one of the following elements in referenceSeq : 1. genomeBuild 2 referenceSeqId 3. referenceSeqPointer 4. referenceSeqString"/>
        <expression value="(genomeBuild.count()+referenceSeqId.count()+ referenceSeqPointer.count()+ referenceSeqString.count()) = 1"/>
        <xpath value="count(f:genomeBuild)+count(f:referenceSeqId)+count(f:referenceSeqPointer)+count(f:referenceSeqString)=1"/>
      </constraint>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.referenceSeq.id">
      <path value="Sequence.referenceSeq.id"/>
      <representation value="xmlAttr"/>
      <short value="xml:id (or equivalent in JSON)"/>
      <definition value="unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces."/>
      <min value="0"/>
      <max value="1"/>
      <base>
        <path value="Element.id"/>
        <min value="0"/>
        <max value="1"/>
      </base>
      <type>
        <code value="string"/>
      </type>
      <mapping>
        <identity value="rim"/>
        <map value="n/a"/>
      </mapping>
    </element>
    <element id="Sequence.referenceSeq.extension">
      <path value="Sequence.referenceSeq.extension"/>
      <short value="Additional Content defined by implementations"/>
      <definition value="May be used to represent additional information that is not part of the basic definition of the element. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension."/>
      <comment value="There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone."/>
      <alias value="extensions"/>
      <alias value="user content"/>
      <min value="0"/>
      <max value="*"/>
      <base>
        <path value="Element.extension"/>
        <min value="0"/>
        <max value="*"/>
      </base>
      <type>
        <code value="Extension"/>
      </type>
      <mapping>
        <identity value="rim"/>
        <map value="n/a"/>
      </mapping>
    </element>
    <element id="Sequence.referenceSeq.modifierExtension">
      <path value="Sequence.referenceSeq.modifierExtension"/>
      <short value="Extensions that cannot be ignored"/>
      <definition value="May be used to represent additional information that is not part of the basic definition of the element, and that modifies the understanding of the element that contains it. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions."/>
      <comment value="There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone."/>
      <alias value="extensions"/>
      <alias value="user content"/>
      <alias value="modifiers"/>
      <min value="0"/>
      <max value="*"/>
      <base>
        <path value="BackboneElement.modifierExtension"/>
        <min value="0"/>
        <max value="*"/>
      </base>
      <type>
        <code value="Extension"/>
      </type>
      <isModifier value="true"/>
      <isSummary value="true"/>
      <mapping>
        <identity value="rim"/>
        <map value="N/A"/>
      </mapping>
    </element>
    <element id="Sequence.referenceSeq.chromosome">
      <path value="Sequence.referenceSeq.chromosome"/>
      <short value="Chromosome containing genetic finding"/>
      <definition value="Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340))."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="CodeableConcept"/>
      </type>
      <isSummary value="true"/>
      <binding>
        <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
          <valueString value="chromosome-human"/>
        </extension>
        <strength value="example"/>
        <description value="Chromosome number for human"/>
        <valueSetReference>
          <reference value="http://hl7.org/fhir/ValueSet/chromosome-human"/>
        </valueSetReference>
      </binding>
    </element>
    <element id="Sequence.referenceSeq.genomeBuild">
      <path value="Sequence.referenceSeq.genomeBuild"/>
      <short value="The Genome Build used for reference, following GRCh build versions e.g. &apos;GRCh 37&apos;"/>
      <definition value="The Genome Build used for reference, following GRCh build versions e.g. &apos;GRCh 37&apos;. Version number must be included if a versioned release of a primary build was used."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.referenceSeq.referenceSeqId">
      <path value="Sequence.referenceSeq.referenceSeqId"/>
      <short value="Reference identifier"/>
      <definition value="Reference identifier of reference sequence submitted to NCBI. It must match the type in the Sequence.type field. For example, the prefix, &#x201C;NG_&#x201D; identifies reference sequence for genes, &#x201C;NM_&#x201D; for messenger RNA transcripts, and &#x201C;NP_&#x201D; for amino acid sequences."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="CodeableConcept"/>
      </type>
      <isSummary value="true"/>
      <binding>
        <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
          <valueString value="sequenceReference"/>
        </extension>
        <strength value="example"/>
        <description value="Reference identifier"/>
        <valueSetReference>
          <reference value="http://hl7.org/fhir/ValueSet/sequence-referenceSeq"/>
        </valueSetReference>
      </binding>
    </element>
    <element id="Sequence.referenceSeq.referenceSeqPointer">
      <path value="Sequence.referenceSeq.referenceSeqPointer"/>
      <short value="A Pointer to another Sequence entity as reference sequence"/>
      <definition value="A Pointer to another Sequence entity as reference sequence."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="Reference"/>
        <targetProfile value="http://hl7.org/fhir/StructureDefinition/Sequence"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.referenceSeq.referenceSeqString">
      <path value="Sequence.referenceSeq.referenceSeqString"/>
      <short value="A string to represent reference sequence"/>
      <definition value="A string like &quot;ACGT&quot;."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.referenceSeq.strand">
      <path value="Sequence.referenceSeq.strand"/>
      <short value="Directionality of DNA ( +1/-1)"/>
      <definition value="Directionality of DNA sequence. Available values are &quot;1&quot; for the plus strand (5&apos; to 3&apos;)/Watson/Sense/positive and &quot;-1&quot; for the minus strand(3&apos; to 5&apos;)/Crick/Antisense/negative."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="integer"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.referenceSeq.windowStart">
      <path value="Sequence.referenceSeq.windowStart"/>
      <short value="Start position of the window on the reference sequence"/>
      <definition value="Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive."/>
      <min value="1"/>
      <max value="1"/>
      <type>
        <code value="integer"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.referenceSeq.windowEnd">
      <path value="Sequence.referenceSeq.windowEnd"/>
      <short value="End position of the window on the reference sequence"/>
      <definition value="End position of the window on the reference sequence. If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position."/>
      <min value="1"/>
      <max value="1"/>
      <type>
        <code value="integer"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.variant">
      <path value="Sequence.variant"/>
      <short value="Variant in sequence"/>
      <definition value="The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string."/>
      <min value="0"/>
      <max value="*"/>
      <type>
        <code value="BackboneElement"/>
      </type>
      <constraint>
        <key value="ele-1"/>
        <severity value="error"/>
        <human value="All FHIR elements must have a @value or children"/>
        <expression value="hasValue() | (children().count() &gt; id.count())"/>
        <xpath value="@value|f:*|h:div"/>
        <source value="Element"/>
      </constraint>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.variant.id">
      <path value="Sequence.variant.id"/>
      <representation value="xmlAttr"/>
      <short value="xml:id (or equivalent in JSON)"/>
      <definition value="unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces."/>
      <min value="0"/>
      <max value="1"/>
      <base>
        <path value="Element.id"/>
        <min value="0"/>
        <max value="1"/>
      </base>
      <type>
        <code value="string"/>
      </type>
      <mapping>
        <identity value="rim"/>
        <map value="n/a"/>
      </mapping>
    </element>
    <element id="Sequence.variant.extension">
      <path value="Sequence.variant.extension"/>
      <short value="Additional Content defined by implementations"/>
      <definition value="May be used to represent additional information that is not part of the basic definition of the element. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension."/>
      <comment value="There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone."/>
      <alias value="extensions"/>
      <alias value="user content"/>
      <min value="0"/>
      <max value="*"/>
      <base>
        <path value="Element.extension"/>
        <min value="0"/>
        <max value="*"/>
      </base>
      <type>
        <code value="Extension"/>
      </type>
      <mapping>
        <identity value="rim"/>
        <map value="n/a"/>
      </mapping>
    </element>
    <element id="Sequence.variant.modifierExtension">
      <path value="Sequence.variant.modifierExtension"/>
      <short value="Extensions that cannot be ignored"/>
      <definition value="May be used to represent additional information that is not part of the basic definition of the element, and that modifies the understanding of the element that contains it. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions."/>
      <comment value="There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone."/>
      <alias value="extensions"/>
      <alias value="user content"/>
      <alias value="modifiers"/>
      <min value="0"/>
      <max value="*"/>
      <base>
        <path value="BackboneElement.modifierExtension"/>
        <min value="0"/>
        <max value="*"/>
      </base>
      <type>
        <code value="Extension"/>
      </type>
      <isModifier value="true"/>
      <isSummary value="true"/>
      <mapping>
        <identity value="rim"/>
        <map value="N/A"/>
      </mapping>
    </element>
    <element id="Sequence.variant.start">
      <path value="Sequence.variant.start"/>
      <short value="Start position of the variant on the reference sequence"/>
      <definition value="Start position of the variant on the reference sequence.If the coordinate system is either 0-based or 1-based, then start position is inclusive."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="integer"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.variant.end">
      <path value="Sequence.variant.end"/>
      <short value="End position of the variant on the reference sequence"/>
      <definition value="End position of the variant on the reference sequence.If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="integer"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.variant.observedAllele">
      <path value="Sequence.variant.observedAllele"/>
      <short value="Allele that was observed"/>
      <definition value="An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.variant.referenceAllele">
      <path value="Sequence.variant.referenceAllele"/>
      <short value="Allele in the reference sequence"/>
      <definition value="An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.variant.cigar">
      <path value="Sequence.variant.cigar"/>
      <short value="Extended CIGAR string for aligning the sequence with reference bases"/>
      <definition value="Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm)."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.variant.variantPointer">
      <path value="Sequence.variant.variantPointer"/>
      <short value="Pointer to observed variant information"/>
      <definition value="A pointer to an Observation containing variant information."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="Reference"/>
        <targetProfile value="http://hl7.org/fhir/StructureDefinition/Observation"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.observedSeq">
      <path value="Sequence.observedSeq"/>
      <short value="Sequence that was observed"/>
      <definition value="Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts from referenceSeq.windowStart and end by referenceSeq.windowEnd."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality">
      <path value="Sequence.quality"/>
      <short value="An set of value as quality of sequence"/>
      <definition value="An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686))."/>
      <min value="0"/>
      <max value="*"/>
      <type>
        <code value="BackboneElement"/>
      </type>
      <constraint>
        <key value="ele-1"/>
        <severity value="error"/>
        <human value="All FHIR elements must have a @value or children"/>
        <expression value="hasValue() | (children().count() &gt; id.count())"/>
        <xpath value="@value|f:*|h:div"/>
        <source value="Element"/>
      </constraint>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.id">
      <path value="Sequence.quality.id"/>
      <representation value="xmlAttr"/>
      <short value="xml:id (or equivalent in JSON)"/>
      <definition value="unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces."/>
      <min value="0"/>
      <max value="1"/>
      <base>
        <path value="Element.id"/>
        <min value="0"/>
        <max value="1"/>
      </base>
      <type>
        <code value="string"/>
      </type>
      <mapping>
        <identity value="rim"/>
        <map value="n/a"/>
      </mapping>
    </element>
    <element id="Sequence.quality.extension">
      <path value="Sequence.quality.extension"/>
      <short value="Additional Content defined by implementations"/>
      <definition value="May be used to represent additional information that is not part of the basic definition of the element. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension."/>
      <comment value="There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone."/>
      <alias value="extensions"/>
      <alias value="user content"/>
      <min value="0"/>
      <max value="*"/>
      <base>
        <path value="Element.extension"/>
        <min value="0"/>
        <max value="*"/>
      </base>
      <type>
        <code value="Extension"/>
      </type>
      <mapping>
        <identity value="rim"/>
        <map value="n/a"/>
      </mapping>
    </element>
    <element id="Sequence.quality.modifierExtension">
      <path value="Sequence.quality.modifierExtension"/>
      <short value="Extensions that cannot be ignored"/>
      <definition value="May be used to represent additional information that is not part of the basic definition of the element, and that modifies the understanding of the element that contains it. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions."/>
      <comment value="There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone."/>
      <alias value="extensions"/>
      <alias value="user content"/>
      <alias value="modifiers"/>
      <min value="0"/>
      <max value="*"/>
      <base>
        <path value="BackboneElement.modifierExtension"/>
        <min value="0"/>
        <max value="*"/>
      </base>
      <type>
        <code value="Extension"/>
      </type>
      <isModifier value="true"/>
      <isSummary value="true"/>
      <mapping>
        <identity value="rim"/>
        <map value="N/A"/>
      </mapping>
    </element>
    <element id="Sequence.quality.type">
      <path value="Sequence.quality.type"/>
      <short value="indel | snp | unknown"/>
      <definition value="INDEL / SNP / Undefined variant."/>
      <min value="1"/>
      <max value="1"/>
      <type>
        <code value="code"/>
      </type>
      <isSummary value="true"/>
      <binding>
        <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
          <valueString value="qualityType"/>
        </extension>
        <strength value="required"/>
        <description value="Type for quality report"/>
        <valueSetReference>
          <reference value="http://hl7.org/fhir/ValueSet/quality-type"/>
        </valueSetReference>
      </binding>
    </element>
    <element id="Sequence.quality.standardSequence">
      <path value="Sequence.quality.standardSequence"/>
      <short value="Standard sequence for comparison"/>
      <definition value="Gold standard sequence used for comparing against."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="CodeableConcept"/>
      </type>
      <isSummary value="true"/>
      <binding>
        <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
          <valueString value="qualityStandardSequence"/>
        </extension>
        <strength value="example"/>
        <description value="Reference identifier of the sequence that used to mark the quality of tested samples."/>
        <valueSetReference>
          <reference value="http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence"/>
        </valueSetReference>
      </binding>
    </element>
    <element id="Sequence.quality.start">
      <path value="Sequence.quality.start"/>
      <short value="Start position of the sequence"/>
      <definition value="Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="integer"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.end">
      <path value="Sequence.quality.end"/>
      <short value="End position of the sequence"/>
      <definition value="End position of the sequence.If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="integer"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.score">
      <path value="Sequence.quality.score"/>
      <short value="Quality score for the comparison"/>
      <definition value="The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685))."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="Quantity"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.method">
      <path value="Sequence.quality.method"/>
      <short value="Method to get quality"/>
      <definition value="Which method is used to get sequence quality."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="CodeableConcept"/>
      </type>
      <isSummary value="true"/>
      <binding>
        <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
          <valueString value="qualityMethod"/>
        </extension>
        <strength value="example"/>
        <description value="The method used to evaluate the numerical quality of the observed sequence."/>
        <valueSetReference>
          <reference value="http://hl7.org/fhir/ValueSet/sequence-quality-method"/>
        </valueSetReference>
      </binding>
    </element>
    <element id="Sequence.quality.truthTP">
      <path value="Sequence.quality.truthTP"/>
      <short value="True positives from the perspective of the truth data"/>
      <definition value="True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="decimal"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.queryTP">
      <path value="Sequence.quality.queryTP"/>
      <short value="True positives from the perspective of the query data"/>
      <definition value="True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="decimal"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.truthFN">
      <path value="Sequence.quality.truthFN"/>
      <short value="False negatives"/>
      <definition value="False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="decimal"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.queryFP">
      <path value="Sequence.quality.queryFP"/>
      <short value="False positives"/>
      <definition value="False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="decimal"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.gtFP">
      <path value="Sequence.quality.gtFP"/>
      <short value="False positives where the non-REF alleles in the Truth and Query Call Sets match"/>
      <definition value="The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar)."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="decimal"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.precision">
      <path value="Sequence.quality.precision"/>
      <short value="Precision of comparison"/>
      <definition value="QUERY.TP / (QUERY.TP + QUERY.FP)."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="decimal"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.recall">
      <path value="Sequence.quality.recall"/>
      <short value="Recall of comparison"/>
      <definition value="TRUTH.TP / (TRUTH.TP + TRUTH.FN)."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="decimal"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.fScore">
      <path value="Sequence.quality.fScore"/>
      <short value="F-score"/>
      <definition value="Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall)."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="decimal"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.readCoverage">
      <path value="Sequence.readCoverage"/>
      <short value="Average number of reads representing a given nucleotide in the reconstructed sequence"/>
      <definition value="Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="integer"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.repository">
      <path value="Sequence.repository"/>
      <short value="External repository which contains detailed report related with observedSeq in this resource"/>
      <definition value="Configurations of the external repository. The repository shall store target&apos;s observedSeq or records related with target&apos;s observedSeq."/>
      <min value="0"/>
      <max value="*"/>
      <type>
        <code value="BackboneElement"/>
      </type>
      <constraint>
        <key value="ele-1"/>
        <severity value="error"/>
        <human value="All FHIR elements must have a @value or children"/>
        <expression value="hasValue() | (children().count() &gt; id.count())"/>
        <xpath value="@value|f:*|h:div"/>
        <source value="Element"/>
      </constraint>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.repository.id">
      <path value="Sequence.repository.id"/>
      <representation value="xmlAttr"/>
      <short value="xml:id (or equivalent in JSON)"/>
      <definition value="unique id for the element within a resource (for internal references). This may be any string value that does not contain spaces."/>
      <min value="0"/>
      <max value="1"/>
      <base>
        <path value="Element.id"/>
        <min value="0"/>
        <max value="1"/>
      </base>
      <type>
        <code value="string"/>
      </type>
      <mapping>
        <identity value="rim"/>
        <map value="n/a"/>
      </mapping>
    </element>
    <element id="Sequence.repository.extension">
      <path value="Sequence.repository.extension"/>
      <short value="Additional Content defined by implementations"/>
      <definition value="May be used to represent additional information that is not part of the basic definition of the element. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension."/>
      <comment value="There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone."/>
      <alias value="extensions"/>
      <alias value="user content"/>
      <min value="0"/>
      <max value="*"/>
      <base>
        <path value="Element.extension"/>
        <min value="0"/>
        <max value="*"/>
      </base>
      <type>
        <code value="Extension"/>
      </type>
      <mapping>
        <identity value="rim"/>
        <map value="n/a"/>
      </mapping>
    </element>
    <element id="Sequence.repository.modifierExtension">
      <path value="Sequence.repository.modifierExtension"/>
      <short value="Extensions that cannot be ignored"/>
      <definition value="May be used to represent additional information that is not part of the basic definition of the element, and that modifies the understanding of the element that contains it. Usually modifier elements provide negation or qualification. In order to make the use of extensions safe and manageable, there is a strict set of governance applied to the definition and use of extensions. Though any implementer is allowed to define an extension, there is a set of requirements that SHALL be met as part of the definition of the extension. Applications processing a resource are required to check for modifier extensions."/>
      <comment value="There can be no stigma associated with the use of extensions by any application, project, or standard - regardless of the institution or jurisdiction that uses or defines the extensions. The use of extensions is what allows the FHIR specification to retain a core level of simplicity for everyone."/>
      <alias value="extensions"/>
      <alias value="user content"/>
      <alias value="modifiers"/>
      <min value="0"/>
      <max value="*"/>
      <base>
        <path value="BackboneElement.modifierExtension"/>
        <min value="0"/>
        <max value="*"/>
      </base>
      <type>
        <code value="Extension"/>
      </type>
      <isModifier value="true"/>
      <isSummary value="true"/>
      <mapping>
        <identity value="rim"/>
        <map value="N/A"/>
      </mapping>
    </element>
    <element id="Sequence.repository.type">
      <path value="Sequence.repository.type"/>
      <short value="directlink | openapi | login | oauth | other"/>
      <definition value="Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource."/>
      <min value="1"/>
      <max value="1"/>
      <type>
        <code value="code"/>
      </type>
      <isSummary value="true"/>
      <binding>
        <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
          <valueString value="repositoryType"/>
        </extension>
        <strength value="required"/>
        <description value="Type for access of external URI"/>
        <valueSetReference>
          <reference value="http://hl7.org/fhir/ValueSet/repository-type"/>
        </valueSetReference>
      </binding>
    </element>
    <element id="Sequence.repository.url">
      <path value="Sequence.repository.url"/>
      <short value="URI of the repository"/>
      <definition value="URI of an external repository which contains further details about the genetics data."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="uri"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.repository.name">
      <path value="Sequence.repository.name"/>
      <short value="Repository&apos;s name"/>
      <definition value="URI of an external repository which contains further details about the genetics data."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.repository.datasetId">
      <path value="Sequence.repository.datasetId"/>
      <short value="Id of the dataset that used to call for dataset in repository"/>
      <definition value="Id of the variant in this external repository. The server will understand how to use this id to call for more info about datasets in external repository."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.repository.variantsetId">
      <path value="Sequence.repository.variantsetId"/>
      <short value="Id of the variantset that used to call for variantset in repository"/>
      <definition value="Id of the variantset in this external repository. The server will understand how to use this id to call for more info about variantsets in external repository."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.repository.readsetId">
      <path value="Sequence.repository.readsetId"/>
      <short value="Id of the read"/>
      <definition value="Id of the read in this external repository."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.pointer">
      <path value="Sequence.pointer"/>
      <short value="Pointer to next atomic sequence"/>
      <definition value="Pointer to next atomic sequence which at most contains one variant."/>
      <min value="0"/>
      <max value="*"/>
      <type>
        <code value="Reference"/>
        <targetProfile value="http://hl7.org/fhir/StructureDefinition/Sequence"/>
      </type>
      <isSummary value="true"/>
    </element>
  </snapshot>
  <differential>
    <element id="Sequence">
      <path value="Sequence"/>
      <short value="Information about a biological sequence"/>
      <definition value="Raw data describing a biological sequence."/>
      <min value="0"/>
      <max value="*"/>
      <constraint>
        <key value="seq-3"/>
        <severity value="error"/>
        <human value="Only 0 and 1 are valid for coordinateSystem"/>
        <expression value="coordinateSystem = 1 or coordinateSystem = 0"/>
        <xpath value="count(f:coordinateSystem[@value=0 and @value=1]) = 1"/>
      </constraint>
      <mapping>
        <identity value="w5"/>
        <map value="clinical.diagnostics"/>
      </mapping>
    </element>
    <element id="Sequence.identifier">
      <path value="Sequence.identifier"/>
      <short value="Unique ID for this particular sequence. This is a FHIR-defined id"/>
      <definition value="A unique identifier for this particular sequence instance. This is a FHIR-defined id."/>
      <requirements value="Allows sequences to be distinguished and referenced."/>
      <min value="0"/>
      <max value="*"/>
      <type>
        <code value="Identifier"/>
      </type>
      <isSummary value="true"/>
      <mapping>
        <identity value="w5"/>
        <map value="id"/>
      </mapping>
    </element>
    <element id="Sequence.type">
      <path value="Sequence.type"/>
      <short value="aa | dna | rna"/>
      <definition value="Amino Acid Sequence/ DNA Sequence / RNA Sequence."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="code"/>
      </type>
      <isSummary value="true"/>
      <binding>
        <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
          <valueString value="sequenceType"/>
        </extension>
        <strength value="example"/>
        <description value="Type if a sequence -- DNA, RNA, or amino acid sequence"/>
        <valueSetReference>
          <reference value="http://hl7.org/fhir/ValueSet/sequence-type"/>
        </valueSetReference>
      </binding>
    </element>
    <element id="Sequence.coordinateSystem">
      <path value="Sequence.coordinateSystem"/>
      <short value="Base number of coordinate system (0 for 0-based numbering or coordinates, inclusive start, exclusive end, 1 for 1-based numbering, inclusive start, inclusive end)"/>
      <definition value="Whether the sequence is numbered starting at 0 (0-based numbering or coordinates, inclusive start, exclusive end) or starting at 1 (1-based numbering, inclusive start and inclusive end)."/>
      <min value="1"/>
      <max value="1"/>
      <type>
        <code value="integer"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.patient">
      <path value="Sequence.patient"/>
      <short value="Who and/or what this is about"/>
      <definition value="The patient whose sequencing results are described by this resource."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="Reference"/>
        <targetProfile value="http://hl7.org/fhir/StructureDefinition/Patient"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.specimen">
      <path value="Sequence.specimen"/>
      <short value="Specimen used for sequencing"/>
      <definition value="Specimen used for sequencing."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="Reference"/>
        <targetProfile value="http://hl7.org/fhir/StructureDefinition/Specimen"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.device">
      <path value="Sequence.device"/>
      <short value="The method for sequencing"/>
      <definition value="The method for sequencing, for example, chip information."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="Reference"/>
        <targetProfile value="http://hl7.org/fhir/StructureDefinition/Device"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.performer">
      <path value="Sequence.performer"/>
      <short value="Who should be responsible for test result"/>
      <definition value="The organization or lab that should be responsible for this result."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="Reference"/>
        <targetProfile value="http://hl7.org/fhir/StructureDefinition/Organization"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quantity">
      <path value="Sequence.quantity"/>
      <short value="The number of copies of the seqeunce of interest. (RNASeq)"/>
      <definition value="The number of copies of the seqeunce of interest. (RNASeq)."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="Quantity"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.referenceSeq">
      <path value="Sequence.referenceSeq"/>
      <short value="A sequence used as reference"/>
      <definition value="A sequence that is used as a reference to describe variants that are present in a sequence analyzed."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="BackboneElement"/>
      </type>
      <constraint>
        <key value="seq-4"/>
        <severity value="error"/>
        <human value="Only +1 and -1 are valid for strand"/>
        <expression value="strand.empty() or strand = 1 or strand = -1"/>
        <xpath value="not(exists(f:strand)) or count(f:strand[@value=-1 and @value=1]) = 1"/>
      </constraint>
      <constraint>
        <key value="seq-5"/>
        <severity value="error"/>
        <human value="GenomeBuild and chromosome must be both contained if either one of them is contained"/>
        <expression value="(chromosome.empty() and genomeBuild.empty()) or (chromosome.exists() and genomeBuild.exists())"/>
        <xpath value="(exists(f:chromosome) and exists(f:genomeBuild)) or (not(exists(f:chromosome)) and not(exists(f:genomeBuild)))"/>
      </constraint>
      <constraint>
        <key value="seq-6"/>
        <severity value="error"/>
        <human value="Have and only have one of the following elements in referenceSeq : 1. genomeBuild 2 referenceSeqId 3. referenceSeqPointer 4. referenceSeqString"/>
        <expression value="(genomeBuild.count()+referenceSeqId.count()+ referenceSeqPointer.count()+ referenceSeqString.count()) = 1"/>
        <xpath value="count(f:genomeBuild)+count(f:referenceSeqId)+count(f:referenceSeqPointer)+count(f:referenceSeqString)=1"/>
      </constraint>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.referenceSeq.chromosome">
      <path value="Sequence.referenceSeq.chromosome"/>
      <short value="Chromosome containing genetic finding"/>
      <definition value="Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication ([SO:0000340](http://www.sequenceontology.org/browser/current_svn/term/SO:0000340))."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="CodeableConcept"/>
      </type>
      <isSummary value="true"/>
      <binding>
        <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
          <valueString value="chromosome-human"/>
        </extension>
        <strength value="example"/>
        <description value="Chromosome number for human"/>
        <valueSetReference>
          <reference value="http://hl7.org/fhir/ValueSet/chromosome-human"/>
        </valueSetReference>
      </binding>
    </element>
    <element id="Sequence.referenceSeq.genomeBuild">
      <path value="Sequence.referenceSeq.genomeBuild"/>
      <short value="The Genome Build used for reference, following GRCh build versions e.g. &apos;GRCh 37&apos;"/>
      <definition value="The Genome Build used for reference, following GRCh build versions e.g. &apos;GRCh 37&apos;. Version number must be included if a versioned release of a primary build was used."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.referenceSeq.referenceSeqId">
      <path value="Sequence.referenceSeq.referenceSeqId"/>
      <short value="Reference identifier"/>
      <definition value="Reference identifier of reference sequence submitted to NCBI. It must match the type in the Sequence.type field. For example, the prefix, &#x201C;NG_&#x201D; identifies reference sequence for genes, &#x201C;NM_&#x201D; for messenger RNA transcripts, and &#x201C;NP_&#x201D; for amino acid sequences."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="CodeableConcept"/>
      </type>
      <isSummary value="true"/>
      <binding>
        <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
          <valueString value="sequenceReference"/>
        </extension>
        <strength value="example"/>
        <description value="Reference identifier"/>
        <valueSetReference>
          <reference value="http://hl7.org/fhir/ValueSet/sequence-referenceSeq"/>
        </valueSetReference>
      </binding>
    </element>
    <element id="Sequence.referenceSeq.referenceSeqPointer">
      <path value="Sequence.referenceSeq.referenceSeqPointer"/>
      <short value="A Pointer to another Sequence entity as reference sequence"/>
      <definition value="A Pointer to another Sequence entity as reference sequence."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="Reference"/>
        <targetProfile value="http://hl7.org/fhir/StructureDefinition/Sequence"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.referenceSeq.referenceSeqString">
      <path value="Sequence.referenceSeq.referenceSeqString"/>
      <short value="A string to represent reference sequence"/>
      <definition value="A string like &quot;ACGT&quot;."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.referenceSeq.strand">
      <path value="Sequence.referenceSeq.strand"/>
      <short value="Directionality of DNA ( +1/-1)"/>
      <definition value="Directionality of DNA sequence. Available values are &quot;1&quot; for the plus strand (5&apos; to 3&apos;)/Watson/Sense/positive and &quot;-1&quot; for the minus strand(3&apos; to 5&apos;)/Crick/Antisense/negative."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="integer"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.referenceSeq.windowStart">
      <path value="Sequence.referenceSeq.windowStart"/>
      <short value="Start position of the window on the reference sequence"/>
      <definition value="Start position of the window on the reference sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive."/>
      <min value="1"/>
      <max value="1"/>
      <type>
        <code value="integer"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.referenceSeq.windowEnd">
      <path value="Sequence.referenceSeq.windowEnd"/>
      <short value="End position of the window on the reference sequence"/>
      <definition value="End position of the window on the reference sequence. If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position."/>
      <min value="1"/>
      <max value="1"/>
      <type>
        <code value="integer"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.variant">
      <path value="Sequence.variant"/>
      <short value="Variant in sequence"/>
      <definition value="The definition of variant here originates from Sequence ontology ([variant_of](http://www.sequenceontology.org/browser/current_svn/term/variant_of)). This element can represent amino acid or nucleic sequence change(including insertion,deletion,SNP,etc.) It can represent some complex mutation or segment variation with the assist of CIGAR string."/>
      <min value="0"/>
      <max value="*"/>
      <type>
        <code value="BackboneElement"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.variant.start">
      <path value="Sequence.variant.start"/>
      <short value="Start position of the variant on the reference sequence"/>
      <definition value="Start position of the variant on the reference sequence.If the coordinate system is either 0-based or 1-based, then start position is inclusive."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="integer"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.variant.end">
      <path value="Sequence.variant.end"/>
      <short value="End position of the variant on the reference sequence"/>
      <definition value="End position of the variant on the reference sequence.If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="integer"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.variant.observedAllele">
      <path value="Sequence.variant.observedAllele"/>
      <short value="Allele that was observed"/>
      <definition value="An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the observed sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.variant.referenceAllele">
      <path value="Sequence.variant.referenceAllele"/>
      <short value="Allele in the reference sequence"/>
      <definition value="An allele is one of a set of coexisting sequence variants of a gene ([SO:0001023](http://www.sequenceontology.org/browser/current_svn/term/SO:0001023)). Nucleotide(s)/amino acids from start position of sequence to stop position of sequence on the positive (+) strand of the reference sequence. When the sequence type is DNA, it should be the sequence on the positive (+) strand. This will lay in the range between variant.start and variant.end."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.variant.cigar">
      <path value="Sequence.variant.cigar"/>
      <short value="Extended CIGAR string for aligning the sequence with reference bases"/>
      <definition value="Extended CIGAR string for aligning the sequence with reference bases. See detailed documentation [here](http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_ExtendedCIGARFormat.htm)."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.variant.variantPointer">
      <path value="Sequence.variant.variantPointer"/>
      <short value="Pointer to observed variant information"/>
      <definition value="A pointer to an Observation containing variant information."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="Reference"/>
        <targetProfile value="http://hl7.org/fhir/StructureDefinition/Observation"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.observedSeq">
      <path value="Sequence.observedSeq"/>
      <short value="Sequence that was observed"/>
      <definition value="Sequence that was observed. It is the result marked by referenceSeq along with variant records on referenceSeq. This shall starts from referenceSeq.windowStart and end by referenceSeq.windowEnd."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality">
      <path value="Sequence.quality"/>
      <short value="An set of value as quality of sequence"/>
      <definition value="An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score ([SO:0001686](http://www.sequenceontology.org/browser/current_svn/term/SO:0001686))."/>
      <min value="0"/>
      <max value="*"/>
      <type>
        <code value="BackboneElement"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.type">
      <path value="Sequence.quality.type"/>
      <short value="indel | snp | unknown"/>
      <definition value="INDEL / SNP / Undefined variant."/>
      <min value="1"/>
      <max value="1"/>
      <type>
        <code value="code"/>
      </type>
      <isSummary value="true"/>
      <binding>
        <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
          <valueString value="qualityType"/>
        </extension>
        <strength value="required"/>
        <description value="Type for quality report"/>
        <valueSetReference>
          <reference value="http://hl7.org/fhir/ValueSet/quality-type"/>
        </valueSetReference>
      </binding>
    </element>
    <element id="Sequence.quality.standardSequence">
      <path value="Sequence.quality.standardSequence"/>
      <short value="Standard sequence for comparison"/>
      <definition value="Gold standard sequence used for comparing against."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="CodeableConcept"/>
      </type>
      <isSummary value="true"/>
      <binding>
        <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
          <valueString value="qualityStandardSequence"/>
        </extension>
        <strength value="example"/>
        <description value="Reference identifier of the sequence that used to mark the quality of tested samples."/>
        <valueSetReference>
          <reference value="http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence"/>
        </valueSetReference>
      </binding>
    </element>
    <element id="Sequence.quality.start">
      <path value="Sequence.quality.start"/>
      <short value="Start position of the sequence"/>
      <definition value="Start position of the sequence. If the coordinate system is either 0-based or 1-based, then start position is inclusive."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="integer"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.end">
      <path value="Sequence.quality.end"/>
      <short value="End position of the sequence"/>
      <definition value="End position of the sequence.If the coordinate system is 0-based then end is is exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="integer"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.score">
      <path value="Sequence.quality.score"/>
      <short value="Quality score for the comparison"/>
      <definition value="The score of an experimentally derived feature such as a p-value ([SO:0001685](http://www.sequenceontology.org/browser/current_svn/term/SO:0001685))."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="Quantity"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.method">
      <path value="Sequence.quality.method"/>
      <short value="Method to get quality"/>
      <definition value="Which method is used to get sequence quality."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="CodeableConcept"/>
      </type>
      <isSummary value="true"/>
      <binding>
        <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
          <valueString value="qualityMethod"/>
        </extension>
        <strength value="example"/>
        <description value="The method used to evaluate the numerical quality of the observed sequence."/>
        <valueSetReference>
          <reference value="http://hl7.org/fhir/ValueSet/sequence-quality-method"/>
        </valueSetReference>
      </binding>
    </element>
    <element id="Sequence.quality.truthTP">
      <path value="Sequence.quality.truthTP"/>
      <short value="True positives from the perspective of the truth data"/>
      <definition value="True positives, from the perspective of the truth data, i.e. the number of sites in the Truth Call Set for which there are paths through the Query Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="decimal"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.queryTP">
      <path value="Sequence.quality.queryTP"/>
      <short value="True positives from the perspective of the query data"/>
      <definition value="True positives, from the perspective of the query data, i.e. the number of sites in the Query Call Set for which there are paths through the Truth Call Set that are consistent with all of the alleles at this site, and for which there is an accurate genotype call for the event."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="decimal"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.truthFN">
      <path value="Sequence.quality.truthFN"/>
      <short value="False negatives"/>
      <definition value="False negatives, i.e. the number of sites in the Truth Call Set for which there is no path through the Query Call Set that is consistent with all of the alleles at this site, or sites for which there is an inaccurate genotype call for the event. Sites with correct variant but incorrect genotype are counted here."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="decimal"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.queryFP">
      <path value="Sequence.quality.queryFP"/>
      <short value="False positives"/>
      <definition value="False positives, i.e. the number of sites in the Query Call Set for which there is no path through the Truth Call Set that is consistent with this site. Sites with correct variant but incorrect genotype are counted here."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="decimal"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.gtFP">
      <path value="Sequence.quality.gtFP"/>
      <short value="False positives where the non-REF alleles in the Truth and Query Call Sets match"/>
      <definition value="The number of false positives where the non-REF alleles in the Truth and Query Call Sets match (i.e. cases where the truth is 1/1 and the query is 0/1 or similar)."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="decimal"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.precision">
      <path value="Sequence.quality.precision"/>
      <short value="Precision of comparison"/>
      <definition value="QUERY.TP / (QUERY.TP + QUERY.FP)."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="decimal"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.recall">
      <path value="Sequence.quality.recall"/>
      <short value="Recall of comparison"/>
      <definition value="TRUTH.TP / (TRUTH.TP + TRUTH.FN)."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="decimal"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.quality.fScore">
      <path value="Sequence.quality.fScore"/>
      <short value="F-score"/>
      <definition value="Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall)."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="decimal"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.readCoverage">
      <path value="Sequence.readCoverage"/>
      <short value="Average number of reads representing a given nucleotide in the reconstructed sequence"/>
      <definition value="Coverage (read depth or depth) is the average number of reads representing a given nucleotide in the reconstructed sequence."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="integer"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.repository">
      <path value="Sequence.repository"/>
      <short value="External repository which contains detailed report related with observedSeq in this resource"/>
      <definition value="Configurations of the external repository. The repository shall store target&apos;s observedSeq or records related with target&apos;s observedSeq."/>
      <min value="0"/>
      <max value="*"/>
      <type>
        <code value="BackboneElement"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.repository.type">
      <path value="Sequence.repository.type"/>
      <short value="directlink | openapi | login | oauth | other"/>
      <definition value="Click and see / RESTful API / Need login to see / RESTful API with authentication / Other ways to see resource."/>
      <min value="1"/>
      <max value="1"/>
      <type>
        <code value="code"/>
      </type>
      <isSummary value="true"/>
      <binding>
        <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName">
          <valueString value="repositoryType"/>
        </extension>
        <strength value="required"/>
        <description value="Type for access of external URI"/>
        <valueSetReference>
          <reference value="http://hl7.org/fhir/ValueSet/repository-type"/>
        </valueSetReference>
      </binding>
    </element>
    <element id="Sequence.repository.url">
      <path value="Sequence.repository.url"/>
      <short value="URI of the repository"/>
      <definition value="URI of an external repository which contains further details about the genetics data."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="uri"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.repository.name">
      <path value="Sequence.repository.name"/>
      <short value="Repository&apos;s name"/>
      <definition value="URI of an external repository which contains further details about the genetics data."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.repository.datasetId">
      <path value="Sequence.repository.datasetId"/>
      <short value="Id of the dataset that used to call for dataset in repository"/>
      <definition value="Id of the variant in this external repository. The server will understand how to use this id to call for more info about datasets in external repository."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.repository.variantsetId">
      <path value="Sequence.repository.variantsetId"/>
      <short value="Id of the variantset that used to call for variantset in repository"/>
      <definition value="Id of the variantset in this external repository. The server will understand how to use this id to call for more info about variantsets in external repository."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.repository.readsetId">
      <path value="Sequence.repository.readsetId"/>
      <short value="Id of the read"/>
      <definition value="Id of the read in this external repository."/>
      <min value="0"/>
      <max value="1"/>
      <type>
        <code value="string"/>
      </type>
      <isSummary value="true"/>
    </element>
    <element id="Sequence.pointer">
      <path value="Sequence.pointer"/>
      <short value="Pointer to next atomic sequence"/>
      <definition value="Pointer to next atomic sequence which at most contains one variant."/>
      <min value="0"/>
      <max value="*"/>
      <type>
        <code value="Reference"/>
        <targetProfile value="http://hl7.org/fhir/StructureDefinition/Sequence"/>
      </type>
      <isSummary value="true"/>
    </element>
  </differential>
</StructureDefinition>