Cg im moldef work in progress 2

source/moleculardefinition/DocumentReference-example-genomicFile-af1961831-url.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+
+<DocumentReference xmlns="http://hl7.org/fhir">
+  <id value="example-genomicFile-af1961831-url"/>
+  <text>
+    <status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "genomicFile1" </p></div><p><b>identifier</b>: id: 11111</p><p><b>status</b>: current</p><p><b>docStatus</b>: preliminary</p><p><b>subject</b>: <a href="Patient-denovoChild.html">Patient/denovoChild: Child Junior Doe</a> " DOE"</p><p><b>description</b>: A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.</p><p><b>securityLabel</b>: Restricted <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v3-Confidentiality.html">Confidentiality</a>#R)</span></p><blockquote><p><b>content</b></p></blockquote></div>
+  </text>
+  <identifier>
+    <system value="http://www.somesystemabc.net/identifiers/files"/>
+    <value value="11111"/>
+  </identifier>
+  <status value="current"/>
+  <docStatus value="preliminary"/>
+  <description value="A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline."/>
+  <securityLabel>
+    <coding>
+      <system value="http://terminology.hl7.org/CodeSystem/v3-Confidentiality"/>
+      <code value="R"/>
+      <display value="Restricted"/>
+    </coding>
+  </securityLabel>
+  <description value="Homo sapiens MHC class I antigen (HLA-B) gene"/>
+  <content>
+    <attachment>
+      <title value="Homo sapiens MHC class I antigen (HLA-B) gene"/>
+      <contentType value="text/html"/>
+      <url value="https://www.ebi.ac.uk/ena/browser/api/fasta/AF196183.1 "/>
+    </attachment>
+  </content>
+</DocumentReference>

source/moleculardefinition/DocumentReference-example-genomicFile-cyp2c19-accession.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+
+<DocumentReference xmlns="http://hl7.org/fhir">
+  <id value="example-genomicFile-cyp2c19-accession"/>
+  <text>
+    <status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "genomicFile1" </p></div><p><b>identifier</b>: id: 11111</p><p><b>status</b>: current</p><p><b>docStatus</b>: preliminary</p><p><b>subject</b>: <a href="Patient-denovoChild.html">Patient/denovoChild: Child Junior Doe</a> " DOE"</p><p><b>description</b>: A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.</p><p><b>securityLabel</b>: Restricted <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v3-Confidentiality.html">Confidentiality</a>#R)</span></p><blockquote><p><b>content</b></p></blockquote></div>
+  </text>
+  <identifier>
+    <system value="https://www.ncbi.nlm.nih.gov/nuccore"/>
+    <value value="NG_008384.3"/>
+  </identifier>
+  <status value="current"/>
+  <docStatus value="preliminary"/>
+  <description value="A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline."/>
+  <securityLabel>
+    <coding>
+      <system value="http://terminology.hl7.org/CodeSystem/v3-Confidentiality"/>
+      <code value="R"/>
+      <display value="Restricted"/>
+    </coding>
+  </securityLabel>
+  <description value="CYP2C19 gene sequence"/>
+  <content>
+    <attachment>
+      <title value="Homo sapiens cytochrome P450 family 2 subfamily C member 19 (CYP2C19), RefSeqGene (LRG_584) on chromosome 10"/>
+      <contentType value="text/html"/>
+      <url value="https://www.ncbi.nlm.nih.gov/nuccore/NG_008384"/>
+    </attachment>
+  </content>
+</DocumentReference>

source/moleculardefinition/DocumentReference-example-genomicFile-cyp2c19-url.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+
+<DocumentReference xmlns="http://hl7.org/fhir">
+  <id value="example-genomicFile-cyp2c19-url"/>
+  <text>
+    <status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "genomicFile1" </p></div><p><b>identifier</b>: id: 11111</p><p><b>status</b>: current</p><p><b>docStatus</b>: preliminary</p><p><b>subject</b>: <a href="Patient-denovoChild.html">Patient/denovoChild: Child Junior Doe</a> " DOE"</p><p><b>description</b>: A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.</p><p><b>securityLabel</b>: Restricted <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v3-Confidentiality.html">Confidentiality</a>#R)</span></p><blockquote><p><b>content</b></p></blockquote></div>
+  </text>
+  <identifier>
+    <system value="http://www.somesystemabc.net/identifiers/files"/>
+    <value value="11111"/>
+  </identifier>
+  <status value="current"/>
+  <docStatus value="preliminary"/>
+  <description value="A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline."/>
+  <securityLabel>
+    <coding>
+      <system value="http://terminology.hl7.org/CodeSystem/v3-Confidentiality"/>
+      <code value="R"/>
+      <display value="Restricted"/>
+    </coding>
+  </securityLabel>
+  <description value="CYP2C19 gene sequence"/>
+  <content>
+    <attachment>
+      <title value="Homo sapiens cytochrome P450 family 2 subfamily C member 19 (CYP2C19), RefSeqGene (LRG_584) on chromosome 10"/>
+      <contentType value="text/html"/>
+      <url value="https://www.ncbi.nlm.nih.gov/nuccore/NG_008384"/>
+    </attachment>
+  </content>
+</DocumentReference>

source/moleculardefinition/DocumentReference-example-genomicFile-hla00001.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+
+<DocumentReference xmlns="http://hl7.org/fhir">
+  <id value="example-genomicFile-hla00001"/>
+  <text>
+    <status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "genomicFile1" </p></div><p><b>identifier</b>: id: 11111</p><p><b>status</b>: current</p><p><b>docStatus</b>: preliminary</p><p><b>subject</b>: <a href="Patient-denovoChild.html">Patient/denovoChild: Child Junior Doe</a> " DOE"</p><p><b>description</b>: A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.</p><p><b>securityLabel</b>: Restricted <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v3-Confidentiality.html">Confidentiality</a>#R)</span></p><blockquote><p><b>content</b></p></blockquote></div>
+  </text>
+  <identifier>
+    <system value="http://www.somesystemabc.net/identifiers/files"/>
+    <value value="11111"/>
+  </identifier>
+  <status value="current"/>
+  <docStatus value="preliminary"/>
+  <description value="A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline."/>
+  <securityLabel>
+    <coding>
+      <system value="http://terminology.hl7.org/CodeSystem/v3-Confidentiality"/>
+      <code value="R"/>
+      <display value="Restricted"/>
+    </coding>
+  </securityLabel>
+  <content>
+    <attachment>
+      <contentType value="text/html"/>
+      <url value="https://www.ebi.ac.uk/Tools/dbfetch/dbfetch?db=imgthla;id=HLA00001;format=fasta;style=raw"/>
+    </attachment>
+  </content>
+</DocumentReference>

source/moleculardefinition/DocumentReference-example-genomicFile-mw7162561.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+
+<DocumentReference xmlns="http://hl7.org/fhir">
+  <id value="example-genomicFile-mw7162561"/>
+  <text>
+    <status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "genomicFile1" </p></div><p><b>identifier</b>: id: 11111</p><p><b>status</b>: current</p><p><b>docStatus</b>: preliminary</p><p><b>subject</b>: <a href="Patient-denovoChild.html">Patient/denovoChild: Child Junior Doe</a> " DOE"</p><p><b>description</b>: A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.</p><p><b>securityLabel</b>: Restricted <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v3-Confidentiality.html">Confidentiality</a>#R)</span></p><blockquote><p><b>content</b></p></blockquote></div>
+  </text>
+  <identifier>
+    <system value="http://www.somesystemabc.net/identifiers/files"/>
+    <value value="11111"/>
+  </identifier>
+  <status value="current"/>
+  <docStatus value="preliminary"/>
+  <description value="A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline."/>
+  <securityLabel>
+    <coding>
+      <system value="http://terminology.hl7.org/CodeSystem/v3-Confidentiality"/>
+      <code value="R"/>
+      <display value="Restricted"/>
+    </coding>
+  </securityLabel>
+  <content>
+    <attachment>
+      <contentType value="text/html"/>
+      <url value="https://www.ncbi.nlm.nih.gov/nuccore/MW716256.1?report=fasta"/>
+    </attachment>
+  </content>
+</DocumentReference>

source/moleculardefinition/DocumentReference-example-genomicFile-ng0083843.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+
+<DocumentReference xmlns="http://hl7.org/fhir">
+  <id value="example-genomicFile-ng0083843"/>
+  <text>
+    <status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "genomicFile1" </p></div><p><b>identifier</b>: id: 11111</p><p><b>status</b>: current</p><p><b>docStatus</b>: preliminary</p><p><b>subject</b>: <a href="Patient-denovoChild.html">Patient/denovoChild: Child Junior Doe</a> " DOE"</p><p><b>description</b>: A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.</p><p><b>securityLabel</b>: Restricted <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v3-Confidentiality.html">Confidentiality</a>#R)</span></p><blockquote><p><b>content</b></p></blockquote></div>
+  </text>
+  <identifier>
+    <system value="http://www.somesystemabc.net/identifiers/files"/>
+    <value value="11111"/>
+  </identifier>
+  <status value="current"/>
+  <docStatus value="preliminary"/>
+  <description value="A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline."/>
+  <securityLabel>
+    <coding>
+      <system value="http://terminology.hl7.org/CodeSystem/v3-Confidentiality"/>
+      <code value="R"/>
+      <display value="Restricted"/>
+    </coding>
+  </securityLabel>
+  <content>
+    <attachment>
+      <contentType value="text/html"/>
+      <url value="https://www.ncbi.nlm.nih.gov/nuccore/NG_008384.3?report=fasta"/>
+    </attachment>
+  </content>
+</DocumentReference>

source/moleculardefinition/DocumentReference-example-genomicFile-nm0002513.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+
+<DocumentReference xmlns="http://hl7.org/fhir">
+  <id value="example-genomicFile-nm0002513"/>
+  <text>
+    <status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "genomicFile1" </p></div><p><b>identifier</b>: id: 11111</p><p><b>status</b>: current</p><p><b>docStatus</b>: preliminary</p><p><b>subject</b>: <a href="Patient-denovoChild.html">Patient/denovoChild: Child Junior Doe</a> " DOE"</p><p><b>description</b>: A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.</p><p><b>securityLabel</b>: Restricted <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v3-Confidentiality.html">Confidentiality</a>#R)</span></p><blockquote><p><b>content</b></p></blockquote></div>
+  </text>
+  <identifier>
+    <system value="http://www.somesystemabc.net/identifiers/files"/>
+    <value value="11111"/>
+  </identifier>
+  <status value="current"/>
+  <docStatus value="preliminary"/>
+  <description value="A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline."/>
+  <securityLabel>
+    <coding>
+      <system value="http://terminology.hl7.org/CodeSystem/v3-Confidentiality"/>
+      <code value="R"/>
+      <display value="Restricted"/>
+    </coding>
+  </securityLabel>
+  <content>
+    <attachment>
+      <contentType value="text/html"/>
+      <url value="https://www.ncbi.nlm.nih.gov/nuccore/NM_000251.3?report=fasta"/>
+    </attachment>
+  </content>
+</DocumentReference>

source/moleculardefinition/DocumentReference-example-genomicFile-nm0007694.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+
+<DocumentReference xmlns="http://hl7.org/fhir">
+  <id value="example-genomicFile-nm0007694"/>
+  <text>
+    <status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "genomicFile1" </p></div><p><b>identifier</b>: id: 11111</p><p><b>status</b>: current</p><p><b>docStatus</b>: preliminary</p><p><b>subject</b>: <a href="Patient-denovoChild.html">Patient/denovoChild: Child Junior Doe</a> " DOE"</p><p><b>description</b>: A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.</p><p><b>securityLabel</b>: Restricted <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v3-Confidentiality.html">Confidentiality</a>#R)</span></p><blockquote><p><b>content</b></p></blockquote></div>
+  </text>
+  <identifier>
+    <system value="http://www.somesystemabc.net/identifiers/files"/>
+    <value value="11111"/>
+  </identifier>
+  <status value="current"/>
+  <docStatus value="preliminary"/>
+  <description value="(CYP2C19), mRNA"/>
+  <securityLabel>
+    <coding>
+      <system value="http://terminology.hl7.org/CodeSystem/v3-Confidentiality"/>
+      <code value="R"/>
+      <display value="Restricted"/>
+    </coding>
+  </securityLabel>
+  <content>
+    <attachment>
+      <title value="Homo sapiens cytochrome P450 family 2 subfamily C member 19 (CYP2C19), mRNA"/>
+      <contentType value="text/html"/>
+      <url value="https://www.ncbi.nlm.nih.gov/nuccore/NM_000769.4?report=fasta"/>
+    </attachment>
+  </content>
+</DocumentReference>

source/moleculardefinition/DocumentReference-example-genomicFile-nm0020245.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+
+<DocumentReference xmlns="http://hl7.org/fhir">
+  <id value="example-genomicFile-nm0020245"/>
+  <text>
+    <status value="generated"/><div xmlns="http://www.w3.org/1999/xhtml"><p><b>Generated Narrative</b></p><div style="display: inline-block; background-color: #d9e0e7; padding: 6px; margin: 4px; border: 1px solid #8da1b4; border-radius: 5px; line-height: 60%"><p style="margin-bottom: 0px">Resource "genomicFile1" </p></div><p><b>identifier</b>: id: 11111</p><p><b>status</b>: current</p><p><b>docStatus</b>: preliminary</p><p><b>subject</b>: <a href="Patient-denovoChild.html">Patient/denovoChild: Child Junior Doe</a> " DOE"</p><p><b>description</b>: A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline.</p><p><b>securityLabel</b>: Restricted <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/3.1.0/CodeSystem-v3-Confidentiality.html">Confidentiality</a>#R)</span></p><blockquote><p><b>content</b></p></blockquote></div>
+  </text>
+  <identifier>
+    <system value="http://www.somesystemabc.net/identifiers/files"/>
+    <value value="11111"/>
+  </identifier>
+  <status value="current"/>
+  <docStatus value="preliminary"/>
+  <description value="A sample Document Reference instance representing a generic genomic file that may ber used as input or output of a genomic analysis pipeline."/>
+  <securityLabel>
+    <coding>
+      <system value="http://terminology.hl7.org/CodeSystem/v3-Confidentiality"/>
+      <code value="R"/>
+      <display value="Restricted"/>
+    </coding>
+  </securityLabel>
+  <content>
+    <attachment>
+      <contentType value="text/html"/>
+      <url value="https://www.ncbi.nlm.nih.gov/nuccore/NM_002024.5?report=fasta"/>
+    </attachment>
+  </content>
+</DocumentReference>

source/moleculardefinition/codesystem-moleculardefinition-encoding.xml

@@ -0,0 +1,54 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<CodeSystem xmlns="http://hl7.org/fhir">
+  <id value="moleculardefinition-encoding"/>
+  <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-encoding"/>
+  <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="MolecularDefinitionEncoding"/>
+  <title value="Molecular Definition Encoding"/>
+  <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="[email protected]"/>
+    </telecom>
+  </contact>
+  <description value="The encoding of the molecular definition sequences, e.g., IUPAC-DNA, IUPAC-Protein"/>
+  <caseSensitive value="true"/>
+  <valueSet value="http://hl7.org/fhir/ValueSet/moleculardefinition-encoding"/>
+  <content value="example"/>
+  <concept>
+    <code value="iupac-nucleotide"/>
+    <display value="IUPAC-Nucleotide "/>
+    <definition value="International Union of Pure and Applied Chemistry-DNA Nucleotide Codes."/>
+  </concept>
+  <concept>
+    <code value="iupac-protein"/>
+    <display value="IUPAC-Protein"/>
+    <definition value="International Union of Pure and Applied Chemistry-Amino Acid Codes."/>
+  </concept>
+</CodeSystem>