<status value="active" /> <date value="2025-11-04" /> <publisher value="Robert Koch-Institut" /> <contact> <telecom> <system value="email" /> <value value="demis-support@rki.de" /> </telecom> </contact> <description value="Die Sequenz umfasst Informationen zu einer biologischen Sequenz, hier DNA-Sequenz. Es kann sich hierbei auch um Sequenzrohdaten oder assemblierte Daten handeln, jeweils mit den dazugehörigen Metadaten (z.B. Datum der Probennahme, Sequenzierungsgerät, Adapter für die Library Preparation, Upload in eine Online-Datenbank (Repositorium), etc.) handeln." /> <jurisdiction> <coding> <system value="urn:iso:std:iso:3166" /> <version value="ALPHA-2" /> <code value="DE" /> </coding> </jurisdiction> <copyright value="Copyright (C) 2021-2025 Robert Koch-Institut" /> <fhirVersion value="4.0.1" /> <kind value="resource" /> <abstract value="false" /> <type value="MolecularSequence" /> <baseDefinition value="http://hl7.org/fhir/StructureDefinition/MolecularSequence" /> <derivation value="constraint" /> <snapshot> <element id="MolecularSequence"> <path value="MolecularSequence" /> <short value="Information about a biological sequence" /> <definition value="Raw data describing a biological sequence." /> <min value="0" /> <max value="*" /> <base> <path value="MolecularSequence" /> <min value="0" /> <max value="*" /> </base> <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="http://hl7.org/fhir/StructureDefinition/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="http://hl7.org/fhir/StructureDefinition/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 or SHALL refer to the containing resource" /> <expression value="contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()" /> <xpath value="not(exists(for $id in f:contained/*/f:id/@value return $contained[not(parent::*/descendant::f:reference/@value=concat('#', $contained/*/id/@value) or descendant::f:reference[@value='#'])]))" /> <source value="http://hl7.org/fhir/StructureDefinition/DomainResource" /> </constraint> <constraint> <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice"> <valueBoolean value="true" /> </extension> <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bestpractice-explanation"> <valueMarkdown value="When a resource has no narrative, only systems that fully understand the data can display the resource to a human safely. Including a human readable representation in the resource makes for a much more robust eco-system and cheaper handling of resources by intermediary systems. Some ecosystems restrict distribution of resources to only those systems that do fully understand the resources, and as a consequence implementers may believe that the narrative is superfluous. However experience shows that such eco-systems often open up to new participants over time." /> </extension> <key value="dom-6" /> <severity value="warning" /> <human value="A resource should have narrative for robust management" /> <expression value="text.`div`.exists()" /> <xpath value="exists(f:text/h:div)" /> <source value="http://hl7.org/fhir/StructureDefinition/DomainResource" /> </constraint> <constraint> <key value="dom-5" /> <severity value="error" /> <human value="If a resource is contained in another resource, it SHALL NOT have a security label" /> <expression value="contained.meta.security.empty()" /> <xpath value="not(exists(f:contained/*/f:meta/f:security))" /> <source value="http://hl7.org/fhir/StructureDefinition/DomainResource" /> </constraint> <constraint> <key value="msq-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" /> <source value="http://hl7.org/fhir/StructureDefinition/MolecularSequence" /> </constraint> <mapping> <identity value="rim" /> <map value="Entity. Role, or Act" /> </mapping> </element> <element id="MolecularSequence.id"> <path value="MolecularSequence.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> <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type"> <valueUrl value="string" /> </extension> <code value="http://hl7.org/fhirpath/System.String" /> </type> <isSummary value="true" /> </element> <element id="MolecularSequence.meta"> <path value="MolecularSequence.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 might not always be associated with version changes to the resource." /> <min value="1" /> <max value="1" /> <base> <path value="Resource.meta" /> <min value="0" /> <max value="1" /> </base> <type> <code value="Meta" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <mustSupport value="true" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.meta.id"> <path value="MolecularSequence.meta.id" /> <representation value="xmlAttr" /> <short value="Unique id for inter-element referencing" /> <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> <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type"> <valueUrl value="string" /> </extension> <code value="http://hl7.org/fhirpath/System.String" /> </type> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.meta.extension"> <path value="MolecularSequence.meta.extension" /> <slicing> <discriminator> <type value="value" /> <path value="url" /> </discriminator> <description value="Extensions are always sliced by (at least) url" /> <rules value="open" /> </slicing> <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. 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 can 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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.meta.versionId"> <path value="MolecularSequence.meta.versionId" /> <short value="Version specific identifier" /> <definition value="The version specific identifier, as it appears in the version portion of the URL. This value changes when the resource is created, updated, or deleted." /> <comment value="The server assigns this value, and ignores what the client specifies, except in the case that the server is imposing version integrity on updates/deletes." /> <min value="0" /> <max value="1" /> <base> <path value="Meta.versionId" /> <min value="0" /> <max value="1" /> </base> <type> <code value="id" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.meta.lastUpdated"> <path value="MolecularSequence.meta.lastUpdated" /> <short value="When the resource version last changed" /> <definition value="When the resource last changed - e.g. when the version changed." /> <comment value="This value is always populated except when the resource is first being created. The server / resource manager sets this value; what a client provides is irrelevant. This is equivalent to the HTTP Last-Modified and SHOULD have the same value on a [read](http.html#read) interaction." /> <min value="0" /> <max value="1" /> <base> <path value="Meta.lastUpdated" /> <min value="0" /> <max value="1" /> </base> <type> <code value="instant" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.meta.source"> <path value="MolecularSequence.meta.source" /> <short value="Identifies where the resource comes from" /> <definition value="A uri that identifies the source system of the resource. This provides a minimal amount of [Provenance](provenance.html#) information that can be used to track or differentiate the source of information in the resource. The source may identify another FHIR server, document, message, database, etc." /> <comment value="In the provenance resource, this corresponds to Provenance.entity.what[x]. The exact use of the source (and the implied Provenance.entity.role) is left to implementer discretion. Only one nominated source is allowed; for additional provenance details, a full Provenance resource should be used. This element can be used to indicate where the current master source of a resource that has a canonical URL if the resource is no longer hosted at the canonical URL." /> <min value="0" /> <max value="1" /> <base> <path value="Meta.source" /> <min value="0" /> <max value="1" /> </base> <type> <code value="uri" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.meta.profile"> <path value="MolecularSequence.meta.profile" /> <short value="Profiles this resource claims to conform to" /> <definition value="A list of profiles (references to [StructureDefinition](structuredefinition.html#) resources) that this resource claims to conform to. The URL is a reference to [StructureDefinition.url](structuredefinition-definitions.html#StructureDefinition.url)." /> <comment value="It is up to the server and/or other infrastructure of policy to determine whether/how these claims are verified and/or updated over time. The list of profile URLs is a set." /> <min value="1" /> <max value="1" /> <base> <path value="Meta.profile" /> <min value="0" /> <max value="*" /> </base> <type> <code value="canonical" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/StructureDefinition" /> </type> <patternCanonical value="https://demis.rki.de/fhir/igs/StructureDefinition/Sequence" /> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <mustSupport value="true" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.meta.security"> <path value="MolecularSequence.meta.security" /> <short value="Security Labels applied to this resource" /> <definition value="Security labels applied to this resource. These tags connect specific resources to the overall security policy and infrastructure." /> <comment value="The security labels can be updated without changing the stated version of the resource. The list of security labels is a set. Uniqueness is based the system/code, and version and display are ignored." /> <min value="0" /> <max value="*" /> <base> <path value="Meta.security" /> <min value="0" /> <max value="*" /> </base> <type> <code value="Coding" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <binding> <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName"> <valueString value="SecurityLabels" /> </extension> <strength value="extensible" /> <description value="Security Labels from the Healthcare Privacy and Security Classification System." /> <valueSet value="http://hl7.org/fhir/ValueSet/security-labels" /> </binding> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="v2" /> <map value="CE/CNE/CWE subset one of the sets of component 1-3 or 4-6" /> </mapping> <mapping> <identity value="rim" /> <map value="CV" /> </mapping> <mapping> <identity value="orim" /> <map value="fhir:Coding rdfs:subClassOf dt:CDCoding" /> </mapping> </element> <element id="MolecularSequence.meta.tag"> <path value="MolecularSequence.meta.tag" /> <short value="Tags applied to this resource" /> <definition value="Tags applied to this resource. Tags are intended to be used to identify and relate resources to process and workflow, and applications are not required to consider the tags when interpreting the meaning of a resource." /> <comment value="The tags can be updated without changing the stated version of the resource. The list of tags is a set. Uniqueness is based the system/code, and version and display are ignored." /> <min value="0" /> <max value="*" /> <base> <path value="Meta.tag" /> <min value="0" /> <max value="*" /> </base> <type> <code value="Coding" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <binding> <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName"> <valueString value="Tags" /> </extension> <strength value="example" /> <description value="Codes that represent various types of tags, commonly workflow-related; e.g. "Needs review by Dr. Jones"." /> <valueSet value="http://hl7.org/fhir/ValueSet/common-tags" /> </binding> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="v2" /> <map value="CE/CNE/CWE subset one of the sets of component 1-3 or 4-6" /> </mapping> <mapping> <identity value="rim" /> <map value="CV" /> </mapping> <mapping> <identity value="orim" /> <map value="fhir:Coding rdfs:subClassOf dt:CDCoding" /> </mapping> </element> <element id="MolecularSequence.implicitRules"> <path value="MolecularSequence.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. Often, this is a reference to an implementation guide that defines the special rules along with other profiles etc." /> <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. Often, when used, the URL is a reference to an implementation guide that defines these special rules as part of it's narrative along with other profiles, value sets, etc." /> <min value="0" /> <max value="1" /> <base> <path value="Resource.implicitRules" /> <min value="0" /> <max value="1" /> </base> <type> <code value="uri" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isModifier value="true" /> <isModifierReason value="This element is labeled as a modifier because the implicit rules may provide additional knowledge about the resource that modifies it's meaning or interpretation" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.language"> <path value="MolecularSequence.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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <binding> <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"> <valueCanonical value="http://hl7.org/fhir/ValueSet/all-languages" /> </extension> <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName"> <valueString value="Language" /> </extension> <strength value="preferred" /> <description value="A human language." /> <valueSet value="http://hl7.org/fhir/ValueSet/languages" /> </binding> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.text"> <path value="MolecularSequence.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 can 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 "clinically safe" 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 "text blob" or where text is additionally entered raw or narrated and encoded information 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="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> <mapping> <identity value="rim" /> <map value="Act.text?" /> </mapping> </element> <element id="MolecularSequence.contained"> <path value="MolecularSequence.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. Contained resources may have profiles and tags In their meta elements, but SHALL NOT have security labels." /> <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="Entity. Role, or Act" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.extension"> <path value="MolecularSequence.extension" /> <slicing> <discriminator> <type value="value" /> <path value="url" /> </discriminator> <description value="Extensions are always sliced by (at least) url" /> <rules value="open" /> </slicing> <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. 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 can 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="1" /> <max value="*" /> <base> <path value="DomainResource.extension" /> <min value="0" /> <max value="*" /> </base> <type> <code value="Extension" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mustSupport value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.extension:sequenceAuthor"> <path value="MolecularSequence.extension" /> <sliceName value="sequenceAuthor" /> <short value="Person/Labor, die/das verantwortlich für die Sequenz ist" /> <definition value="Person/Labor, die/das verantwortlich für die Sequenz ist" /> <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="1" /> <base> <path value="DomainResource.extension" /> <min value="0" /> <max value="*" /> </base> <type> <code value="Extension" /> <profile value="https://demis.rki.de/fhir/igs/StructureDefinition/SequenceAuthor" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mustSupport value="true" /> <isModifier value="false" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.extension:sequencingReason"> <path value="MolecularSequence.extension" /> <sliceName value="sequencingReason" /> <short value="Grund der Sequenzierung" /> <definition value="Grund der Sequenzierung" /> <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="1" /> <base> <path value="DomainResource.extension" /> <min value="0" /> <max value="*" /> </base> <type> <code value="Extension" /> <profile value="https://demis.rki.de/fhir/igs/StructureDefinition/SequencingReason" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mustSupport value="true" /> <isModifier value="false" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.extension:sequenceDocumentReference"> <path value="MolecularSequence.extension" /> <sliceName value="sequenceDocumentReference" /> <short value="Referenz auf die Sequenz" /> <definition value="Referenz auf die Sequenz" /> <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="1" /> <max value="*" /> <base> <path value="DomainResource.extension" /> <min value="0" /> <max value="*" /> </base> <type> <code value="Extension" /> <profile value="https://demis.rki.de/fhir/igs/StructureDefinition/SequenceDocumentReference" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mustSupport value="true" /> <isModifier value="false" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.modifierExtension"> <path value="MolecularSequence.modifierExtension" /> <slicing> <discriminator> <type value="value" /> <path value="url" /> </discriminator> <description value="Extensions are always sliced by (at least) url" /> <rules value="open" /> </slicing> <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 and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself)." /> <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." /> <requirements value="Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](extensibility.html#modifierExtension)." /> <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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <isModifier value="true" /> <isModifierReason value="Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.identifier"> <path value="MolecularSequence.identifier" /> <short value="Laboreigener Identifier der Probe" /> <definition value="Eineindeutiger Identifier der Probe, die vom einreichenden Labor verwendet wird." /> <requirements value="Allows sequences to be distinguished and referenced." /> <min value="1" /> <max value="1" /> <base> <path value="MolecularSequence.identifier" /> <min value="0" /> <max value="*" /> </base> <type> <code value="Identifier" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <mustSupport value="true" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="v2" /> <map value="CX / EI (occasionally, more often EI maps to a resource id or a URL)" /> </mapping> <mapping> <identity value="rim" /> <map value="II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT]" /> </mapping> <mapping> <identity value="servd" /> <map value="Identifier" /> </mapping> <mapping> <identity value="w5" /> <map value="FiveWs.identifier" /> </mapping> </element> <element id="MolecularSequence.type"> <path value="MolecularSequence.type" /> <short value="Typ der Sequenz" /> <definition value="Für DEMIS ist der Typ grundsätzlich mit dem Wert „dna“ zu belegen." /> <comment value="Note that FHIR strings SHALL NOT exceed 1MB in size" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.type" /> <min value="0" /> <max value="1" /> </base> <type> <code value="code" /> </type> <fixedCode value="dna" /> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <mustSupport value="true" /> <isSummary value="true" /> <binding> <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName"> <valueString value="sequenceType" /> </extension> <strength value="required" /> <description value="Type if a sequence -- DNA, RNA, or amino acid sequence." /> <valueSet value="http://hl7.org/fhir/ValueSet/sequence-type|4.0.1" /> </binding> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.coordinateSystem"> <path value="MolecularSequence.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)." /> <comment value="32 bit number; for values larger than this, use decimal" /> <min value="1" /> <max value="1" /> <base> <path value="MolecularSequence.coordinateSystem" /> <min value="1" /> <max value="1" /> </base> <type> <code value="integer" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.patient"> <path value="MolecularSequence.patient" /> <short value="Who and/or what this is about" /> <definition value="The patient whose sequencing results are described by this resource." /> <comment value="References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository." /> <min value="0" /> <max value="0" /> <base> <path value="MolecularSequence.patient" /> <min value="0" /> <max value="1" /> </base> <type> <code value="Reference" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/Patient" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ref-1" /> <severity value="error" /> <human value="SHALL have a contained resource if a local reference is provided" /> <expression value="reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))" /> <xpath value="not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Reference" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="The target of a resource reference is a RIM entry point (Act, Role, or Entity)" /> </mapping> </element> <element id="MolecularSequence.specimen"> <path value="MolecularSequence.specimen" /> <short value="Verweis auf die Sequenz-Probe" /> <definition value="Verweis auf die Sequenz-Probe" /> <comment value="References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository." /> <min value="1" /> <max value="1" /> <base> <path value="MolecularSequence.specimen" /> <min value="0" /> <max value="1" /> </base> <type> <code value="Reference" /> <targetProfile value="https://demis.rki.de/fhir/igs/StructureDefinition/SpecimenSequence" /> <aggregation value="bundled" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ref-1" /> <severity value="error" /> <human value="SHALL have a contained resource if a local reference is provided" /> <expression value="reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))" /> <xpath value="not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Reference" /> </constraint> <mustSupport value="true" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="The target of a resource reference is a RIM entry point (Act, Role, or Entity)" /> </mapping> </element> <element id="MolecularSequence.specimen.id"> <path value="MolecularSequence.specimen.id" /> <representation value="xmlAttr" /> <short value="Unique id for inter-element referencing" /> <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> <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type"> <valueUrl value="string" /> </extension> <code value="http://hl7.org/fhirpath/System.String" /> </type> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.specimen.extension"> <path value="MolecularSequence.specimen.extension" /> <slicing> <discriminator> <type value="value" /> <path value="url" /> </discriminator> <description value="Extensions are always sliced by (at least) url" /> <rules value="open" /> </slicing> <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. 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 can 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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.specimen.reference"> <path value="MolecularSequence.specimen.reference" /> <short value="Literal reference, Relative, internal or absolute URL" /> <definition value="A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources." /> <comment value="Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure "/[type]/[id]" then it should be assumed that the reference is to a FHIR RESTful server." /> <min value="1" /> <max value="1" /> <base> <path value="Reference.reference" /> <min value="0" /> <max value="1" /> </base> <type> <code value="string" /> </type> <condition value="ele-1" /> <condition value="ref-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <mustSupport value="true" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.specimen.type"> <path value="MolecularSequence.specimen.type" /> <short value="Type the reference refers to (e.g. "Patient")" /> <definition value="The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent. The type is the Canonical URL of Resource Definition that is the type this reference refers to. References are URLs that are relative to http://hl7.org/fhir/StructureDefinition/ e.g. "Patient" is a reference to http://hl7.org/fhir/StructureDefinition/Patient. Absolute URLs are only allowed for logical models (and can only be used in references in logical models, not resources)." /> <comment value="This element is used to indicate the type of the target of the reference. This may be used which ever of the other elements are populated (or not). In some cases, the type of the target may be determined by inspection of the reference (e.g. a RESTful URL) or by resolving the target of the reference; if both the type and a reference is provided, the reference SHALL resolve to a resource of the same type as that specified." /> <min value="0" /> <max value="1" /> <base> <path value="Reference.type" /> <min value="0" /> <max value="1" /> </base> <type> <code value="uri" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <binding> <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName"> <valueString value="FHIRResourceTypeExt" /> </extension> <strength value="extensible" /> <description value="Aa resource (or, for logical models, the URI of the logical model)." /> <valueSet value="http://hl7.org/fhir/ValueSet/resource-types" /> </binding> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.specimen.identifier"> <path value="MolecularSequence.specimen.identifier" /> <short value="Logical reference, when literal reference is not known" /> <definition value="An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference." /> <comment value="When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it. Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any)." /> <min value="0" /> <max value="1" /> <base> <path value="Reference.identifier" /> <min value="0" /> <max value="1" /> </base> <type> <code value="Identifier" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="v2" /> <map value="CX / EI (occasionally, more often EI maps to a resource id or a URL)" /> </mapping> <mapping> <identity value="rim" /> <map value="II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT]" /> </mapping> <mapping> <identity value="servd" /> <map value="Identifier" /> </mapping> <mapping> <identity value="rim" /> <map value=".identifier" /> </mapping> </element> <element id="MolecularSequence.specimen.display"> <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable"> <valueBoolean value="true" /> </extension> <path value="MolecularSequence.specimen.display" /> <short value="Text alternative for the resource" /> <definition value="Plain text narrative that identifies the resource in addition to the resource reference." /> <comment value="This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it." /> <min value="0" /> <max value="1" /> <base> <path value="Reference.display" /> <min value="0" /> <max value="1" /> </base> <type> <code value="string" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.device"> <path value="MolecularSequence.device" /> <short value="Verweis auf das Sequenziergerät" /> <definition value="Verweis auf das Sequenziergerät" /> <comment value="References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository." /> <min value="1" /> <max value="1" /> <base> <path value="MolecularSequence.device" /> <min value="0" /> <max value="1" /> </base> <type> <code value="Reference" /> <targetProfile value="https://demis.rki.de/fhir/igs/StructureDefinition/SequencingDevice" /> <aggregation value="bundled" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ref-1" /> <severity value="error" /> <human value="SHALL have a contained resource if a local reference is provided" /> <expression value="reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))" /> <xpath value="not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Reference" /> </constraint> <mustSupport value="true" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="The target of a resource reference is a RIM entry point (Act, Role, or Entity)" /> </mapping> </element> <element id="MolecularSequence.device.id"> <path value="MolecularSequence.device.id" /> <representation value="xmlAttr" /> <short value="Unique id for inter-element referencing" /> <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> <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type"> <valueUrl value="string" /> </extension> <code value="http://hl7.org/fhirpath/System.String" /> </type> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.device.extension"> <path value="MolecularSequence.device.extension" /> <slicing> <discriminator> <type value="value" /> <path value="url" /> </discriminator> <description value="Extensions are always sliced by (at least) url" /> <rules value="open" /> </slicing> <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. 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 can 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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.device.reference"> <path value="MolecularSequence.device.reference" /> <short value="Literal reference, Relative, internal or absolute URL" /> <definition value="A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources." /> <comment value="Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure "/[type]/[id]" then it should be assumed that the reference is to a FHIR RESTful server." /> <min value="1" /> <max value="1" /> <base> <path value="Reference.reference" /> <min value="0" /> <max value="1" /> </base> <type> <code value="string" /> </type> <condition value="ele-1" /> <condition value="ref-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <mustSupport value="true" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.device.type"> <path value="MolecularSequence.device.type" /> <short value="Type the reference refers to (e.g. "Patient")" /> <definition value="The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent. The type is the Canonical URL of Resource Definition that is the type this reference refers to. References are URLs that are relative to http://hl7.org/fhir/StructureDefinition/ e.g. "Patient" is a reference to http://hl7.org/fhir/StructureDefinition/Patient. Absolute URLs are only allowed for logical models (and can only be used in references in logical models, not resources)." /> <comment value="This element is used to indicate the type of the target of the reference. This may be used which ever of the other elements are populated (or not). In some cases, the type of the target may be determined by inspection of the reference (e.g. a RESTful URL) or by resolving the target of the reference; if both the type and a reference is provided, the reference SHALL resolve to a resource of the same type as that specified." /> <min value="0" /> <max value="1" /> <base> <path value="Reference.type" /> <min value="0" /> <max value="1" /> </base> <type> <code value="uri" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <binding> <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName"> <valueString value="FHIRResourceTypeExt" /> </extension> <strength value="extensible" /> <description value="Aa resource (or, for logical models, the URI of the logical model)." /> <valueSet value="http://hl7.org/fhir/ValueSet/resource-types" /> </binding> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.device.identifier"> <path value="MolecularSequence.device.identifier" /> <short value="Logical reference, when literal reference is not known" /> <definition value="An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference." /> <comment value="When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it. Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any)." /> <min value="0" /> <max value="1" /> <base> <path value="Reference.identifier" /> <min value="0" /> <max value="1" /> </base> <type> <code value="Identifier" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="v2" /> <map value="CX / EI (occasionally, more often EI maps to a resource id or a URL)" /> </mapping> <mapping> <identity value="rim" /> <map value="II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT]" /> </mapping> <mapping> <identity value="servd" /> <map value="Identifier" /> </mapping> <mapping> <identity value="rim" /> <map value=".identifier" /> </mapping> </element> <element id="MolecularSequence.device.display"> <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable"> <valueBoolean value="true" /> </extension> <path value="MolecularSequence.device.display" /> <short value="Text alternative for the resource" /> <definition value="Plain text narrative that identifies the resource in addition to the resource reference." /> <comment value="This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it." /> <min value="0" /> <max value="1" /> <base> <path value="Reference.display" /> <min value="0" /> <max value="1" /> </base> <type> <code value="string" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.performer"> <path value="MolecularSequence.performer" /> <short value="Verweis auf die Melder-Einrichtung" /> <definition value="Verweis auf die Melder-Einrichtung" /> <comment value="References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository." /> <min value="1" /> <max value="1" /> <base> <path value="MolecularSequence.performer" /> <min value="0" /> <max value="1" /> </base> <type> <code value="Reference" /> <targetProfile value="https://demis.rki.de/fhir/StructureDefinition/NotifierFacility" /> <aggregation value="bundled" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ref-1" /> <severity value="error" /> <human value="SHALL have a contained resource if a local reference is provided" /> <expression value="reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))" /> <xpath value="not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Reference" /> </constraint> <mustSupport value="true" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="The target of a resource reference is a RIM entry point (Act, Role, or Entity)" /> </mapping> </element> <element id="MolecularSequence.performer.id"> <path value="MolecularSequence.performer.id" /> <representation value="xmlAttr" /> <short value="Unique id for inter-element referencing" /> <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> <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type"> <valueUrl value="string" /> </extension> <code value="http://hl7.org/fhirpath/System.String" /> </type> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.performer.extension"> <path value="MolecularSequence.performer.extension" /> <slicing> <discriminator> <type value="value" /> <path value="url" /> </discriminator> <description value="Extensions are always sliced by (at least) url" /> <rules value="open" /> </slicing> <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. 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 can 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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.performer.reference"> <path value="MolecularSequence.performer.reference" /> <short value="Literal reference, Relative, internal or absolute URL" /> <definition value="A reference to a location at which the other resource is found. The reference may be a relative reference, in which case it is relative to the service base URL, or an absolute URL that resolves to the location where the resource is found. The reference may be version specific or not. If the reference is not to a FHIR RESTful server, then it should be assumed to be version specific. Internal fragment references (start with '#') refer to contained resources." /> <comment value="Using absolute URLs provides a stable scalable approach suitable for a cloud/web context, while using relative/logical references provides a flexible approach suitable for use when trading across closed eco-system boundaries. Absolute URLs do not need to point to a FHIR RESTful server, though this is the preferred approach. If the URL conforms to the structure "/[type]/[id]" then it should be assumed that the reference is to a FHIR RESTful server." /> <min value="1" /> <max value="1" /> <base> <path value="Reference.reference" /> <min value="0" /> <max value="1" /> </base> <type> <code value="string" /> </type> <condition value="ele-1" /> <condition value="ref-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <mustSupport value="true" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.performer.type"> <path value="MolecularSequence.performer.type" /> <short value="Type the reference refers to (e.g. "Patient")" /> <definition value="The expected type of the target of the reference. If both Reference.type and Reference.reference are populated and Reference.reference is a FHIR URL, both SHALL be consistent. The type is the Canonical URL of Resource Definition that is the type this reference refers to. References are URLs that are relative to http://hl7.org/fhir/StructureDefinition/ e.g. "Patient" is a reference to http://hl7.org/fhir/StructureDefinition/Patient. Absolute URLs are only allowed for logical models (and can only be used in references in logical models, not resources)." /> <comment value="This element is used to indicate the type of the target of the reference. This may be used which ever of the other elements are populated (or not). In some cases, the type of the target may be determined by inspection of the reference (e.g. a RESTful URL) or by resolving the target of the reference; if both the type and a reference is provided, the reference SHALL resolve to a resource of the same type as that specified." /> <min value="0" /> <max value="1" /> <base> <path value="Reference.type" /> <min value="0" /> <max value="1" /> </base> <type> <code value="uri" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <binding> <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName"> <valueString value="FHIRResourceTypeExt" /> </extension> <strength value="extensible" /> <description value="Aa resource (or, for logical models, the URI of the logical model)." /> <valueSet value="http://hl7.org/fhir/ValueSet/resource-types" /> </binding> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.performer.identifier"> <path value="MolecularSequence.performer.identifier" /> <short value="Logical reference, when literal reference is not known" /> <definition value="An identifier for the target resource. This is used when there is no way to reference the other resource directly, either because the entity it represents is not available through a FHIR server, or because there is no way for the author of the resource to convert a known identifier to an actual location. There is no requirement that a Reference.identifier point to something that is actually exposed as a FHIR instance, but it SHALL point to a business concept that would be expected to be exposed as a FHIR instance, and that instance would need to be of a FHIR resource type allowed by the reference." /> <comment value="When an identifier is provided in place of a reference, any system processing the reference will only be able to resolve the identifier to a reference if it understands the business context in which the identifier is used. Sometimes this is global (e.g. a national identifier) but often it is not. For this reason, none of the useful mechanisms described for working with references (e.g. chaining, includes) are possible, nor should servers be expected to be able resolve the reference. Servers may accept an identifier based reference untouched, resolve it, and/or reject it - see CapabilityStatement.rest.resource.referencePolicy. When both an identifier and a literal reference are provided, the literal reference is preferred. Applications processing the resource are allowed - but not required - to check that the identifier matches the literal reference Applications converting a logical reference to a literal reference may choose to leave the logical reference present, or remove it. Reference is intended to point to a structure that can potentially be expressed as a FHIR resource, though there is no need for it to exist as an actual FHIR resource instance - except in as much as an application wishes to actual find the target of the reference. The content referred to be the identifier must meet the logical constraints implied by any limitations on what resource types are permitted for the reference. For example, it would not be legitimate to send the identifier for a drug prescription if the type were Reference(Observation|DiagnosticReport). One of the use-cases for Reference.identifier is the situation where no FHIR representation exists (where the type is Reference (Any)." /> <min value="0" /> <max value="1" /> <base> <path value="Reference.identifier" /> <min value="0" /> <max value="1" /> </base> <type> <code value="Identifier" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="v2" /> <map value="CX / EI (occasionally, more often EI maps to a resource id or a URL)" /> </mapping> <mapping> <identity value="rim" /> <map value="II - The Identifier class is a little looser than the v3 type II because it allows URIs as well as registered OIDs or GUIDs. Also maps to Role[classCode=IDENT]" /> </mapping> <mapping> <identity value="servd" /> <map value="Identifier" /> </mapping> <mapping> <identity value="rim" /> <map value=".identifier" /> </mapping> </element> <element id="MolecularSequence.performer.display"> <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable"> <valueBoolean value="true" /> </extension> <path value="MolecularSequence.performer.display" /> <short value="Text alternative for the resource" /> <definition value="Plain text narrative that identifies the resource in addition to the resource reference." /> <comment value="This is generally not the same as the Resource.text of the referenced resource. The purpose is to identify what's being referenced, not to fully describe it." /> <min value="0" /> <max value="1" /> <base> <path value="Reference.display" /> <min value="0" /> <max value="1" /> </base> <type> <code value="string" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.quantity"> <path value="MolecularSequence.quantity" /> <short value="The number of copies of the sequence of interest. (RNASeq)" /> <definition value="The number of copies of the sequence of interest. (RNASeq)." /> <comment value="The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator." /> <min value="0" /> <max value="0" /> <base> <path value="MolecularSequence.quantity" /> <min value="0" /> <max value="1" /> </base> <type> <code value="Quantity" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="qty-3" /> <severity value="error" /> <human value="If a code for the unit is present, the system SHALL also be present" /> <expression value="code.empty() or system.exists()" /> <xpath value="not(exists(f:code)) or exists(f:system)" /> <source value="http://hl7.org/fhir/StructureDefinition/Quantity" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="v2" /> <map value="SN (see also Range) or CQ" /> </mapping> <mapping> <identity value="rim" /> <map value="PQ, IVL<PQ>, MO, CO, depending on the values" /> </mapping> </element> <element id="MolecularSequence.referenceSeq"> <path value="MolecularSequence.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="0" /> <base> <path value="MolecularSequence.referenceSeq" /> <min value="0" /> <max value="1" /> </base> <type> <code value="BackboneElement" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="msq-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" /> <source value="http://hl7.org/fhir/StructureDefinition/MolecularSequence" /> </constraint> <constraint> <key value="msq-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)))" /> <source value="http://hl7.org/fhir/StructureDefinition/MolecularSequence" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.referenceSeq.id"> <path value="MolecularSequence.referenceSeq.id" /> <representation value="xmlAttr" /> <short value="Unique id for inter-element referencing" /> <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> <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type"> <valueUrl value="string" /> </extension> <code value="http://hl7.org/fhirpath/System.String" /> </type> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.referenceSeq.extension"> <path value="MolecularSequence.referenceSeq.extension" /> <slicing> <discriminator> <type value="value" /> <path value="url" /> </discriminator> <description value="Extensions are always sliced by (at least) url" /> <rules value="open" /> </slicing> <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. 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 can 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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.referenceSeq.modifierExtension"> <path value="MolecularSequence.referenceSeq.modifierExtension" /> <short value="Extensions that cannot be ignored even if unrecognized" /> <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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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 can 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. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself)." /> <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." /> <requirements value="Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](extensibility.html#modifierExtension)." /> <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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <isModifier value="true" /> <isModifierReason value="Modifier extensions are expected to modify the meaning or interpretation of the element that contains them" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.referenceSeq.chromosome"> <path value="MolecularSequence.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))." /> <comment value="Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination." /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.referenceSeq.chromosome" /> <min value="0" /> <max value="1" /> </base> <type> <code value="CodeableConcept" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <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." /> <valueSet value="http://hl7.org/fhir/ValueSet/chromosome-human" /> </binding> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="v2" /> <map value="CE/CNE/CWE" /> </mapping> <mapping> <identity value="rim" /> <map value="CD" /> </mapping> <mapping> <identity value="orim" /> <map value="fhir:CodeableConcept rdfs:subClassOf dt:CD" /> </mapping> </element> <element id="MolecularSequence.referenceSeq.genomeBuild"> <path value="MolecularSequence.referenceSeq.genomeBuild" /> <short value="The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'" /> <definition value="The Genome Build used for reference, following GRCh build versions e.g. 'GRCh 37'. Version number must be included if a versioned release of a primary build was used." /> <comment value="Note that FHIR strings SHALL NOT exceed 1MB in size" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.referenceSeq.genomeBuild" /> <min value="0" /> <max value="1" /> </base> <type> <code value="string" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.referenceSeq.orientation"> <path value="MolecularSequence.referenceSeq.orientation" /> <short value="sense | antisense" /> <definition value="A relative reference to a DNA strand based on gene orientation. The strand that contains the open reading frame of the gene is the "sense" strand, and the opposite complementary strand is the "antisense" strand." /> <comment value="Note that FHIR strings SHALL NOT exceed 1MB in size" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.referenceSeq.orientation" /> <min value="0" /> <max value="1" /> </base> <type> <code value="code" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <binding> <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName"> <valueString value="orientationType" /> </extension> <strength value="required" /> <description value="Type for orientation." /> <valueSet value="http://hl7.org/fhir/ValueSet/orientation-type|4.0.1" /> </binding> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.referenceSeq.referenceSeqId"> <path value="MolecularSequence.referenceSeq.referenceSeqId" /> <short value="Reference identifier" /> <definition value="Reference identifier of reference sequence submitted to NCBI. It must match the type in the MolecularSequence.type field. For example, the prefix, “NG_” identifies reference sequence for genes, “NM_” for messenger RNA transcripts, and “NP_” for amino acid sequences." /> <comment value="Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination." /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.referenceSeq.referenceSeqId" /> <min value="0" /> <max value="1" /> </base> <type> <code value="CodeableConcept" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <binding> <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName"> <valueString value="sequenceReference" /> </extension> <strength value="example" /> <description value="Reference identifier." /> <valueSet value="http://hl7.org/fhir/ValueSet/sequence-referenceSeq" /> </binding> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="v2" /> <map value="CE/CNE/CWE" /> </mapping> <mapping> <identity value="rim" /> <map value="CD" /> </mapping> <mapping> <identity value="orim" /> <map value="fhir:CodeableConcept rdfs:subClassOf dt:CD" /> </mapping> </element> <element id="MolecularSequence.referenceSeq.referenceSeqPointer"> <path value="MolecularSequence.referenceSeq.referenceSeqPointer" /> <short value="A pointer to another MolecularSequence entity as reference sequence" /> <definition value="A pointer to another MolecularSequence entity as reference sequence." /> <comment value="References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository." /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.referenceSeq.referenceSeqPointer" /> <min value="0" /> <max value="1" /> </base> <type> <code value="Reference" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/MolecularSequence" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ref-1" /> <severity value="error" /> <human value="SHALL have a contained resource if a local reference is provided" /> <expression value="reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))" /> <xpath value="not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Reference" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="The target of a resource reference is a RIM entry point (Act, Role, or Entity)" /> </mapping> </element> <element id="MolecularSequence.referenceSeq.referenceSeqString"> <path value="MolecularSequence.referenceSeq.referenceSeqString" /> <short value="A string to represent reference sequence" /> <definition value="A string like "ACGT"." /> <comment value="Note that FHIR strings SHALL NOT exceed 1MB in size" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.referenceSeq.referenceSeqString" /> <min value="0" /> <max value="1" /> </base> <type> <code value="string" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.referenceSeq.strand"> <path value="MolecularSequence.referenceSeq.strand" /> <short value="watson | crick" /> <definition value="An absolute reference to a strand. The Watson strand is the strand whose 5'-end is on the short arm of the chromosome, and the Crick strand as the one whose 5'-end is on the long arm." /> <comment value="Note that FHIR strings SHALL NOT exceed 1MB in size" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.referenceSeq.strand" /> <min value="0" /> <max value="1" /> </base> <type> <code value="code" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <binding> <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName"> <valueString value="strandType" /> </extension> <strength value="required" /> <description value="Type for strand." /> <valueSet value="http://hl7.org/fhir/ValueSet/strand-type|4.0.1" /> </binding> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.referenceSeq.windowStart"> <path value="MolecularSequence.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." /> <comment value="32 bit number; for values larger than this, use decimal" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.referenceSeq.windowStart" /> <min value="0" /> <max value="1" /> </base> <type> <code value="integer" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.referenceSeq.windowEnd"> <path value="MolecularSequence.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 exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position." /> <comment value="32 bit number; for values larger than this, use decimal" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.referenceSeq.windowEnd" /> <min value="0" /> <max value="1" /> </base> <type> <code value="integer" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.variant"> <path value="MolecularSequence.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="0" /> <base> <path value="MolecularSequence.variant" /> <min value="0" /> <max value="*" /> </base> <type> <code value="BackboneElement" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.variant.id"> <path value="MolecularSequence.variant.id" /> <representation value="xmlAttr" /> <short value="Unique id for inter-element referencing" /> <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> <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type"> <valueUrl value="string" /> </extension> <code value="http://hl7.org/fhirpath/System.String" /> </type> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.variant.extension"> <path value="MolecularSequence.variant.extension" /> <slicing> <discriminator> <type value="value" /> <path value="url" /> </discriminator> <description value="Extensions are always sliced by (at least) url" /> <rules value="open" /> </slicing> <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. 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 can 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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.variant.modifierExtension"> <path value="MolecularSequence.variant.modifierExtension" /> <short value="Extensions that cannot be ignored even if unrecognized" /> <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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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 can 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. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself)." /> <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." /> <requirements value="Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](extensibility.html#modifierExtension)." /> <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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <isModifier value="true" /> <isModifierReason value="Modifier extensions are expected to modify the meaning or interpretation of the element that contains them" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.variant.start"> <path value="MolecularSequence.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." /> <comment value="32 bit number; for values larger than this, use decimal" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.variant.start" /> <min value="0" /> <max value="1" /> </base> <type> <code value="integer" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.variant.end"> <path value="MolecularSequence.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 exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position." /> <comment value="32 bit number; for values larger than this, use decimal" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.variant.end" /> <min value="0" /> <max value="1" /> </base> <type> <code value="integer" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.variant.observedAllele"> <path value="MolecularSequence.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." /> <comment value="Note that FHIR strings SHALL NOT exceed 1MB in size" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.variant.observedAllele" /> <min value="0" /> <max value="1" /> </base> <type> <code value="string" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.variant.referenceAllele"> <path value="MolecularSequence.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." /> <comment value="Note that FHIR strings SHALL NOT exceed 1MB in size" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.variant.referenceAllele" /> <min value="0" /> <max value="1" /> </base> <type> <code value="string" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.variant.cigar"> <path value="MolecularSequence.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)." /> <comment value="Note that FHIR strings SHALL NOT exceed 1MB in size" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.variant.cigar" /> <min value="0" /> <max value="1" /> </base> <type> <code value="string" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.variant.variantPointer"> <path value="MolecularSequence.variant.variantPointer" /> <short value="Pointer to observed variant information" /> <definition value="A pointer to an Observation containing variant information." /> <comment value="References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository." /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.variant.variantPointer" /> <min value="0" /> <max value="1" /> </base> <type> <code value="Reference" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/Observation" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ref-1" /> <severity value="error" /> <human value="SHALL have a contained resource if a local reference is provided" /> <expression value="reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))" /> <xpath value="not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Reference" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="The target of a resource reference is a RIM entry point (Act, Role, or Entity)" /> </mapping> </element> <element id="MolecularSequence.observedSeq"> <path value="MolecularSequence.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 start from referenceSeq.windowStart and end by referenceSeq.windowEnd." /> <comment value="Note that FHIR strings SHALL NOT exceed 1MB in size" /> <min value="0" /> <max value="0" /> <base> <path value="MolecularSequence.observedSeq" /> <min value="0" /> <max value="1" /> </base> <type> <code value="string" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality"> <path value="MolecularSequence.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="0" /> <base> <path value="MolecularSequence.quality" /> <min value="0" /> <max value="*" /> </base> <type> <code value="BackboneElement" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.id"> <path value="MolecularSequence.quality.id" /> <representation value="xmlAttr" /> <short value="Unique id for inter-element referencing" /> <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> <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type"> <valueUrl value="string" /> </extension> <code value="http://hl7.org/fhirpath/System.String" /> </type> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.extension"> <path value="MolecularSequence.quality.extension" /> <slicing> <discriminator> <type value="value" /> <path value="url" /> </discriminator> <description value="Extensions are always sliced by (at least) url" /> <rules value="open" /> </slicing> <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. 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 can 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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.quality.modifierExtension"> <path value="MolecularSequence.quality.modifierExtension" /> <short value="Extensions that cannot be ignored even if unrecognized" /> <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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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 can 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. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself)." /> <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." /> <requirements value="Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](extensibility.html#modifierExtension)." /> <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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <isModifier value="true" /> <isModifierReason value="Modifier extensions are expected to modify the meaning or interpretation of the element that contains them" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.quality.type"> <path value="MolecularSequence.quality.type" /> <short value="indel | snp | unknown" /> <definition value="INDEL / SNP / Undefined variant." /> <comment value="Note that FHIR strings SHALL NOT exceed 1MB in size" /> <min value="1" /> <max value="1" /> <base> <path value="MolecularSequence.quality.type" /> <min value="1" /> <max value="1" /> </base> <type> <code value="code" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <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." /> <valueSet value="http://hl7.org/fhir/ValueSet/quality-type|4.0.1" /> </binding> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.standardSequence"> <path value="MolecularSequence.quality.standardSequence" /> <short value="Standard sequence for comparison" /> <definition value="Gold standard sequence used for comparing against." /> <comment value="Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination." /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.quality.standardSequence" /> <min value="0" /> <max value="1" /> </base> <type> <code value="CodeableConcept" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <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." /> <valueSet value="http://hl7.org/fhir/ValueSet/sequence-quality-standardSequence" /> </binding> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="v2" /> <map value="CE/CNE/CWE" /> </mapping> <mapping> <identity value="rim" /> <map value="CD" /> </mapping> <mapping> <identity value="orim" /> <map value="fhir:CodeableConcept rdfs:subClassOf dt:CD" /> </mapping> </element> <element id="MolecularSequence.quality.start"> <path value="MolecularSequence.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." /> <comment value="32 bit number; for values larger than this, use decimal" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.quality.start" /> <min value="0" /> <max value="1" /> </base> <type> <code value="integer" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.end"> <path value="MolecularSequence.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 exclusive and does not include the last position. If the coordinate system is 1-base, then end is inclusive and includes the last position." /> <comment value="32 bit number; for values larger than this, use decimal" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.quality.end" /> <min value="0" /> <max value="1" /> </base> <type> <code value="integer" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.score"> <path value="MolecularSequence.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))." /> <comment value="The context of use may frequently define what kind of quantity this is and therefore what kind of units can be used. The context of use may also restrict the values for the comparator." /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.quality.score" /> <min value="0" /> <max value="1" /> </base> <type> <code value="Quantity" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="qty-3" /> <severity value="error" /> <human value="If a code for the unit is present, the system SHALL also be present" /> <expression value="code.empty() or system.exists()" /> <xpath value="not(exists(f:code)) or exists(f:system)" /> <source value="http://hl7.org/fhir/StructureDefinition/Quantity" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="v2" /> <map value="SN (see also Range) or CQ" /> </mapping> <mapping> <identity value="rim" /> <map value="PQ, IVL<PQ>, MO, CO, depending on the values" /> </mapping> </element> <element id="MolecularSequence.quality.method"> <path value="MolecularSequence.quality.method" /> <short value="Method to get quality" /> <definition value="Which method is used to get sequence quality." /> <comment value="Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination." /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.quality.method" /> <min value="0" /> <max value="1" /> </base> <type> <code value="CodeableConcept" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <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." /> <valueSet value="http://hl7.org/fhir/ValueSet/sequence-quality-method" /> </binding> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="v2" /> <map value="CE/CNE/CWE" /> </mapping> <mapping> <identity value="rim" /> <map value="CD" /> </mapping> <mapping> <identity value="orim" /> <map value="fhir:CodeableConcept rdfs:subClassOf dt:CD" /> </mapping> </element> <element id="MolecularSequence.quality.truthTP"> <path value="MolecularSequence.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." /> <comment value="Do not use an IEEE type floating point type, instead use something that works like a true decimal, with inbuilt precision (e.g. Java BigInteger)" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.quality.truthTP" /> <min value="0" /> <max value="1" /> </base> <type> <code value="decimal" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.queryTP"> <path value="MolecularSequence.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." /> <comment value="Do not use an IEEE type floating point type, instead use something that works like a true decimal, with inbuilt precision (e.g. Java BigInteger)" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.quality.queryTP" /> <min value="0" /> <max value="1" /> </base> <type> <code value="decimal" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.truthFN"> <path value="MolecularSequence.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." /> <comment value="Do not use an IEEE type floating point type, instead use something that works like a true decimal, with inbuilt precision (e.g. Java BigInteger)" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.quality.truthFN" /> <min value="0" /> <max value="1" /> </base> <type> <code value="decimal" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.queryFP"> <path value="MolecularSequence.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." /> <comment value="Do not use an IEEE type floating point type, instead use something that works like a true decimal, with inbuilt precision (e.g. Java BigInteger)" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.quality.queryFP" /> <min value="0" /> <max value="1" /> </base> <type> <code value="decimal" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.gtFP"> <path value="MolecularSequence.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)." /> <comment value="Do not use an IEEE type floating point type, instead use something that works like a true decimal, with inbuilt precision (e.g. Java BigInteger)" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.quality.gtFP" /> <min value="0" /> <max value="1" /> </base> <type> <code value="decimal" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.precision"> <path value="MolecularSequence.quality.precision" /> <short value="Precision of comparison" /> <definition value="QUERY.TP / (QUERY.TP + QUERY.FP)." /> <comment value="Do not use an IEEE type floating point type, instead use something that works like a true decimal, with inbuilt precision (e.g. Java BigInteger)" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.quality.precision" /> <min value="0" /> <max value="1" /> </base> <type> <code value="decimal" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.recall"> <path value="MolecularSequence.quality.recall" /> <short value="Recall of comparison" /> <definition value="TRUTH.TP / (TRUTH.TP + TRUTH.FN)." /> <comment value="Do not use an IEEE type floating point type, instead use something that works like a true decimal, with inbuilt precision (e.g. Java BigInteger)" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.quality.recall" /> <min value="0" /> <max value="1" /> </base> <type> <code value="decimal" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.fScore"> <path value="MolecularSequence.quality.fScore" /> <short value="F-score" /> <definition value="Harmonic mean of Recall and Precision, computed as: 2 * precision * recall / (precision + recall)." /> <comment value="Do not use an IEEE type floating point type, instead use something that works like a true decimal, with inbuilt precision (e.g. Java BigInteger)" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.quality.fScore" /> <min value="0" /> <max value="1" /> </base> <type> <code value="decimal" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.roc"> <path value="MolecularSequence.quality.roc" /> <short value="Receiver Operator Characteristic (ROC) Curve" /> <definition value="Receiver Operator Characteristic (ROC) Curve to give sensitivity/specificity tradeoff." /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.quality.roc" /> <min value="0" /> <max value="1" /> </base> <type> <code value="BackboneElement" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.roc.id"> <path value="MolecularSequence.quality.roc.id" /> <representation value="xmlAttr" /> <short value="Unique id for inter-element referencing" /> <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> <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type"> <valueUrl value="string" /> </extension> <code value="http://hl7.org/fhirpath/System.String" /> </type> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.roc.extension"> <path value="MolecularSequence.quality.roc.extension" /> <slicing> <discriminator> <type value="value" /> <path value="url" /> </discriminator> <description value="Extensions are always sliced by (at least) url" /> <rules value="open" /> </slicing> <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. 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 can 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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.quality.roc.modifierExtension"> <path value="MolecularSequence.quality.roc.modifierExtension" /> <short value="Extensions that cannot be ignored even if unrecognized" /> <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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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 can 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. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself)." /> <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." /> <requirements value="Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](extensibility.html#modifierExtension)." /> <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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <isModifier value="true" /> <isModifierReason value="Modifier extensions are expected to modify the meaning or interpretation of the element that contains them" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.quality.roc.score"> <path value="MolecularSequence.quality.roc.score" /> <short value="Genotype quality score" /> <definition value="Invidual data point representing the GQ (genotype quality) score threshold." /> <comment value="32 bit number; for values larger than this, use decimal" /> <min value="0" /> <max value="*" /> <base> <path value="MolecularSequence.quality.roc.score" /> <min value="0" /> <max value="*" /> </base> <type> <code value="integer" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.roc.numTP"> <path value="MolecularSequence.quality.roc.numTP" /> <short value="Roc score true positive numbers" /> <definition value="The number of true positives if the GQ score threshold was set to "score" field value." /> <comment value="32 bit number; for values larger than this, use decimal" /> <min value="0" /> <max value="*" /> <base> <path value="MolecularSequence.quality.roc.numTP" /> <min value="0" /> <max value="*" /> </base> <type> <code value="integer" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.roc.numFP"> <path value="MolecularSequence.quality.roc.numFP" /> <short value="Roc score false positive numbers" /> <definition value="The number of false positives if the GQ score threshold was set to "score" field value." /> <comment value="32 bit number; for values larger than this, use decimal" /> <min value="0" /> <max value="*" /> <base> <path value="MolecularSequence.quality.roc.numFP" /> <min value="0" /> <max value="*" /> </base> <type> <code value="integer" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.roc.numFN"> <path value="MolecularSequence.quality.roc.numFN" /> <short value="Roc score false negative numbers" /> <definition value="The number of false negatives if the GQ score threshold was set to "score" field value." /> <comment value="32 bit number; for values larger than this, use decimal" /> <min value="0" /> <max value="*" /> <base> <path value="MolecularSequence.quality.roc.numFN" /> <min value="0" /> <max value="*" /> </base> <type> <code value="integer" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.roc.precision"> <path value="MolecularSequence.quality.roc.precision" /> <short value="Precision of the GQ score" /> <definition value="Calculated precision if the GQ score threshold was set to "score" field value." /> <comment value="Do not use an IEEE type floating point type, instead use something that works like a true decimal, with inbuilt precision (e.g. Java BigInteger)" /> <min value="0" /> <max value="*" /> <base> <path value="MolecularSequence.quality.roc.precision" /> <min value="0" /> <max value="*" /> </base> <type> <code value="decimal" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.roc.sensitivity"> <path value="MolecularSequence.quality.roc.sensitivity" /> <short value="Sensitivity of the GQ score" /> <definition value="Calculated sensitivity if the GQ score threshold was set to "score" field value." /> <comment value="Do not use an IEEE type floating point type, instead use something that works like a true decimal, with inbuilt precision (e.g. Java BigInteger)" /> <min value="0" /> <max value="*" /> <base> <path value="MolecularSequence.quality.roc.sensitivity" /> <min value="0" /> <max value="*" /> </base> <type> <code value="decimal" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.quality.roc.fMeasure"> <path value="MolecularSequence.quality.roc.fMeasure" /> <short value="FScore of the GQ score" /> <definition value="Calculated fScore if the GQ score threshold was set to "score" field value." /> <comment value="Do not use an IEEE type floating point type, instead use something that works like a true decimal, with inbuilt precision (e.g. Java BigInteger)" /> <min value="0" /> <max value="*" /> <base> <path value="MolecularSequence.quality.roc.fMeasure" /> <min value="0" /> <max value="*" /> </base> <type> <code value="decimal" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.readCoverage"> <path value="MolecularSequence.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." /> <comment value="32 bit number; for values larger than this, use decimal" /> <min value="0" /> <max value="0" /> <base> <path value="MolecularSequence.readCoverage" /> <min value="0" /> <max value="1" /> </base> <type> <code value="integer" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.repository"> <path value="MolecularSequence.repository" /> <short value="Repositorium, in welches die Sequenz hochgeladen wird" /> <definition value="Repositorium, in welches die Sequenz hochgeladen wird" /> <min value="0" /> <max value="*" /> <base> <path value="MolecularSequence.repository" /> <min value="0" /> <max value="*" /> </base> <type> <code value="BackboneElement" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <mustSupport value="true" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.repository.id"> <path value="MolecularSequence.repository.id" /> <representation value="xmlAttr" /> <short value="Unique id for inter-element referencing" /> <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> <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type"> <valueUrl value="string" /> </extension> <code value="http://hl7.org/fhirpath/System.String" /> </type> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.repository.extension"> <path value="MolecularSequence.repository.extension" /> <slicing> <discriminator> <type value="value" /> <path value="url" /> </discriminator> <description value="Extensions are always sliced by (at least) url" /> <rules value="open" /> </slicing> <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. 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 can 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="1" /> <max value="*" /> <base> <path value="Element.extension" /> <min value="0" /> <max value="*" /> </base> <type> <code value="Extension" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mustSupport value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.repository.extension:sequenceUploadDate"> <path value="MolecularSequence.repository.extension" /> <sliceName value="sequenceUploadDate" /> <short value="Datum des Sequenz-Uploads" /> <definition value="Datum des Sequenz-Uploads" /> <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="1" /> <base> <path value="Element.extension" /> <min value="0" /> <max value="*" /> </base> <type> <code value="Extension" /> <profile value="https://demis.rki.de/fhir/igs/StructureDefinition/SequenceUploadDate" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mustSupport value="true" /> <isModifier value="false" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.repository.extension:sequenceUploadSubmitter"> <path value="MolecularSequence.repository.extension" /> <sliceName value="sequenceUploadSubmitter" /> <short value="Verantwortliche/es Person/Labor für den Sequenz-Upload" /> <definition value="Verantwortliche/es Person/Labor für den Sequenz-Upload." /> <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="1" /> <base> <path value="Element.extension" /> <min value="0" /> <max value="*" /> </base> <type> <code value="Extension" /> <profile value="https://demis.rki.de/fhir/igs/StructureDefinition/SequenceUploadSubmitter" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mustSupport value="true" /> <isModifier value="false" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.repository.extension:sequenceUploadStatus"> <path value="MolecularSequence.repository.extension" /> <sliceName value="sequenceUploadStatus" /> <short value="Status des Sequenz-Uploads" /> <definition value="Status des Sequenz-Uploads." /> <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="1" /> <max value="1" /> <base> <path value="Element.extension" /> <min value="0" /> <max value="*" /> </base> <type> <code value="Extension" /> <profile value="https://demis.rki.de/fhir/igs/StructureDefinition/SequenceUploadStatus" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mustSupport value="true" /> <isModifier value="false" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.repository.modifierExtension"> <path value="MolecularSequence.repository.modifierExtension" /> <short value="Extensions that cannot be ignored even if unrecognized" /> <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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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 can 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. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself)." /> <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." /> <requirements value="Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](extensibility.html#modifierExtension)." /> <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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <isModifier value="true" /> <isModifierReason value="Modifier extensions are expected to modify the meaning or interpretation of the element that contains them" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.repository.type"> <path value="MolecularSequence.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." /> <comment value="Note that FHIR strings SHALL NOT exceed 1MB in size" /> <min value="1" /> <max value="1" /> <base> <path value="MolecularSequence.repository.type" /> <min value="1" /> <max value="1" /> </base> <type> <code value="code" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <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." /> <valueSet value="http://hl7.org/fhir/ValueSet/repository-type|4.0.1" /> </binding> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.repository.url"> <path value="MolecularSequence.repository.url" /> <short value="Hyperlink auf die Sequenz im Repositorium" /> <definition value="Hyperlink auf die Sequenz im Repositorium." /> <comment value="see http://en.wikipedia.org/wiki/Uniform_resource_identifier" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.repository.url" /> <min value="0" /> <max value="1" /> </base> <type> <code value="uri" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <mustSupport value="true" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.repository.name"> <path value="MolecularSequence.repository.name" /> <short value="Name des Repositoriums" /> <definition value="Name des Repositoriums, in welches die Sequenz hochgeladen wird. Der Wert muss entsprechend des vom RKI definierten ValueSets https://demis.rki.de/fhir/igs/ValueSet/repositoryName dargestellt werden." /> <comment value="Note that FHIR strings SHALL NOT exceed 1MB in size" /> <min value="1" /> <max value="1" /> <base> <path value="MolecularSequence.repository.name" /> <min value="0" /> <max value="1" /> </base> <type> <code value="string" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <mustSupport value="true" /> <isSummary value="true" /> <binding> <strength value="required" /> <valueSet value="https://demis.rki.de/fhir/igs/ValueSet/repositoryName" /> </binding> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.repository.datasetId"> <path value="MolecularSequence.repository.datasetId" /> <short value="Identifier der Sequenz im Repositorium" /> <definition value="Identifier der Sequenz im Repositorium." /> <comment value="Note that FHIR strings SHALL NOT exceed 1MB in size" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.repository.datasetId" /> <min value="0" /> <max value="1" /> </base> <type> <code value="string" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <mustSupport value="true" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.repository.variantsetId"> <path value="MolecularSequence.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." /> <comment value="Note that FHIR strings SHALL NOT exceed 1MB in size" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.repository.variantsetId" /> <min value="0" /> <max value="1" /> </base> <type> <code value="string" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.repository.readsetId"> <path value="MolecularSequence.repository.readsetId" /> <short value="Id of the read" /> <definition value="Id of the read in this external repository." /> <comment value="Note that FHIR strings SHALL NOT exceed 1MB in size" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.repository.readsetId" /> <min value="0" /> <max value="1" /> </base> <type> <code value="string" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.pointer"> <path value="MolecularSequence.pointer" /> <short value="Pointer to next atomic sequence" /> <definition value="Pointer to next atomic sequence which at most contains one variant." /> <comment value="References SHALL be a reference to an actual FHIR resource, and SHALL be resolveable (allowing for access control, temporary unavailability, etc.). Resolution can be either by retrieval from the URL, or, where applicable by resource type, by treating an absolute reference as a canonical URL and looking it up in a local registry/repository." /> <min value="0" /> <max value="0" /> <base> <path value="MolecularSequence.pointer" /> <min value="0" /> <max value="*" /> </base> <type> <code value="Reference" /> <targetProfile value="http://hl7.org/fhir/StructureDefinition/MolecularSequence" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ref-1" /> <severity value="error" /> <human value="SHALL have a contained resource if a local reference is provided" /> <expression value="reference.startsWith('#').not() or (reference.substring(1).trace('url') in %rootResource.contained.id.trace('ids'))" /> <xpath value="not(starts-with(f:reference/@value, '#')) or exists(ancestor::*[self::f:entry or self::f:parameter]/f:resource/f:*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')]|/*/f:contained/f:*[f:id/@value=substring-after(current()/f:reference/@value, '#')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Reference" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="The target of a resource reference is a RIM entry point (Act, Role, or Entity)" /> </mapping> </element> <element id="MolecularSequence.structureVariant"> <path value="MolecularSequence.structureVariant" /> <short value="Structural variant" /> <definition value="Information about chromosome structure variation." /> <min value="0" /> <max value="0" /> <base> <path value="MolecularSequence.structureVariant" /> <min value="0" /> <max value="*" /> </base> <type> <code value="BackboneElement" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.structureVariant.id"> <path value="MolecularSequence.structureVariant.id" /> <representation value="xmlAttr" /> <short value="Unique id for inter-element referencing" /> <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> <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type"> <valueUrl value="string" /> </extension> <code value="http://hl7.org/fhirpath/System.String" /> </type> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.structureVariant.extension"> <path value="MolecularSequence.structureVariant.extension" /> <slicing> <discriminator> <type value="value" /> <path value="url" /> </discriminator> <description value="Extensions are always sliced by (at least) url" /> <rules value="open" /> </slicing> <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. 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 can 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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.structureVariant.modifierExtension"> <path value="MolecularSequence.structureVariant.modifierExtension" /> <short value="Extensions that cannot be ignored even if unrecognized" /> <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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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 can 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. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself)." /> <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." /> <requirements value="Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](extensibility.html#modifierExtension)." /> <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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <isModifier value="true" /> <isModifierReason value="Modifier extensions are expected to modify the meaning or interpretation of the element that contains them" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.structureVariant.variantType"> <path value="MolecularSequence.structureVariant.variantType" /> <short value="Structural variant change type" /> <definition value="Information about chromosome structure variation DNA change type." /> <comment value="Not all terminology uses fit this general pattern. In some cases, models should not use CodeableConcept and use Coding directly and provide their own structure for managing text, codings, translations and the relationship between elements and pre- and post-coordination." /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.structureVariant.variantType" /> <min value="0" /> <max value="1" /> </base> <type> <code value="CodeableConcept" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <binding> <extension url="http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName"> <valueString value="LOINC LL379-9 answerlist" /> </extension> <strength value="required" /> <description value="DNA change type." /> <valueSet value="http://loinc.org/vs/LL379-9|4.0.1" /> </binding> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="v2" /> <map value="CE/CNE/CWE" /> </mapping> <mapping> <identity value="rim" /> <map value="CD" /> </mapping> <mapping> <identity value="orim" /> <map value="fhir:CodeableConcept rdfs:subClassOf dt:CD" /> </mapping> </element> <element id="MolecularSequence.structureVariant.exact"> <path value="MolecularSequence.structureVariant.exact" /> <short value="Does the structural variant have base pair resolution breakpoints?" /> <definition value="Used to indicate if the outer and inner start-end values have the same meaning." /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.structureVariant.exact" /> <min value="0" /> <max value="1" /> </base> <type> <code value="boolean" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.structureVariant.length"> <path value="MolecularSequence.structureVariant.length" /> <short value="Structural variant length" /> <definition value="Length of the variant chromosome." /> <comment value="32 bit number; for values larger than this, use decimal" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.structureVariant.length" /> <min value="0" /> <max value="1" /> </base> <type> <code value="integer" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.structureVariant.outer"> <path value="MolecularSequence.structureVariant.outer" /> <short value="Structural variant outer" /> <definition value="Structural variant outer." /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.structureVariant.outer" /> <min value="0" /> <max value="1" /> </base> <type> <code value="BackboneElement" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.structureVariant.outer.id"> <path value="MolecularSequence.structureVariant.outer.id" /> <representation value="xmlAttr" /> <short value="Unique id for inter-element referencing" /> <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> <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type"> <valueUrl value="string" /> </extension> <code value="http://hl7.org/fhirpath/System.String" /> </type> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.structureVariant.outer.extension"> <path value="MolecularSequence.structureVariant.outer.extension" /> <slicing> <discriminator> <type value="value" /> <path value="url" /> </discriminator> <description value="Extensions are always sliced by (at least) url" /> <rules value="open" /> </slicing> <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. 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 can 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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.structureVariant.outer.modifierExtension"> <path value="MolecularSequence.structureVariant.outer.modifierExtension" /> <short value="Extensions that cannot be ignored even if unrecognized" /> <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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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 can 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. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself)." /> <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." /> <requirements value="Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](extensibility.html#modifierExtension)." /> <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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <isModifier value="true" /> <isModifierReason value="Modifier extensions are expected to modify the meaning or interpretation of the element that contains them" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.structureVariant.outer.start"> <path value="MolecularSequence.structureVariant.outer.start" /> <short value="Structural variant outer start" /> <definition value="Structural variant outer start. If the coordinate system is either 0-based or 1-based, then start position is inclusive." /> <comment value="32 bit number; for values larger than this, use decimal" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.structureVariant.outer.start" /> <min value="0" /> <max value="1" /> </base> <type> <code value="integer" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.structureVariant.outer.end"> <path value="MolecularSequence.structureVariant.outer.end" /> <short value="Structural variant outer end" /> <definition value="Structural variant outer end. If the coordinate system is 0-based then end 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." /> <comment value="32 bit number; for values larger than this, use decimal" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.structureVariant.outer.end" /> <min value="0" /> <max value="1" /> </base> <type> <code value="integer" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.structureVariant.inner"> <path value="MolecularSequence.structureVariant.inner" /> <short value="Structural variant inner" /> <definition value="Structural variant inner." /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.structureVariant.inner" /> <min value="0" /> <max value="1" /> </base> <type> <code value="BackboneElement" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.structureVariant.inner.id"> <path value="MolecularSequence.structureVariant.inner.id" /> <representation value="xmlAttr" /> <short value="Unique id for inter-element referencing" /> <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> <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fhir-type"> <valueUrl value="string" /> </extension> <code value="http://hl7.org/fhirpath/System.String" /> </type> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.structureVariant.inner.extension"> <path value="MolecularSequence.structureVariant.inner.extension" /> <slicing> <discriminator> <type value="value" /> <path value="url" /> </discriminator> <description value="Extensions are always sliced by (at least) url" /> <rules value="open" /> </slicing> <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. 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 can 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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.structureVariant.inner.modifierExtension"> <path value="MolecularSequence.structureVariant.inner.modifierExtension" /> <short value="Extensions that cannot be ignored even if unrecognized" /> <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 in which it is contained and/or the understanding of the containing element's descendants. Usually modifier elements provide negation or qualification. 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 can 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. Modifier extensions SHALL NOT change the meaning of any elements on Resource or DomainResource (including cannot change the meaning of modifierExtension itself)." /> <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." /> <requirements value="Modifier extensions allow for extensions that *cannot* be safely ignored to be clearly distinguished from the vast majority of extensions which can be safely ignored. This promotes interoperability by eliminating the need for implementers to prohibit the presence of extensions. For further information, see the [definition of modifier extensions](extensibility.html#modifierExtension)." /> <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> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <constraint> <key value="ext-1" /> <severity value="error" /> <human value="Must have either extensions or value[x], not both" /> <expression value="extension.exists() != value.exists()" /> <xpath value="exists(f:extension)!=exists(f:*[starts-with(local-name(.), 'value')])" /> <source value="http://hl7.org/fhir/StructureDefinition/Extension" /> </constraint> <isModifier value="true" /> <isModifierReason value="Modifier extensions are expected to modify the meaning or interpretation of the element that contains them" /> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> <mapping> <identity value="rim" /> <map value="N/A" /> </mapping> </element> <element id="MolecularSequence.structureVariant.inner.start"> <path value="MolecularSequence.structureVariant.inner.start" /> <short value="Structural variant inner start" /> <definition value="Structural variant inner start. If the coordinate system is either 0-based or 1-based, then start position is inclusive." /> <comment value="32 bit number; for values larger than this, use decimal" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.structureVariant.inner.start" /> <min value="0" /> <max value="1" /> </base> <type> <code value="integer" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> <element id="MolecularSequence.structureVariant.inner.end"> <path value="MolecularSequence.structureVariant.inner.end" /> <short value="Structural variant inner end" /> <definition value="Structural variant inner end. If the coordinate system is 0-based then end 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." /> <comment value="32 bit number; for values larger than this, use decimal" /> <min value="0" /> <max value="1" /> <base> <path value="MolecularSequence.structureVariant.inner.end" /> <min value="0" /> <max value="1" /> </base> <type> <code value="integer" /> </type> <condition value="ele-1" /> <constraint> <key value="ele-1" /> <severity value="error" /> <human value="All FHIR elements must have a @value or children" /> <expression value="hasValue() or (children().count() > id.count())" /> <xpath value="@value|f:*|h:div" /> <source value="http://hl7.org/fhir/StructureDefinition/Element" /> </constraint> <isSummary value="true" /> <mapping> <identity value="rim" /> <map value="n/a" /> </mapping> </element> </snapshot> <differential> <element id="MolecularSequence.meta"> <path value="MolecularSequence.meta" /> <min value="1" /> <mustSupport value="true" /> </element> <element id="MolecularSequence.meta.profile"> <path value="MolecularSequence.meta.profile" /> <min value="1" /> <max value="1" /> <patternCanonical value="https://demis.rki.de/fhir/igs/StructureDefinition/Sequence" /> <mustSupport value="true" /> </element> <element id="MolecularSequence.extension"> <path value="MolecularSequence.extension" /> <slicing> <discriminator> <type value="value" /> <path value="url" /> </discriminator> <rules value="open" /> </slicing> <min value="1" /> <mustSupport value="true" /> </element> <element id="MolecularSequence.extension:sequenceAuthor"> <path value="MolecularSequence.extension" /> <sliceName value="sequenceAuthor" /> <short value="Person/Labor, die/das verantwortlich für die Sequenz ist" /> <definition value="Person/Labor, die/das verantwortlich für die Sequenz ist" /> <min value="0" /> <max value="1" /> <type> <code value="Extension" /> <profile value="https://demis.rki.de/fhir/igs/StructureDefinition/SequenceAuthor" /> </type> <mustSupport value="true" /> <isModifier value="false" /> </element> <element id="MolecularSequence.extension:sequencingReason"> <path value="MolecularSequence.extension" /> <sliceName value="sequencingReason" /> <short value="Grund der Sequenzierung" /> <definition value="Grund der Sequenzierung" /> <min value="0" /> <max value="1" /> <type> <code value="Extension" /> <profile value="https://demis.rki.de/fhir/igs/StructureDefinition/SequencingReason" /> </type> <mustSupport value="true" /> <isModifier value="false" /> </element> <element id="MolecularSequence.extension:sequenceDocumentReference"> <path value="MolecularSequence.extension" /> <sliceName value="sequenceDocumentReference" /> <short value="Referenz auf die Sequenz" /> <definition value="Referenz auf die Sequenz" /> <min value="1" /> <type> <code value="Extension" /> <profile value="https://demis.rki.de/fhir/igs/StructureDefinition/SequenceDocumentReference" /> </type> <mustSupport value="true" /> <isModifier value="false" /> </element> <element id="MolecularSequence.identifier"> <path value="MolecularSequence.identifier" /> <short value="Laboreigener Identifier der Probe" /> <definition value="Eineindeutiger Identifier der Probe, die vom einreichenden Labor verwendet wird." /> <min value="1" /> <max value="1" /> <mustSupport value="true" /> </element> <element id="MolecularSequence.type"> <path value="MolecularSequence.type" /> <short value="Typ der Sequenz" /> <definition value="Für DEMIS ist der Typ grundsätzlich mit dem Wert „dna“ zu belegen." /> <fixedCode value="dna" /> <mustSupport value="true" /> </element> <element id="MolecularSequence.patient"> <path value="MolecularSequence.patient" /> <max value="0" /> </element> <element id="MolecularSequence.specimen"> <path value="MolecularSequence.specimen" /> <short value="Verweis auf die Sequenz-Probe" /> <definition value="Verweis auf die Sequenz-Probe" /> <min value="1" /> <type> <code value="Reference" /> <targetProfile value="https://demis.rki.de/fhir/igs/StructureDefinition/SpecimenSequence" /> <aggregation value="bundled" /> </type> <mustSupport value="true" /> </element> <element id="MolecularSequence.specimen.reference"> <path value="MolecularSequence.specimen.reference" /> <min value="1" /> <mustSupport value="true" /> </element> <element id="MolecularSequence.device"> <path value="MolecularSequence.device" /> <short value="Verweis auf das Sequenziergerät" /> <definition value="Verweis auf das Sequenziergerät" /> <min value="1" /> <type> <code value="Reference" /> <targetProfile value="https://demis.rki.de/fhir/igs/StructureDefinition/SequencingDevice" /> <aggregation value="bundled" /> </type> <mustSupport value="true" /> </element> <element id="MolecularSequence.device.reference"> <path value="MolecularSequence.device.reference" /> <min value="1" /> <mustSupport value="true" /> </element> <element id="MolecularSequence.performer"> <path value="MolecularSequence.performer" /> <short value="Verweis auf die Melder-Einrichtung" /> <definition value="Verweis auf die Melder-Einrichtung" /> <min value="1" /> <type> <code value="Reference" /> <targetProfile value="https://demis.rki.de/fhir/StructureDefinition/NotifierFacility" /> <aggregation value="bundled" /> </type> <mustSupport value="true" /> </element> <element id="MolecularSequence.performer.reference"> <path value="MolecularSequence.performer.reference" /> <min value="1" /> <mustSupport value="true" /> </element> <element id="MolecularSequence.quantity"> <path value="MolecularSequence.quantity" /> <max value="0" /> </element> <element id="MolecularSequence.referenceSeq"> <path value="MolecularSequence.referenceSeq" /> <max value="0" /> </element> <element id="MolecularSequence.variant"> <path value="MolecularSequence.variant" /> <max value="0" /> </element> <element id="MolecularSequence.observedSeq"> <path value="MolecularSequence.observedSeq" /> <max value="0" /> </element> <element id="MolecularSequence.quality"> <path value="MolecularSequence.quality" /> <max value="0" /> </element> <element id="MolecularSequence.readCoverage"> <path value="MolecularSequence.readCoverage" /> <max value="0" /> </element> <element id="MolecularSequence.repository"> <path value="MolecularSequence.repository" /> <short value="Repositorium, in welches die Sequenz hochgeladen wird" /> <definition value="Repositorium, in welches die Sequenz hochgeladen wird" /> <mustSupport value="true" /> </element> <element id="MolecularSequence.repository.extension"> <path value="MolecularSequence.repository.extension" /> <slicing> <discriminator> <type value="value" /> <path value="url" /> </discriminator> <rules value="open" /> </slicing> <min value="1" /> <mustSupport value="true" /> </element> <element id="MolecularSequence.repository.extension:sequenceUploadDate"> <path value="MolecularSequence.repository.extension" /> <sliceName value="sequenceUploadDate" /> <short value="Datum des Sequenz-Uploads" /> <definition value="Datum des Sequenz-Uploads" /> <min value="0" /> <max value="1" /> <type> <code value="Extension" /> <profile value="https://demis.rki.de/fhir/igs/StructureDefinition/SequenceUploadDate" /> </type> <mustSupport value="true" /> <isModifier value="false" /> </element> <element id="MolecularSequence.repository.extension:sequenceUploadSubmitter"> <path value="MolecularSequence.repository.extension" /> <sliceName value="sequenceUploadSubmitter" /> <short value="Verantwortliche/es Person/Labor für den Sequenz-Upload" /> <definition value="Verantwortliche/es Person/Labor für den Sequenz-Upload." /> <min value="0" /> <max value="1" /> <type> <code value="Extension" /> <profile value="https://demis.rki.de/fhir/igs/StructureDefinition/SequenceUploadSubmitter" /> </type> <mustSupport value="true" /> <isModifier value="false" /> </element> <element id="MolecularSequence.repository.extension:sequenceUploadStatus"> <path value="MolecularSequence.repository.extension" /> <sliceName value="sequenceUploadStatus" /> <short value="Status des Sequenz-Uploads" /> <definition value="Status des Sequenz-Uploads." /> <min value="1" /> <max value="1" /> <type> <code value="Extension" /> <profile value="https://demis.rki.de/fhir/igs/StructureDefinition/SequenceUploadStatus" /> </type> <mustSupport value="true" /> <isModifier value="false" /> </element> <element id="MolecularSequence.repository.url"> <path value="MolecularSequence.repository.url" /> <short value="Hyperlink auf die Sequenz im Repositorium" /> <definition value="Hyperlink auf die Sequenz im Repositorium." /> <mustSupport value="true" /> </element> <element id="MolecularSequence.repository.name"> <path value="MolecularSequence.repository.name" /> <short value="Name des Repositoriums" /> <definition value="Name des Repositoriums, in welches die Sequenz hochgeladen wird. Der Wert muss entsprechend des vom RKI definierten ValueSets https://demis.rki.de/fhir/igs/ValueSet/repositoryName dargestellt werden." /> <min value="1" /> <mustSupport value="true" /> <binding> <strength value="required" /> <valueSet value="https://demis.rki.de/fhir/igs/ValueSet/repositoryName" /> </binding> </element> <element id="MolecularSequence.repository.datasetId"> <path value="MolecularSequence.repository.datasetId" /> <short value="Identifier der Sequenz im Repositorium" /> <definition value="Identifier der Sequenz im Repositorium." /> <mustSupport value="true" /> </element> <element id="MolecularSequence.pointer"> <path value="MolecularSequence.pointer" /> <max value="0" /> </element> <element id="MolecularSequence.structureVariant"> <path value="MolecularSequence.structureVariant" /> <max value="0" /> </element> </differential> </StructureDefinition>