Extensions for Using Data Elements from FHIR R5 in FHIR R4
0.1.0 - STU
Extensions for Using Data Elements from FHIR R5 in FHIR R4
0.1.0 - STU
Extensions for Using Data Elements from FHIR R5 in FHIR R4 - Downloaded Version null See the Directory of published versions
| Page standards status: Trial-use | Maturity Level: 0 |
XML representation of the profile-MolecularSequence resource profile.
<StructureDefinition xmlns="http://hl7.org/fhir">
<id value="profile-MolecularSequence"/>
<text>
<status value="extensions"/>
<div xmlns="http://www.w3.org/1999/xhtml"><p class="res-header-id"><b>Generated Narrative: StructureDefinition profile-MolecularSequence</b></p><a name="profile-MolecularSequence"> </a><a name="hcprofile-MolecularSequence"> </a><table border="0" cellpadding="0" cellspacing="0" style="border: 0px #F0F0F0 solid; font-size: 11px; font-family: verdana; vertical-align: top;"><tr style="border: 1px #F0F0F0 solid; font-size: 11px; font-family: verdana; vertical-align: top"><th style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; padding-top: 3px; padding-bottom: 3px" class="hierarchy"><a href="https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views" title="The logical name of the element">Name</a></th><th style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; padding-top: 3px; padding-bottom: 3px" class="hierarchy"><a href="https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views" title="Information about the use of the element">Flags</a></th><th style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; padding-top: 3px; padding-bottom: 3px" class="hierarchy"><a href="https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views" title="Minimum and Maximum # of times the element can appear in the instance">Card.</a></th><th style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; padding-top: 3px; padding-bottom: 3px; width: 100px" class="hierarchy"><a href="https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views" title="Reference to the type of the element">Type</a></th><th style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; padding-top: 3px; padding-bottom: 3px" class="hierarchy"><a href="https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views" title="Additional information about the element">Description & Constraints</a><span style="float: right"><a href="https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views" title="Legend for this format"><img src="data:image/png;base64,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" alt="doco" style="background-color: inherit"/></a></span></th></tr><tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_resource.png" alt="." style="background-color: white; background-color: inherit" title="Resource" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence">MolecularSequence</a><a name="MolecularSequence"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="opacity: 0.5">0</span><span style="opacity: 0.5">..</span><span style="opacity: 0.5">*</span></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="http://hl7.org/fhir/R4/molecularsequence.html">MolecularSequence(4.0.1)</a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="opacity: 0.5">Information about a biological sequence</span></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck13.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_extension_simple.png" alt="." style="background-color: #F7F7F7; background-color: inherit" title="Simple Extension" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.extension">Slices for extension</a><a name="MolecularSequence.extension"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">1..*</td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a style="opacity: 0.5; opacity: 0.5" href="http://hl7.org/fhir/R4/extensibility.html#Extension">Extension</a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="opacity: 0.5">Extension</span><br/><span style="font-weight:bold">Slice: </span>Unordered, Open by value:url<br/></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck134.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_slice_item.png" alt="." style="background-color: white; background-color: inherit" title="Slice Item" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.extension:focus" title="Extension URL = http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.focus">extension:focus</a><a name="MolecularSequence.extension.2"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">0..*</td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="http://hl7.org/fhir/R4/references.html">Reference</a>(<a href="StructureDefinition-profile-Resource.html">Cross-version Profile for R5.Resource for use in FHIR R4(0.1.0)</a> | <a href="http://hl7.org/fhir/R4/resource.html">Resource</a>)</td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">R5: What the molecular sequence is about, when it is not about the subject of record (new)<br/><span style="font-weight:bold">URL: </span><a href="StructureDefinition-ext-R5-MolecularSequence.focus.html">http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.focus</a><br/></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck134.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_slice_item.png" alt="." style="background-color: #F7F7F7; background-color: inherit" title="Slice Item" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.extension:formatted" title="Extension URL = http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.formatted">extension:formatted</a><a name="MolecularSequence.extension.3"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">0..*</td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="http://hl7.org/fhir/R4/datatypes.html#Attachment">Attachment</a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">R5: Embedded file or a link (URL) which contains content to represent the sequence (new)<br/><span style="font-weight:bold">URL: </span><a href="StructureDefinition-ext-R5-MolecularSequence.formatted.html">http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.formatted</a><br/></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck134.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_slice_item.png" alt="." style="background-color: white; background-color: inherit" title="Slice Item" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.extension:coordinateSystem" title="Extension URL = http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.coordinateSystem">extension:coordinateSystem</a><a name="MolecularSequence.extension.4"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">1..1</td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="http://hl7.org/fhir/R4/datatypes.html#CodeableConcept">CodeableConcept</a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">R5: Ways of identifying nucleotides or amino acids within a sequence (new)<br/><span style="font-weight:bold">URL: </span><a href="StructureDefinition-ext-R5-MolecularSequence.rel.coordinateSystem.html">http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.coordinateSystem</a><br/></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck134.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_slice_item.png" alt="." style="background-color: #F7F7F7; background-color: inherit" title="Slice Item" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.extension:ordinalPosition" title="Extension URL = http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.ordinalPosition">extension:ordinalPosition</a><a name="MolecularSequence.extension.5"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">0..1</td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="http://hl7.org/fhir/R4/datatypes.html#integer">integer</a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">R5: Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together (new)<br/><span style="font-weight:bold">URL: </span><a href="StructureDefinition-ext-R5-MolecularSequence.rel.ordinalPosition.html">http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.ordinalPosition</a><br/></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck124.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_end_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_slice_item.png" alt="." style="background-color: white; background-color: inherit" title="Slice Item" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.extension:sequenceRange" title="Extension URL = http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.sequenceRange">extension:sequenceRange</a><a name="MolecularSequence.extension.6"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">0..1</td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="http://hl7.org/fhir/R4/datatypes.html#Range">Range</a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">R5: Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together (new)<br/><span style="font-weight:bold">URL: </span><a href="StructureDefinition-ext-R5-MolecularSequence.rel.sequenceRange.html">http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.sequenceRange</a><br/></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck11.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_element.gif" alt="." style="background-color: #F7F7F7; background-color: inherit" title="Element" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.patient">patient</a><a name="MolecularSequence.patient"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck103.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_end.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_extension_simple.png" alt="." style="background-color: white; background-color: inherit" title="Simple Extension" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.patient.extension">Slices for extension</a><a name="MolecularSequence.patient.extension"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">0..*</td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a style="opacity: 0.5; opacity: 0.5" href="http://hl7.org/fhir/R4/extensibility.html#Extension">Extension</a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="opacity: 0.5">Extension</span><br/><span style="font-weight:bold">Slice: </span>Unordered, Open by value:url<br/></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1024.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_blank.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_end_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_slice_item.png" alt="." style="background-color: #F7F7F7; background-color: inherit" title="Slice Item" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.patient.extension:subject" title="Extension URL = http://hl7.org/fhir/StructureDefinition/alternate-reference">extension:subject</a><a name="MolecularSequence.patient.extension.2"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">0..1</td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="http://hl7.org/fhir/R4/references.html">Reference</a>(<a href="http://hl7.org/fhir/R4/resource.html">Resource</a>)</td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">R5: Subject this sequence is associated too<br/><span style="font-weight:bold">URL: </span><a href="http://hl7.org/fhir/extensions/5.2.0/StructureDefinition-alternate-reference.html">http://hl7.org/fhir/StructureDefinition/alternate-reference</a><br/></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck11.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_element.gif" alt="." style="background-color: white; background-color: inherit" title="Element" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.referenceSeq">referenceSeq</a><a name="MolecularSequence.referenceSeq"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck113.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_extension_simple.png" alt="." style="background-color: #F7F7F7; background-color: inherit" title="Simple Extension" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.referenceSeq.extension">Slices for extension</a><a name="MolecularSequence.referenceSeq.extension"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">0..*</td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a style="opacity: 0.5; opacity: 0.5" href="http://hl7.org/fhir/R4/extensibility.html#Extension">Extension</a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="opacity: 0.5">Extension</span><br/><span style="font-weight:bold">Slice: </span>Unordered, Open by value:url<br/></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1134.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_slice_item.png" alt="." style="background-color: white; background-color: inherit" title="Slice Item" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.referenceSeq.extension:genomeAssembly" title="Extension URL = http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.genomeAssembly">extension:genomeAssembly</a><a name="MolecularSequence.referenceSeq.extension.2"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">0..1</td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="http://hl7.org/fhir/R4/datatypes.html#CodeableConcept">CodeableConcept</a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">R5: The genome assembly used for starting sequence, e.g. GRCh38 (new)<br/><span style="font-weight:bold">URL: </span><a href="StructureDefinition-ext-R5-MolecularSequence.rel.sta.genomeAssembly.html">http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.genomeAssembly</a><br/></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1124.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_end_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_slice_item.png" alt="." style="background-color: #F7F7F7; background-color: inherit" title="Slice Item" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.referenceSeq.extension:sequence" title="Extension URL = http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.sequence">extension:sequence</a><a name="MolecularSequence.referenceSeq.extension.3"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">0..1</td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="http://hl7.org/fhir/R4/datatypes.html#CodeableConcept">CodeableConcept</a>, <a href="http://hl7.org/fhir/R4/references.html">Reference</a>(<a href="StructureDefinition-profile-MolecularSequence.html">Cross-version Profile for R5.MolecularSequence for use in FHIR R4(0.1.0)</a> | <a href="http://hl7.org/fhir/R4/molecularsequence.html">MolecularSequence</a>)</td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">R5: The reference sequence that represents the starting sequence additional types<br/><span style="font-weight:bold">URL: </span><a href="StructureDefinition-ext-R5-MolecularSequence.rel.sta.sequence.html">http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.sequence</a><br/></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck101.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_end.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_element.gif" alt="." style="background-color: white; background-color: inherit" title="Element" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.referenceSeq.chromosome">chromosome</a><a name="MolecularSequence.referenceSeq.chromosome"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck1003.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_blank.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_end.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_extension_simple.png" alt="." style="background-color: #F7F7F7; background-color: inherit" title="Simple Extension" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.referenceSeq.chromosome.extension">Slices for extension</a><a name="MolecularSequence.referenceSeq.chromosome.extension"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">0..*</td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a style="opacity: 0.5; opacity: 0.5" href="http://hl7.org/fhir/R4/extensibility.html#Extension">Extension</a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="opacity: 0.5">Extension</span><br/><span style="font-weight:bold">Slice: </span>Unordered, Open by value:url<br/></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck10024.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vline.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_blank.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_blank.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_end_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_slice_item.png" alt="." style="background-color: white; background-color: inherit" title="Slice Item" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.referenceSeq.chromosome.extension:chromosome" title="Extension URL = http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.chromosome">extension:chromosome</a><a name="MolecularSequence.referenceSeq.chromosome.extension.2"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">0..1</td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="http://hl7.org/fhir/R4/datatypes.html#CodeableConcept">CodeableConcept</a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">R5: Chromosome Identifier<br/><span style="font-weight:bold">URL: </span><a href="StructureDefinition-ext-R5-MolecularSequence.rel.sta.chromosome.html">http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.chromosome</a><br/></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck01.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_end.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_element.gif" alt="." style="background-color: #F7F7F7; background-color: inherit" title="Element" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.variant">variant</a><a name="MolecularSequence.variant"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: white"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck003.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_blank.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_end.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_extension_simple.png" alt="." style="background-color: white; background-color: inherit" title="Simple Extension" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.variant.extension">Slices for extension</a><a name="MolecularSequence.variant.extension"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">0..*</td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a style="opacity: 0.5; opacity: 0.5" href="http://hl7.org/fhir/R4/extensibility.html#Extension">Extension</a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: white; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><span style="opacity: 0.5">Extension</span><br/><span style="font-weight:bold">Slice: </span>Unordered, Open by value:url<br/></td></tr>
<tr style="border: 0px #F0F0F0 solid; padding:0px; vertical-align: top; background-color: #F7F7F7"><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px; white-space: nowrap; background-image: url(tbl_bck0024.png)" class="hierarchy"><img src="tbl_spacer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_blank.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_blank.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="tbl_vjoin_end_slicer.png" alt="." style="background-color: inherit" class="hierarchy"/><img src="icon_slice_item.png" alt="." style="background-color: #F7F7F7; background-color: inherit" title="Slice Item" class="hierarchy"/> <a href="StructureDefinition-profile-MolecularSequence-definitions.html#MolecularSequence.variant.extension:start" title="Extension URL = http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.edit.start">extension:start</a><a name="MolecularSequence.variant.extension.2"> </a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"/><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">0..1</td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy"><a href="http://hl7.org/fhir/R4/datatypes.html#integer">integer</a></td><td style="vertical-align: top; text-align : var(--ig-left,left); background-color: #F7F7F7; border: 0px #F0F0F0 solid; padding:0px 4px 0px 4px" class="hierarchy">R5: Start position of the edit on the starting sequence (new)<br/><span style="font-weight:bold">URL: </span><a href="StructureDefinition-ext-R5-MolecularSequence.rel.edi.start.html">http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.edit.start</a><br/></td></tr>
<tr><td colspan="5" class="hierarchy"><br/><a href="https://build.fhir.org/ig/FHIR/ig-guidance/readingIgs.html#table-views" title="Legend for this format"><img src="data:image/png;base64,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" alt="doco" style="background-color: inherit"/> Documentation for this format</a></td></tr></table></div>
</text>
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
<valueCode value="fhir"/>
</extension>
<extension url="http://hl7.org/fhir/StructureDefinition/package-source">
<extension url="packageId">
<valueId value="hl7.fhir.uv.xver-r5.r4"/>
</extension>
<extension url="version">
<valueString value="0.1.0"/>
</extension>
</extension>
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm">
<valueInteger value="0">
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom">
<valueCanonical
value="http://hl7.org/fhir/uv/xver/ImplementationGuide/hl7.fhir.uv.xver-r5.r4"/>
</extension>
</valueInteger>
</extension>
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
<valueCode value="trial-use">
<extension
url="http://hl7.org/fhir/StructureDefinition/structuredefinition-conformance-derivedFrom">
<valueCanonical
value="http://hl7.org/fhir/uv/xver/ImplementationGuide/hl7.fhir.uv.xver-r5.r4"/>
</extension>
</valueCode>
</extension>
<url
value="http://hl7.org/fhir/5.0/StructureDefinition/profile-MolecularSequence"/>
<version value="0.1.0"/>
<name value="Profile_R5_MolecularSequence_R4"/>
<title
value="Cross-version Profile for R5.MolecularSequence for use in FHIR R4"/>
<status value="active"/>
<experimental value="false"/>
<date value="2026-03-17T16:04:43.1781276-05:00"/>
<publisher value="FHIR Infrastructure"/>
<contact>
<name value="FHIR Infrastructure"/>
<telecom>
<system value="url"/>
<value value="http://www.hl7.org/Special/committees/fiwg"/>
</telecom>
</contact>
<description
value="This cross-version profile allows R5 MolecularSequence content to be represented via FHIR R4 MolecularSequence resources."/>
<jurisdiction>
<coding>
<system value="http://unstats.un.org/unsd/methods/m49/m49.htm"/>
<code value="001"/>
<display value="World"/>
</coding>
</jurisdiction>
<fhirVersion value="4.0.1"/>
<mapping>
<identity value="w5"/>
<uri value="http://hl7.org/fhir/fivews"/>
<name value="FiveWs Pattern Mapping"/>
</mapping>
<mapping>
<identity value="rim"/>
<uri value="http://hl7.org/v3"/>
<name value="RIM Mapping"/>
</mapping>
<kind value="resource"/>
<abstract value="false"/>
<type value="MolecularSequence"/>
<baseDefinition
value="http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.0.1"/>
<derivation value="constraint"/>
<snapshot>
<extension
url="http://hl7.org/fhir/tools/StructureDefinition/snapshot-base-version">
<valueString value="4.0.1"/>
</extension>
<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|4.0.1"/>
</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|4.0.1"/>
</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|4.0.1"/>
</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|4.0.1"/>
</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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
<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="id"/>
</extension>
<code value="http://hl7.org/fhirpath/System.String"/>
</type>
<isModifier value="false"/>
<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="0"/>
<max value="1"/>
<base>
<path value="Resource.meta"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="Meta"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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>
<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|4.0.1"/>
</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"/>
</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>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
<binding>
<extension
url="http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet">
<valueCanonical
value="http://hl7.org/fhir/ValueSet/all-languages|4.0.1"/>
</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|4.0.1"/>
</binding>
</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>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
<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>
<isModifier value="false"/>
<isSummary value="false"/>
<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>
<ordered value="false"/>
<rules value="open"/>
</slicing>
<short value="Extension"/>
<definition value="An Extension"/>
<min value="1"/>
<max value="*"/>
<base>
<path value="DomainResource.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
</type>
<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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element id="MolecularSequence.extension:focus">
<path value="MolecularSequence.extension"/>
<sliceName value="focus"/>
<short
value="R5: What the molecular sequence is about, when it is not about the subject of record (new)"/>
<definition
value="R5: `MolecularSequence.focus` (new:Reference(Resource))"/>
<comment
value="Element `MolecularSequence.focus` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.
Element `MolecularSequence.focus` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element)."/>
<min value="0"/>
<max value="*"/>
<base>
<path value="DomainResource.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.focus|0.1.0"/>
</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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element id="MolecularSequence.extension:formatted">
<path value="MolecularSequence.extension"/>
<sliceName value="formatted"/>
<short
value="R5: Embedded file or a link (URL) which contains content to represent the sequence (new)"/>
<definition value="R5: `MolecularSequence.formatted` (new:Attachment)"/>
<comment
value="Element `MolecularSequence.formatted` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.
Element `MolecularSequence.formatted` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element)."/>
<min value="0"/>
<max value="*"/>
<base>
<path value="DomainResource.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.formatted|0.1.0"/>
</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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element id="MolecularSequence.extension:coordinateSystem">
<path value="MolecularSequence.extension"/>
<sliceName value="coordinateSystem"/>
<short
value="R5: Ways of identifying nucleotides or amino acids within a sequence (new)"/>
<definition
value="R5: `MolecularSequence.relative.coordinateSystem` (new:CodeableConcept)"/>
<comment
value="Element `MolecularSequence.relative.coordinateSystem` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.
Element `MolecularSequence.relative.coordinateSystem` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element)."/>
<min value="1"/>
<max value="1"/>
<base>
<path value="DomainResource.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.coordinateSystem|0.1.0"/>
</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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element id="MolecularSequence.extension:ordinalPosition">
<path value="MolecularSequence.extension"/>
<sliceName value="ordinalPosition"/>
<short
value="R5: Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together (new)"/>
<definition
value="R5: `MolecularSequence.relative.ordinalPosition` (new:integer)"/>
<comment
value="Element `MolecularSequence.relative.ordinalPosition` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.
Element `MolecularSequence.relative.ordinalPosition` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element)."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="DomainResource.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.ordinalPosition|0.1.0"/>
</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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element id="MolecularSequence.extension:sequenceRange">
<path value="MolecularSequence.extension"/>
<sliceName value="sequenceRange"/>
<short
value="R5: Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together (new)"/>
<definition
value="R5: `MolecularSequence.relative.sequenceRange` (new:Range)"/>
<comment
value="Element `MolecularSequence.relative.sequenceRange` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.
Element `MolecularSequence.relative.sequenceRange` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element)."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="DomainResource.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.sequenceRange|0.1.0"/>
</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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element id="MolecularSequence.modifierExtension">
<path value="MolecularSequence.modifierExtension"/>
<short value="Extensions that cannot be ignored"/>
<definition
value="May be used to represent additional information that is not part of the basic definition of the resource and that modifies the understanding of the element that contains it 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](http://hl7.org/fhir/R4/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>
<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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="true"/>
<isModifierReason
value="Modifier extensions are expected to modify the meaning or interpretation of the resource that contains them"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="N/A"/>
</mapping>
</element>
<element id="MolecularSequence.identifier">
<path value="MolecularSequence.identifier"/>
<short
value="Unique ID for this particular sequence. This is a FHIR-defined id"/>
<definition
value="A unique identifier for this particular sequence instance. This is a FHIR-defined id."/>
<requirements
value="Allows sequences to be distinguished and referenced."/>
<min value="0"/>
<max value="*"/>
<base>
<path value="MolecularSequence.identifier"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Identifier"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
<mapping>
<identity value="w5"/>
<map value="FiveWs.identifier"/>
</mapping>
</element>
<element id="MolecularSequence.type">
<path value="MolecularSequence.type"/>
<short value="aa | dna | rna"/>
<definition value="Amino Acid Sequence/ DNA Sequence / RNA Sequence."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.type"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="code"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<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>
</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)."/>
<min value="1"/>
<max value="1"/>
<base>
<path value="MolecularSequence.coordinateSystem"/>
<min value="1"/>
<max value="1"/>
</base>
<type>
<code value="integer"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.patient"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="Reference"/>
<targetProfile
value="http://hl7.org/fhir/StructureDefinition/Patient|4.0.1"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</element>
<element id="MolecularSequence.patient.id">
<path value="MolecularSequence.patient.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>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="n/a"/>
</mapping>
</element>
<element id="MolecularSequence.patient.extension">
<path value="MolecularSequence.patient.extension"/>
<slicing>
<discriminator>
<type value="value"/>
<path value="url"/>
</discriminator>
<description value="Extensions are always sliced by (at least) url"/>
<ordered value="false"/>
<rules value="open"/>
</slicing>
<short value="Extension"/>
<definition value="An Extension"/>
<min value="0"/>
<max value="*"/>
<base>
<path value="Element.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
</type>
<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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element id="MolecularSequence.patient.extension:subject">
<path value="MolecularSequence.patient.extension"/>
<sliceName value="subject"/>
<short value="R5: Subject this sequence is associated too"/>
<definition value="R5: `MolecularSequence.subject`"/>
<comment
value="Element `MolecularSequence.subject` is mapped to FHIR R4 element `MolecularSequence.patient` as `SourceIsBroaderThanTarget`.
The standard extension `alternate-reference` has been mapped as the representation of FHIR R5 element `MolecularSequence.subject` with unmapped reference targets: BiologicallyDerivedProduct, Group, NutritionProduct, Substance."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="Element.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/StructureDefinition/alternate-reference|5.2.0"/>
</type>
<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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element id="MolecularSequence.patient.reference">
<path value="MolecularSequence.patient.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="0"/>
<max value="1"/>
<base>
<path value="Reference.reference"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="string"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
<mapping>
<identity value="rim"/>
<map value="N/A"/>
</mapping>
</element>
<element id="MolecularSequence.patient.type">
<path value="MolecularSequence.patient.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>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<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|4.0.1"/>
</binding>
<mapping>
<identity value="rim"/>
<map value="N/A"/>
</mapping>
</element>
<element id="MolecularSequence.patient.identifier">
<path value="MolecularSequence.patient.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>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
<mapping>
<identity value="rim"/>
<map value=".identifier"/>
</mapping>
</element>
<element id="MolecularSequence.patient.display">
<extension
url="http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable">
<valueBoolean value="true"/>
</extension>
<path value="MolecularSequence.patient.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>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
<mapping>
<identity value="rim"/>
<map value="N/A"/>
</mapping>
</element>
<element id="MolecularSequence.specimen">
<path value="MolecularSequence.specimen"/>
<short value="Specimen used for sequencing"/>
<definition value="Specimen used for sequencing."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.specimen"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="Reference"/>
<targetProfile
value="http://hl7.org/fhir/StructureDefinition/Specimen|4.0.1"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</element>
<element id="MolecularSequence.device">
<path value="MolecularSequence.device"/>
<short value="The method for sequencing"/>
<definition
value="The method for sequencing, for example, chip information."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.device"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="Reference"/>
<targetProfile
value="http://hl7.org/fhir/StructureDefinition/Device|4.0.1"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</element>
<element id="MolecularSequence.performer">
<path value="MolecularSequence.performer"/>
<short value="Who should be responsible for test result"/>
<definition
value="The organization or lab that should be responsible for this result."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.performer"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="Reference"/>
<targetProfile
value="http://hl7.org/fhir/StructureDefinition/Organization|4.0.1"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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)."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.quantity"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="Quantity"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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="1"/>
<base>
<path value="MolecularSequence.referenceSeq"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="BackboneElement"/>
</type>
<constraint>
<key value="ele-1"/>
<severity value="error"/>
<human value="All FHIR elements must have a @value or children"/>
<expression
value="hasValue() or (children().count() > id.count())"/>
<xpath value="@value|f:*|h:div"/>
<source
value="http://hl7.org/fhir/StructureDefinition/Element|4.0.1"/>
</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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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>
<isModifier value="false"/>
<isSummary value="false"/>
<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>
<ordered value="false"/>
<rules value="open"/>
</slicing>
<short value="Extension"/>
<definition value="An Extension"/>
<min value="0"/>
<max value="*"/>
<base>
<path value="Element.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
</type>
<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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element id="MolecularSequence.referenceSeq.extension:genomeAssembly">
<path value="MolecularSequence.referenceSeq.extension"/>
<sliceName value="genomeAssembly"/>
<short
value="R5: The genome assembly used for starting sequence, e.g. GRCh38 (new)"/>
<definition
value="R5: `MolecularSequence.relative.startingSequence.genomeAssembly` (new:CodeableConcept)"/>
<comment
value="Element `MolecularSequence.relative.startingSequence.genomeAssembly` has a context of MolecularSequence.referenceSeq based on following the parent source element upwards and mapping to `MolecularSequence`.
Element `MolecularSequence.relative.startingSequence.genomeAssembly` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element)."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="Element.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.genomeAssembly|0.1.0"/>
</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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element id="MolecularSequence.referenceSeq.extension:sequence">
<path value="MolecularSequence.referenceSeq.extension"/>
<sliceName value="sequence"/>
<short
value="R5: The reference sequence that represents the starting sequence additional types"/>
<definition
value="R5: `MolecularSequence.relative.startingSequence.sequence[x]` additional types (CodeableConcept, Reference(http://hl7.org/fhir/StructureDefinition/MolecularSequence))"/>
<comment
value="Element `MolecularSequence.relative.startingSequence.sequence[x]` is mapped to FHIR R4 element `MolecularSequence.referenceSeq.referenceSeqString` as `SourceIsBroaderThanTarget`.
The mappings for `MolecularSequence.relative.startingSequence.sequence[x]` do not cover the following types: CodeableConcept, Reference.
A starting sequence may be represented in one of three ways:
1. CodeableConcept, using NCBI, LRG or other appropriate code systems
1. a simple string of IUPAC codes
1. a reference to another MolecularSequence resource."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="Element.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.sequence|0.1.0"/>
</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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</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](http://hl7.org/fhir/R4/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>
<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|4.0.1"/>
</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|4.0.1"/>
</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>
</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))."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.referenceSeq.chromosome"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="CodeableConcept"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<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|4.0.1"/>
</binding>
</element>
<element id="MolecularSequence.referenceSeq.chromosome.id">
<path value="MolecularSequence.referenceSeq.chromosome.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>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="n/a"/>
</mapping>
</element>
<element id="MolecularSequence.referenceSeq.chromosome.extension">
<path value="MolecularSequence.referenceSeq.chromosome.extension"/>
<slicing>
<discriminator>
<type value="value"/>
<path value="url"/>
</discriminator>
<description value="Extensions are always sliced by (at least) url"/>
<ordered value="false"/>
<rules value="open"/>
</slicing>
<short value="Extension"/>
<definition value="An Extension"/>
<min value="0"/>
<max value="*"/>
<base>
<path value="Element.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
</type>
<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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element
id="MolecularSequence.referenceSeq.chromosome.extension:chromosome">
<path value="MolecularSequence.referenceSeq.chromosome.extension"/>
<sliceName value="chromosome"/>
<short value="R5: Chromosome Identifier"/>
<definition
value="R5: `MolecularSequence.relative.startingSequence.chromosome`"/>
<comment
value="Element `MolecularSequence.relative.startingSequence.chromosome` is mapped to FHIR R4 element `MolecularSequence.referenceSeq.chromosome` as `Equivalent`."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="Element.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.chromosome|0.1.0"/>
</type>
<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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element id="MolecularSequence.referenceSeq.chromosome.coding">
<path value="MolecularSequence.referenceSeq.chromosome.coding"/>
<short value="Code defined by a terminology system"/>
<definition
value="A reference to a code defined by a terminology system."/>
<comment
value="Codes may be defined very casually in enumerations, or code lists, up to very formal definitions such as SNOMED CT - see the HL7 v3 Core Principles for more information. Ordering of codings is undefined and SHALL NOT be used to infer meaning. Generally, at most only one of the coding values will be labeled as UserSelected = true."/>
<requirements
value="Allows for alternative encodings within a code system, and translations to other code systems."/>
<min value="0"/>
<max value="*"/>
<base>
<path value="CodeableConcept.coding"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Coding"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
<mapping>
<identity value="v2"/>
<map value="C*E.1-8, C*E.10-22"/>
</mapping>
<mapping>
<identity value="rim"/>
<map value="union(., ./translation)"/>
</mapping>
<mapping>
<identity value="orim"/>
<map
value="fhir:CodeableConcept.coding rdfs:subPropertyOf dt:CD.coding"/>
</mapping>
</element>
<element id="MolecularSequence.referenceSeq.chromosome.text">
<extension
url="http://hl7.org/fhir/StructureDefinition/elementdefinition-translatable">
<valueBoolean value="true"/>
</extension>
<path value="MolecularSequence.referenceSeq.chromosome.text"/>
<short value="Plain text representation of the concept"/>
<definition
value="A human language representation of the concept as seen/selected/uttered by the user who entered the data and/or which represents the intended meaning of the user."/>
<comment
value="Very often the text is the same as a displayName of one of the codings."/>
<requirements
value="The codes from the terminologies do not always capture the correct meaning with all the nuances of the human using them, or sometimes there is no appropriate code at all. In these cases, the text is used to capture the full meaning of the source."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="CodeableConcept.text"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="string"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
<mapping>
<identity value="v2"/>
<map value="C*E.9. But note many systems use C*E.2 for this"/>
</mapping>
<mapping>
<identity value="rim"/>
<map
value="./originalText[mediaType/code="text/plain"]/data"/>
</mapping>
<mapping>
<identity value="orim"/>
<map
value="fhir:CodeableConcept.text rdfs:subPropertyOf dt:CD.originalText"/>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.referenceSeq.genomeBuild"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="string"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.referenceSeq.orientation"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="code"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<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>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.referenceSeq.referenceSeqId"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="CodeableConcept"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<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|4.0.1"/>
</binding>
</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."/>
<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|4.0.1"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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"."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.referenceSeq.referenceSeqString"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="string"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.referenceSeq.strand"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="code"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<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>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.referenceSeq.windowStart"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="integer"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.referenceSeq.windowEnd"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="integer"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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="*"/>
<base>
<path value="MolecularSequence.variant"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="BackboneElement"/>
</type>
<constraint>
<key value="ele-1"/>
<severity value="error"/>
<human value="All FHIR elements must have a @value or children"/>
<expression
value="hasValue() or (children().count() > id.count())"/>
<xpath value="@value|f:*|h:div"/>
<source
value="http://hl7.org/fhir/StructureDefinition/Element|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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>
<isModifier value="false"/>
<isSummary value="false"/>
<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>
<ordered value="false"/>
<rules value="open"/>
</slicing>
<short value="Extension"/>
<definition value="An Extension"/>
<min value="0"/>
<max value="*"/>
<base>
<path value="Element.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
</type>
<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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</element>
<element id="MolecularSequence.variant.extension:start">
<path value="MolecularSequence.variant.extension"/>
<sliceName value="start"/>
<short
value="R5: Start position of the edit on the starting sequence (new)"/>
<definition
value="R5: `MolecularSequence.relative.edit.start` (new:integer)"/>
<comment
value="Element `MolecularSequence.relative.edit.start` has a context of MolecularSequence.variant based on following the parent source element upwards and mapping to `MolecularSequence`.
Element `MolecularSequence.relative.edit.start` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element)."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="Element.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.edit.start|0.1.0"/>
</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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
</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](http://hl7.org/fhir/R4/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>
<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|4.0.1"/>
</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|4.0.1"/>
</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>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.variant.start"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="integer"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.variant.end"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="integer"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.variant.observedAllele"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="string"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.variant.referenceAllele"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="string"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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)."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.variant.cigar"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="string"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<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|4.0.1"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.observedSeq"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="string"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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="*"/>
<base>
<path value="MolecularSequence.quality"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="BackboneElement"/>
</type>
<constraint>
<key value="ele-1"/>
<severity value="error"/>
<human value="All FHIR elements must have a @value or children"/>
<expression
value="hasValue() or (children().count() > id.count())"/>
<xpath value="@value|f:*|h:div"/>
<source
value="http://hl7.org/fhir/StructureDefinition/Element|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="n/a"/>
</mapping>
</element>
<element id="MolecularSequence.quality.extension">
<path value="MolecularSequence.quality.extension"/>
<short value="Additional content defined by implementations"/>
<definition
value="May be used to represent additional information that is not part of the basic definition of the element. 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>
<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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
<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](http://hl7.org/fhir/R4/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>
<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|4.0.1"/>
</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|4.0.1"/>
</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>
</element>
<element id="MolecularSequence.quality.type">
<path value="MolecularSequence.quality.type"/>
<short value="indel | snp | unknown"/>
<definition value="INDEL / SNP / Undefined variant."/>
<min value="1"/>
<max value="1"/>
<base>
<path value="MolecularSequence.quality.type"/>
<min value="1"/>
<max value="1"/>
</base>
<type>
<code value="code"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<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>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.quality.standardSequence"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="CodeableConcept"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<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|4.0.1"/>
</binding>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.quality.start"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="integer"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.quality.end"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="integer"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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))."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.quality.score"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="Quantity"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.quality.method"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="CodeableConcept"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<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|4.0.1"/>
</binding>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.quality.truthTP"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="decimal"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.quality.queryTP"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="decimal"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.quality.truthFN"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="decimal"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.quality.queryFP"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="decimal"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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)."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.quality.gtFP"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="decimal"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</element>
<element id="MolecularSequence.quality.precision">
<path value="MolecularSequence.quality.precision"/>
<short value="Precision of comparison"/>
<definition value="QUERY.TP / (QUERY.TP + QUERY.FP)."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.quality.precision"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="decimal"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</element>
<element id="MolecularSequence.quality.recall">
<path value="MolecularSequence.quality.recall"/>
<short value="Recall of comparison"/>
<definition value="TRUTH.TP / (TRUTH.TP + TRUTH.FN)."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.quality.recall"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="decimal"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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)."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.quality.fScore"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="decimal"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="n/a"/>
</mapping>
</element>
<element id="MolecularSequence.quality.roc.extension">
<path value="MolecularSequence.quality.roc.extension"/>
<short value="Additional content defined by implementations"/>
<definition
value="May be used to represent additional information that is not part of the basic definition of the element. 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>
<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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
<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](http://hl7.org/fhir/R4/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>
<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|4.0.1"/>
</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|4.0.1"/>
</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>
</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."/>
<min value="0"/>
<max value="*"/>
<base>
<path value="MolecularSequence.quality.roc.score"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="integer"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="*"/>
<base>
<path value="MolecularSequence.quality.roc.numTP"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="integer"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="*"/>
<base>
<path value="MolecularSequence.quality.roc.numFP"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="integer"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="*"/>
<base>
<path value="MolecularSequence.quality.roc.numFN"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="integer"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="*"/>
<base>
<path value="MolecularSequence.quality.roc.precision"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="decimal"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="*"/>
<base>
<path value="MolecularSequence.quality.roc.sensitivity"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="decimal"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="*"/>
<base>
<path value="MolecularSequence.quality.roc.fMeasure"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="decimal"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.readCoverage"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="integer"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</element>
<element id="MolecularSequence.repository">
<path value="MolecularSequence.repository"/>
<short
value="External repository which contains detailed report related with observedSeq in this resource"/>
<definition
value="Configurations of the external repository. The repository shall store target's observedSeq or records related with target's observedSeq."/>
<min value="0"/>
<max value="*"/>
<base>
<path value="MolecularSequence.repository"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="BackboneElement"/>
</type>
<constraint>
<key value="ele-1"/>
<severity value="error"/>
<human value="All FHIR elements must have a @value or children"/>
<expression
value="hasValue() or (children().count() > id.count())"/>
<xpath value="@value|f:*|h:div"/>
<source
value="http://hl7.org/fhir/StructureDefinition/Element|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="n/a"/>
</mapping>
</element>
<element id="MolecularSequence.repository.extension">
<path value="MolecularSequence.repository.extension"/>
<short value="Additional content defined by implementations"/>
<definition
value="May be used to represent additional information that is not part of the basic definition of the element. 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>
<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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
<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](http://hl7.org/fhir/R4/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>
<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|4.0.1"/>
</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|4.0.1"/>
</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>
</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."/>
<min value="1"/>
<max value="1"/>
<base>
<path value="MolecularSequence.repository.type"/>
<min value="1"/>
<max value="1"/>
</base>
<type>
<code value="code"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<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>
</element>
<element id="MolecularSequence.repository.url">
<path value="MolecularSequence.repository.url"/>
<short value="URI of the repository"/>
<definition
value="URI of an external repository which contains further details about the genetics data."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.repository.url"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="uri"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</element>
<element id="MolecularSequence.repository.name">
<path value="MolecularSequence.repository.name"/>
<short value="Repository's name"/>
<definition
value="URI of an external repository which contains further details about the genetics data."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.repository.name"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="string"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</element>
<element id="MolecularSequence.repository.datasetId">
<path value="MolecularSequence.repository.datasetId"/>
<short
value="Id of the dataset that used to call for dataset in repository"/>
<definition
value="Id of the variant in this external repository. The server will understand how to use this id to call for more info about datasets in external repository."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.repository.datasetId"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="string"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.repository.variantsetId"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="string"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.repository.readsetId"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="string"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<min value="0"/>
<max value="*"/>
<base>
<path value="MolecularSequence.pointer"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Reference"/>
<targetProfile
value="http://hl7.org/fhir/StructureDefinition/MolecularSequence|4.0.1"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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="*"/>
<base>
<path value="MolecularSequence.structureVariant"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="BackboneElement"/>
</type>
<constraint>
<key value="ele-1"/>
<severity value="error"/>
<human value="All FHIR elements must have a @value or children"/>
<expression
value="hasValue() or (children().count() > id.count())"/>
<xpath value="@value|f:*|h:div"/>
<source
value="http://hl7.org/fhir/StructureDefinition/Element|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="n/a"/>
</mapping>
</element>
<element id="MolecularSequence.structureVariant.extension">
<path value="MolecularSequence.structureVariant.extension"/>
<short value="Additional content defined by implementations"/>
<definition
value="May be used to represent additional information that is not part of the basic definition of the element. 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>
<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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
<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](http://hl7.org/fhir/R4/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>
<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|4.0.1"/>
</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|4.0.1"/>
</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>
</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."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.structureVariant.variantType"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="CodeableConcept"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<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>
</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>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</element>
<element id="MolecularSequence.structureVariant.length">
<path value="MolecularSequence.structureVariant.length"/>
<short value="Structural variant length"/>
<definition value="Length of the variant chromosome."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="MolecularSequence.structureVariant.length"/>
<min value="0"/>
<max value="1"/>
</base>
<type>
<code value="integer"/>
</type>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="n/a"/>
</mapping>
</element>
<element id="MolecularSequence.structureVariant.outer.extension">
<path value="MolecularSequence.structureVariant.outer.extension"/>
<short value="Additional content defined by implementations"/>
<definition
value="May be used to represent additional information that is not part of the basic definition of the element. 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>
<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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
<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](http://hl7.org/fhir/R4/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>
<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|4.0.1"/>
</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|4.0.1"/>
</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>
</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."/>
<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>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<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>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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>
<isModifier value="false"/>
<isSummary value="false"/>
<mapping>
<identity value="rim"/>
<map value="n/a"/>
</mapping>
</element>
<element id="MolecularSequence.structureVariant.inner.extension">
<path value="MolecularSequence.structureVariant.inner.extension"/>
<short value="Additional content defined by implementations"/>
<definition
value="May be used to represent additional information that is not part of the basic definition of the element. 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>
<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|4.0.1"/>
</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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="false"/>
<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](http://hl7.org/fhir/R4/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>
<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|4.0.1"/>
</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|4.0.1"/>
</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>
</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."/>
<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>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</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."/>
<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>
<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|4.0.1"/>
</constraint>
<isModifier value="false"/>
<isSummary value="true"/>
</element>
</snapshot>
<differential>
<element id="MolecularSequence">
<path value="MolecularSequence"/>
</element>
<element id="MolecularSequence.extension">
<path value="MolecularSequence.extension"/>
<slicing>
<discriminator>
<type value="value"/>
<path value="url"/>
</discriminator>
<ordered value="false"/>
<rules value="open"/>
</slicing>
<min value="1"/>
<max value="*"/>
</element>
<element id="MolecularSequence.extension:focus">
<path value="MolecularSequence.extension"/>
<sliceName value="focus"/>
<short
value="R5: What the molecular sequence is about, when it is not about the subject of record (new)"/>
<definition
value="R5: `MolecularSequence.focus` (new:Reference(Resource))"/>
<comment
value="Element `MolecularSequence.focus` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.
Element `MolecularSequence.focus` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element)."/>
<min value="0"/>
<max value="*"/>
<base>
<path value="DomainResource.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.focus|0.1.0"/>
</type>
</element>
<element id="MolecularSequence.extension:formatted">
<path value="MolecularSequence.extension"/>
<sliceName value="formatted"/>
<short
value="R5: Embedded file or a link (URL) which contains content to represent the sequence (new)"/>
<definition value="R5: `MolecularSequence.formatted` (new:Attachment)"/>
<comment
value="Element `MolecularSequence.formatted` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.
Element `MolecularSequence.formatted` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element)."/>
<min value="0"/>
<max value="*"/>
<base>
<path value="DomainResource.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.formatted|0.1.0"/>
</type>
</element>
<element id="MolecularSequence.extension:coordinateSystem">
<path value="MolecularSequence.extension"/>
<sliceName value="coordinateSystem"/>
<short
value="R5: Ways of identifying nucleotides or amino acids within a sequence (new)"/>
<definition
value="R5: `MolecularSequence.relative.coordinateSystem` (new:CodeableConcept)"/>
<comment
value="Element `MolecularSequence.relative.coordinateSystem` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.
Element `MolecularSequence.relative.coordinateSystem` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element)."/>
<min value="1"/>
<max value="1"/>
<base>
<path value="DomainResource.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.coordinateSystem|0.1.0"/>
</type>
</element>
<element id="MolecularSequence.extension:ordinalPosition">
<path value="MolecularSequence.extension"/>
<sliceName value="ordinalPosition"/>
<short
value="R5: Indicates the order in which the sequence should be considered when putting multiple 'relative' elements together (new)"/>
<definition
value="R5: `MolecularSequence.relative.ordinalPosition` (new:integer)"/>
<comment
value="Element `MolecularSequence.relative.ordinalPosition` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.
Element `MolecularSequence.relative.ordinalPosition` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element)."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="DomainResource.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.ordinalPosition|0.1.0"/>
</type>
</element>
<element id="MolecularSequence.extension:sequenceRange">
<path value="MolecularSequence.extension"/>
<sliceName value="sequenceRange"/>
<short
value="R5: Indicates the nucleotide range in the composed sequence when multiple 'relative' elements are used together (new)"/>
<definition
value="R5: `MolecularSequence.relative.sequenceRange` (new:Range)"/>
<comment
value="Element `MolecularSequence.relative.sequenceRange` has a context of MolecularSequence based on following the parent source element upwards and mapping to `MolecularSequence`.
Element `MolecularSequence.relative.sequenceRange` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element)."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="DomainResource.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.sequenceRange|0.1.0"/>
</type>
</element>
<element id="MolecularSequence.patient.extension">
<path value="MolecularSequence.patient.extension"/>
<slicing>
<discriminator>
<type value="value"/>
<path value="url"/>
</discriminator>
<ordered value="false"/>
<rules value="open"/>
</slicing>
<min value="0"/>
<max value="*"/>
</element>
<element id="MolecularSequence.patient.extension:subject">
<path value="MolecularSequence.patient.extension"/>
<sliceName value="subject"/>
<short value="R5: Subject this sequence is associated too"/>
<definition value="R5: `MolecularSequence.subject`"/>
<comment
value="Element `MolecularSequence.subject` is mapped to FHIR R4 element `MolecularSequence.patient` as `SourceIsBroaderThanTarget`.
The standard extension `alternate-reference` has been mapped as the representation of FHIR R5 element `MolecularSequence.subject` with unmapped reference targets: BiologicallyDerivedProduct, Group, NutritionProduct, Substance."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="DomainResource.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/StructureDefinition/alternate-reference|5.2.0"/>
</type>
</element>
<element id="MolecularSequence.referenceSeq.extension">
<path value="MolecularSequence.referenceSeq.extension"/>
<slicing>
<discriminator>
<type value="value"/>
<path value="url"/>
</discriminator>
<ordered value="false"/>
<rules value="open"/>
</slicing>
<min value="0"/>
<max value="*"/>
</element>
<element id="MolecularSequence.referenceSeq.extension:genomeAssembly">
<path value="MolecularSequence.referenceSeq.extension"/>
<sliceName value="genomeAssembly"/>
<short
value="R5: The genome assembly used for starting sequence, e.g. GRCh38 (new)"/>
<definition
value="R5: `MolecularSequence.relative.startingSequence.genomeAssembly` (new:CodeableConcept)"/>
<comment
value="Element `MolecularSequence.relative.startingSequence.genomeAssembly` has a context of MolecularSequence.referenceSeq based on following the parent source element upwards and mapping to `MolecularSequence`.
Element `MolecularSequence.relative.startingSequence.genomeAssembly` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element)."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="DomainResource.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.genomeAssembly|0.1.0"/>
</type>
</element>
<element id="MolecularSequence.referenceSeq.extension:sequence">
<path value="MolecularSequence.referenceSeq.extension"/>
<sliceName value="sequence"/>
<short
value="R5: The reference sequence that represents the starting sequence additional types"/>
<definition
value="R5: `MolecularSequence.relative.startingSequence.sequence[x]` additional types (CodeableConcept, Reference(http://hl7.org/fhir/StructureDefinition/MolecularSequence))"/>
<comment
value="Element `MolecularSequence.relative.startingSequence.sequence[x]` is mapped to FHIR R4 element `MolecularSequence.referenceSeq.referenceSeqString` as `SourceIsBroaderThanTarget`.
The mappings for `MolecularSequence.relative.startingSequence.sequence[x]` do not cover the following types: CodeableConcept, Reference.
A starting sequence may be represented in one of three ways:
1. CodeableConcept, using NCBI, LRG or other appropriate code systems
1. a simple string of IUPAC codes
1. a reference to another MolecularSequence resource."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="DomainResource.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.sequence|0.1.0"/>
</type>
</element>
<element id="MolecularSequence.referenceSeq.chromosome.extension">
<path value="MolecularSequence.referenceSeq.chromosome.extension"/>
<slicing>
<discriminator>
<type value="value"/>
<path value="url"/>
</discriminator>
<ordered value="false"/>
<rules value="open"/>
</slicing>
<min value="0"/>
<max value="*"/>
</element>
<element
id="MolecularSequence.referenceSeq.chromosome.extension:chromosome">
<path value="MolecularSequence.referenceSeq.chromosome.extension"/>
<sliceName value="chromosome"/>
<short value="R5: Chromosome Identifier"/>
<definition
value="R5: `MolecularSequence.relative.startingSequence.chromosome`"/>
<comment
value="Element `MolecularSequence.relative.startingSequence.chromosome` is mapped to FHIR R4 element `MolecularSequence.referenceSeq.chromosome` as `Equivalent`."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="DomainResource.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.startingSequence.chromosome|0.1.0"/>
</type>
</element>
<element id="MolecularSequence.variant.extension">
<path value="MolecularSequence.variant.extension"/>
<slicing>
<discriminator>
<type value="value"/>
<path value="url"/>
</discriminator>
<ordered value="false"/>
<rules value="open"/>
</slicing>
<min value="0"/>
<max value="*"/>
</element>
<element id="MolecularSequence.variant.extension:start">
<path value="MolecularSequence.variant.extension"/>
<sliceName value="start"/>
<short
value="R5: Start position of the edit on the starting sequence (new)"/>
<definition
value="R5: `MolecularSequence.relative.edit.start` (new:integer)"/>
<comment
value="Element `MolecularSequence.relative.edit.start` has a context of MolecularSequence.variant based on following the parent source element upwards and mapping to `MolecularSequence`.
Element `MolecularSequence.relative.edit.start` has no mapping targets in FHIR R4. Typically, this is because the element has been added (is a new element)."/>
<min value="0"/>
<max value="1"/>
<base>
<path value="DomainResource.extension"/>
<min value="0"/>
<max value="*"/>
</base>
<type>
<code value="Extension"/>
<profile
value="http://hl7.org/fhir/5.0/StructureDefinition/extension-MolecularSequence.relative.edit.start|0.1.0"/>
</type>
</element>
</differential>
</StructureDefinition>
IG © 2025+ FHIR Infrastructure. Package hl7.fhir.uv.xver-r5.r4#0.1.0 based on FHIR 4.0.1. Generated 2026-03-20
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