MolecularDefinition Resource from CG-IM

implementations/translations.xml

@@ -946,6 +946,9 @@
 		<translation lang="es">SecuenciaMolecular</translation>
 		<translation lang="zh">分子序列</translation>
 	</item>
+	<item id="MolecularDefinition">
+		<translation lang="en">MolecularSequence</translation>
+	</item>
 	<!--item id="ServiceDefinition">
 		<translation lang="en">ServiceDefinition</translation>
 		<translation lang="es">DefinicionDeServicio</translation>

publish.ini

@@ -561,6 +561,7 @@ ImagingSelection = Clinical.Diagnostics
 ImagingStudy = Clinical.Diagnostics
 QuestionnaireResponse = Clinical.Diagnostics
 Sequence = Clinical.Diagnostics
+MolecularDefinition = Clinical.Diagnostics
 MedicationRequest = Clinical.Medications
 MedicationAdministration = Clinical.Medications
 MedicationDispense = Clinical.Medications

source/compartments.xml

@@ -584,7 +584,11 @@
    </Row>
    <Row ss:AutoFitHeight="0">
     <Cell><Data ss:Type="String">MolecularSequence</Data></Cell>
-    <Cell><Data ss:Type="String">subject</Data></Cell>
+    <!--<Cell><Data ss:Type="String">subject</Data></Cell>-->
+   </Row>
+   <Row ss:AutoFitHeight="0">
+    <Cell><Data ss:Type="String">MolecularDefinition</Data></Cell>
+    <!--<Cell><Data ss:Type="String">subject</Data></Cell>-->
    </Row>
    <Row ss:AutoFitHeight="0">
     <Cell><Data ss:Type="String">NamingSystem</Data></Cell>

source/diagnostics-module.html

@@ -53,6 +53,7 @@ <h3>Index</h3>
                     <li><a href="imagingselection.html">ImagingSelection</a></li>
                     <li><a href="imagingstudy.html">ImagingStudy</a></li>
                     <li><a href="molecularsequence.html">MolecularSequence</a></li>
+                    <li><a href="moleculardefinition.html">MolecularDefinition</a></li>
                     <li><a href="genomicstudy.html">GenomicStudy</a></li>
                 </ul>
             </td>

source/fhir.ini

@@ -146,6 +146,7 @@ EnrollmentResponse=1
 EvidenceReport=1
 GraphDefinition=1
 GenomicStudy=1
+MolecularDefinition=0
 Linkage=1
 ResearchStudy=1
 ResearchSubject=1
@@ -353,6 +354,7 @@ biologicallyderivedproductdispense=BiologicallyDerivedProductDispense
 deviceassociation=DeviceAssociation
 testplan=TestPlan
 inventoryitem=InventoryItem
+moleculardefinition=MolecularDefinition
 
 [removed-resources]
 ActionDefinition
@@ -650,6 +652,7 @@ regulatedauthorization=brr
 ingredient=brr
 clinicalusedefinition=brr
 molecularsequence=cg
+moleculardefinition=cg
 substancedefinition=brr
 substancepolymer=brr
 substancereferenceinformation=brr
@@ -861,6 +864,7 @@ riskassessment=patient
 schedule=business
 searchparameter=anonymous
 molecularsequence=patient
+moleculardefinition=not-classified
 slot=business
 specimen=patient
 specimendefinition=anonymous
@@ -1023,6 +1027,7 @@ riskassessment=2
 schedule=3
 searchparameter=5
 molecularsequence=1
+moleculardefinition=0
 slot=3
 specimen=2
 specimendefinition=1
@@ -1182,6 +1187,7 @@ TerminologyCapabilities=draft
 TestReport=draft
 Transport=draft
 GenomicStudy=draft
+MolecularDefinition=draft
 VerificationResult=draft
 ;MedicationDefinition=draft
 DeviceDispense=draft
@@ -1379,6 +1385,7 @@ RelatedPerson=rpp
 RequestOrchestration=rqo
 Schedule=sch
 MolecularSequence=msq
+moleculardefinition=mdf
 SpecimenDefinition=spdf
 Subscription=scr
 SubscriptionStatus=scrs
@@ -1577,6 +1584,7 @@ MessageDefinition = approved
 MessageHeader=approved
 MetadataResource=n/a
 MolecularSequence=approved
+MolecularDefinition= no-proposal
 NamingSystem=approved
 NutritionIntake = no-proposal
 NutritionOrder =  no-proposal

source/hierarchy.xml

@@ -341,6 +341,7 @@ signatures.html
       <page type="resource" resource="ImagingStudy"/>
       <page type="resource" resource="ImagingSelection"/>
       <page type="resource" resource="MolecularSequence"/>
+      <page type="resource" resource="MolecularDefinition"/>
       <page type="resource" resource="Specimen"/>
       <page type="resource" resource="BodyStructure"/>
       <page title="Genomics Implementer Guidance" filename="genomics.html"/>

source/moleculardefinition/bundle-MolecularDefinition-search-params.xml

@@ -0,0 +1,101 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<Bundle xmlns="http://hl7.org/fhir">
+  <id value="MolecularDefinition-search-params"/>
+  <entry>
+    <resource>
+      <SearchParameter>
+        <id value="MolecularDefinition-identifier"/>
+        <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
+          <valueCode value="trial-use"/>
+        </extension>
+        <extension url="http://hl7.org/fhir/build/StructureDefinition/path">
+          <valueString value="MolecularDefinition.identifier"/>
+        </extension>
+        <url value="http://hl7.org/fhir/build/SearchParameter/MolecularDefinition-identifier"/>
+        <description value="The unique identity for a particular sequence"/>
+        <code value="identifier"/>
+        <type value="token"/>
+        <expression value="MolecularDefinition.identifier"/>
+        <processingMode value="normal"/>
+      </SearchParameter>
+    </resource>
+  </entry>
+  <!--  <entry>
+      <resource>
+        <SearchParameter>
+          <id value="MolecularDefinition-subject"/>
+          <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
+            <valueCode value="trial-use"/>
+          </extension>
+          <extension url="http://hl7.org/fhir/build/StructureDefinition/path">
+            <valueString value="MolecularDefinition.subject"/>
+          </extension>
+          <url value="http://hl7.org/fhir/build/SearchParameter/MolecularDefinition-subject"/>
+          <description value="The subject that the sequence is about"/>
+          <code value="subject"/>
+          <type value="reference"/>
+          <expression value="MolecularDefinition.subject"/>
+          <processingMode value="normal"/>
+        </SearchParameter>
+      </resource>
+    </entry>-->
+  <!--  <entry>
+      <resource>
+        <SearchParameter>
+          <id value="MolecularDefinition-patient"/>
+          <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
+            <valueCode value="trial-use"/>
+          </extension>
+          <extension url="http://hl7.org/fhir/build/StructureDefinition/path">
+            <valueString value="MolecularDefinition.subject"/>
+          </extension>
+          <url value="http://hl7.org/fhir/build/SearchParameter/MolecularDefinition-patient"/>
+          <description value="The subject that the sequence is about"/>
+          <code value="patient"/>
+          <type value="reference"/>
+          <expression value="MolecularDefinition.subject.where(resolve() is Patient)"/>
+          <processingMode value="normal"/>
+          <target value="Patient"/>
+        </SearchParameter>
+      </resource>
+    </entry>-->
+  <!--  <entry>
+      <resource>
+        <SearchParameter>
+          <id value="MolecularDefinition-focus"/>
+          <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
+            <valueCode value="trial-use"/>
+          </extension>
+          <extension url="http://hl7.org/fhir/build/StructureDefinition/path">
+            <valueString value="MolecularDefinition.focus"/>
+          </extension>
+          <url value="http://hl7.org/fhir/build/SearchParameter/MolecularDefinition-focus"/>
+          <description value="What the molecular sequence is about, when it is not about the subject of record"/>
+          <code value="focus"/>
+          <type value="reference"/>
+          <expression value="MolecularDefinition.focus"/>
+          <processingMode value="normal"/>
+        </SearchParameter>
+      </resource>
+    </entry>-->
+  <entry>
+    <resource>
+      <SearchParameter>
+        <id value="MolecularDefinition-type"/>
+        <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
+          <valueCode value="trial-use"/>
+        </extension>
+        <extension url="http://hl7.org/fhir/build/StructureDefinition/path">
+          <valueString value="MolecularDefinition.type"/>
+        </extension>
+        <url value="http://hl7.org/fhir/build/SearchParameter/MolecularDefinition-type"/>
+        <description value="Amino Acid Sequence/ DNA Sequence / RNA Sequence"/>
+        <code value="type"/>
+        <type value="token"/>
+        <expression value="MolecularDefinition.type"/>
+        <processingMode value="normal"/>
+      </SearchParameter>
+    </resource>
+  </entry>
+</Bundle>

source/moleculardefinition/codesystem-moleculardefinition-focus.xml

@@ -0,0 +1,64 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<CodeSystem xmlns="http://hl7.org/fhir">
+  <id value="moleculardefinition-focus"/>
+  <meta>
+    <lastUpdated value="2022-08-17T15:47:24.148-05:00"/>
+    <profile value="http://hl7.org/fhir/StructureDefinition/shareablecodesystem"/>
+  </meta>
+  <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-wg">
+    <valueCode value="cg"/>
+  </extension>
+  <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-standards-status">
+    <valueCode value="trial-use"/>
+  </extension>
+  <extension url="http://hl7.org/fhir/StructureDefinition/structuredefinition-fmm">
+    <valueInteger value="1"/>
+  </extension>
+  <url value="http://hl7.org/fhir/moleculardefinition-focus"/>
+  <identifier>
+    <system value="urn:ietf:rfc:3986"/>
+    <value value="urn:oid:2.16.840.1.113883.4.642.4.1977"/>
+  </identifier>
+  <version value="6.0.0"/>
+  <name value="MolecularDefinitionFocus"/>
+  <title value="Molecular Definition Focus"/>
+  <status value="draft"/>
+  <experimental value="true"/>
+  <date value="2022-08-17T15:48:24-05:00"/>
+  <publisher value="HL7 (FHIR Project)"/>
+  <contact>
+    <telecom>
+      <system value="url"/>
+      <value value="http://hl7.org/fhir"/>
+    </telecom>
+    <telecom>
+      <system value="email"/>
+      <value value="fhir@lists.hl7.org"/>
+    </telecom>
+  </contact>
+  <description value="The focus of the molecular definition state, i.e., reference, alternative, or context."/>
+  <caseSensitive value="true"/>
+  <valueSet value="http://hl7.org/fhir/ValueSet/moleculardefinition-focus"/>
+  <content value="complete"/>
+  <concept>
+    <code value="reference-state"/>
+    <display value="Reference State"/>
+    <definition value="The reference sequence."/>
+  </concept>
+  <concept>
+    <code value="alternative-state"/>
+    <display value="Alternative State"/>
+    <definition value="The alternative sequence."/>
+  </concept>
+  <concept>
+    <code value="allele-state"/>
+    <display value="Allele State"/>
+    <definition value="The allele sequence."/>
+  </concept>
+  <concept>
+    <code value="context-state"/>
+    <display value="Context State"/>
+    <definition value="The context sequence, i.e., the current sequence."/>
+  </concept>
+</CodeSystem>

source/moleculardefinition/coord-0base-example.xml

@@ -0,0 +1,56 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<MolecularSequence xmlns="http://hl7.org/fhir">
+    <id value="coord-0-base"/>
+    <type value="dna"/>
+    <representation>
+        <relative>
+            <startingSequence>
+                <sequenceString value="ACGTAGTC"/>
+                <windowStart value="0"/>
+                <windowEnd value="8"/>
+                <strand value="watson"/>
+            </startingSequence>
+            <edit>
+                <coordinateSystem>
+                    <coding>
+                        <system value="http://loinc.org"/>
+                        <code value="LA30101-2"/>
+                        <display value="0-based character counting"/>
+                    </coding>
+                </coordinateSystem>
+                <start value="2"/>
+                <end value="2"/>
+                <replacementSequence value="ATG"/>
+                <replacedSequence value="-"/>
+            </edit>
+            <edit>
+                <coordinateSystem>
+                    <coding>
+                        <system value="http://loinc.org"/>
+                        <code value="LA30101-2"/>
+                        <display value="0-based character counting"/>
+                    </coding>
+                </coordinateSystem>
+                <start value="4"/>
+                <end value="5"/>
+                <replacementSequence value="T"/>
+                <replacedSequence value="A"/>
+            </edit>
+            <edit>
+                <coordinateSystem>
+                    <coding>
+                        <system value="http://loinc.org"/>
+                        <code value="LA30101-2"/>
+                        <display value="0-based character counting"/>
+                    </coding>
+                </coordinateSystem>
+                <start value="6"/>
+                <end value="7"/>
+                <replacementSequence value="-"/>
+                <replacedSequence value="T"/>
+            </edit>
+        </relative>
+    </representation>
+
+</MolecularSequence>