Phenomics Exchange for Research and Diagnostics
0.1.0 - ci-build
Phenomics Exchange for Research and Diagnostics
0.1.0 - ci-build
Phenomics Exchange for Research and Diagnostics, published by HL7 International / Clinical Interoperability Council. This guide is not an authorized publication; it is the continuous build for version 0.1.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/HL7/phenomics-exchange-ig/ and changes regularly. See the Directory of published versions
<Bundle xmlns="http://hl7.org/fhir">
<id value="PhenopacketsBundleExample01"/>
<meta>
<lastUpdated value="2022-02-02T22:22:22Z"/>
</meta>
<identifier>
<system value="urn:ietf:rfc:3986"/>
<value value="urn:uuid:1111-1111-1111-1111"/>
</identifier>
<type value="document"/>
<timestamp value="2022-02-02T22:22:22Z"/>
<entry>
<fullUrl
value="http://phenopackets.org/fhir/Composition/PhenopacketCompositionExample01"/>
<resource>
<Composition>
<id value="PhenopacketCompositionExample01"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Phenopacket"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Composition_PhenopacketCompositionExample01"> </a><p><b>Generated Narrative: Composition </b><a name="PhenopacketCompositionExample01"> </a><a name="hcPhenopacketCompositionExample01"> </a></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">ResourceComposition "PhenopacketCompositionExample01" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-Phenopacket.html">Phenopacket profile</a></p></div><p><b>identifier</b>: <a href="http://terminology.hl7.org/5.5.0/NamingSystem-uri.html" title="As defined by RFC 3986 (http://www.ietf.org/rfc/rfc3986.txt)(with many schemes defined in many RFCs). For OIDs and UUIDs, use the URN form (urn:oid:(note: lowercase) and urn:uuid:). See http://www.ietf.org/rfc/rfc3001.txt and http://www.ietf.org/rfc/rfc4122.txt
This oid is used as an identifier II.root to indicate the the extension is an absolute URI (technically, an IRI). Typically, this is used for OIDs and GUIDs. Note that when this OID is used with OIDs and GUIDs, the II.extension should start with urn:oid or urn:uuid:
Note that this OID is created to aid with interconversion between CDA and FHIR - FHIR uses urn:ietf:rfc:3986 as equivalent to this OID. URIs as identifiers appear more commonly in FHIR.
This OID may also be used in CD.codeSystem.">Uniform Resource Identifier (URI)</a>/urn:uuid:1111-1111-1111-1112</p><p><b>status</b>: preliminary</p><p><b>type</b>: Medical records <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#11503-0)</span></p><p><b>date</b>: 2022-02-02</p><p><b>author</b>: See on this page: Practitioner/PhenopacketPractitionerExample01: John T. Practitioner</p><p><b>title</b>: This is an example of a composition resource that represents some of the Phenopackets data elements</p></div>
</text>
<identifier>
<system value="urn:ietf:rfc:3986"/>
<value value="urn:uuid:1111-1111-1111-1112"/>
</identifier>
<status value="preliminary"/>
<type>
<coding>
<system value="http://loinc.org"/>
<code value="11503-0"/>
<display value="Medical records"/>
</coding>
</type>
<subject>🔗
<reference value="Patient/example-patient"/>
<display value="Anyname A. Anyperson"/>
</subject>
<date value="2022-02-02"/>
<author>🔗
<reference value="Practitioner/PhenopacketPractitionerExample01"/>
<display value="John T. Practitioner"/>
</author>
<title
value="This is an example of a composition resource that represents some of the Phenopackets data elements"/>
<section>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type"/>
<code value="phenotypic_features"/>
</coding>
</code>
<entry>🔗
<reference value="Observation/CHF-with-severity"/>
<display value="Congestive heart failure"/>
</entry>
</section>
<section>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type"/>
<code value="measurements"/>
</coding>
</code>
<entry>🔗
<reference value="Observation/thrombocytopenia"/>
<display value="Thrombocytopenia"/>
</entry>
</section>
<section>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type"/>
<code value="biosamples"/>
</coding>
</code>
<entry>🔗
<reference value="Specimen/bladderCarcinoma"/>
<display value="Bladder Carcinoma"/>
</entry>
</section>
<section>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type"/>
<code value="interpretations"/>
</coding>
</code>
<entry>🔗
<reference
value="DiagnosticReport/PhenopacketsGenomicInterpretationExample02"/>
<display
value="Obesity due to centrosomal protein 19 deficiency (disorder)"/>
</entry>
</section>
<section>
<code>
<coding>
<system
value="http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type"/>
<code value="diseases"/>
</coding>
</code>
<entry>🔗
<reference value="Condition/CHF-stageIII"/>
<display value="CHF-stageIII"/>
</entry>
</section>
</Composition>
</resource>
</entry>
<entry>
<fullUrl value="http://phenopackets.org/fhir/Patient/example-patient"/>
<resource>
<Patient>
<id value="example-patient"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Individual"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Patient_example-patient"> </a><p><b>Generated Narrative: Patient </b><a name="example-patient"> </a><a name="hcexample-patient"> </a></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">ResourcePatient "example-patient" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-Individual.html">Individual</a></p></div><p><b>identifier</b>: Medical Record Number/m123 (use: usual)</p><p><b>name</b>: Anyname A. Anyperson </p><p><b>gender</b>: male</p><p><b>birthDate</b>: 2001-01-20</p><p><b>address</b>: 123 Any St Anytown 12345 US </p><h3>Contacts</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Telecom</b></td></tr><tr><td style="display: none">*</td><td>ph: 777-444-2222(HOME), <a href="mailto:anyname.anyperson@example.com">anyname.anyperson@example.com</a></td></tr></table><h3>Communications</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Language</b></td></tr><tr><td style="display: none">*</td><td>English <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-v3-ietf3066.html">Tags for the Identification of Languages</a>#en-US "English (Region=United States)")</span></td></tr></table></div>
</text>
<identifier>
<use value="usual"/>
<type>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0203"/>
<code value="MR"/>
<display value="Medical Record Number"/>
</coding>
</type>
<system value="http://hospital.example.org"/>
<value value="m123"/>
</identifier>
<name>
<family value="Anyperson"/>
<given value="Anyname"/>
<given value="A."/>
</name>
<gender value="male"/>
<birthDate value="2001-01-20"/>
<address>
<line value="123 Any St"/>
<city value="Anytown"/>
<postalCode value="12345"/>
<country value="US"/>
</address>
<contact>
<telecom>
<system value="phone"/>
<value value="777-444-2222"/>
<use value="home"/>
</telecom>
<telecom>
<system value="email"/>
<value value="anyname.anyperson@example.com"/>
</telecom>
</contact>
<communication>
<language>
<coding>
<system value="urn:ietf:bcp:47"/>
<code value="en-US"/>
<display value="English (Region=United States)"/>
</coding>
<text value="English"/>
</language>
</communication>
</Patient>
</resource>
</entry>
<entry>
<fullUrl
value="http://phenopackets.org/fhir/Practitioner/PhenopacketPractitionerExample01"/>
<resource>
<Practitioner>
<id value="PhenopacketPractitionerExample01"/>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml">This is an incomplete example that used as a placeholder for a curated Practitioner example</div>
</text>
<identifier>
<use value="temp"/>
<value value="03"/>
</identifier>
<name>
<text value="John T. Practitioner"/>
</name>
</Practitioner>
</resource>
</entry>
<entry>
<fullUrl
value="http://phenopackets.org/fhir/Observation/CHF-with-severity"/>
<resource>
<Observation>
<id value="CHF-with-severity"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PhenotypicFeature"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_CHF-with-severity"> </a><p><b>Generated Narrative: Observation </b><a name="CHF-with-severity"> </a><a name="hcCHF-with-severity"> </a></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">ResourceObservation "CHF-with-severity" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-PhenotypicFeature.html">Phenotypic Feature</a></p></div><p><b>status</b>: final</p><p><b>code</b>: Low-output congestive heart failure <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-HPO.html">Human Phenotype Ontology</a>#HP:0009805)</span></p><p><b>subject</b>: See on this page: Patient/example-patient</p><p><b>effective</b>: 2018-03-06</p><p><b>value</b>: Present <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#LA9633-4)</span></p><h3>Components</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Code</b></td><td><b>Value[x]</b></td></tr><tr><td style="display: none">*</td><td>Severity <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-HPO.html">Human Phenotype Ontology</a>#HP:0012824)</span></td><td>Severe <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-HPO.html">Human Phenotype Ontology</a>#HP:0012828)</span></td></tr></table></div>
</text>
<status value="final"/>
<code>
<coding>
<system value="http://human-phenotype-ontology.org"/>
<code value="HP:0009805"/>
<display value="Low-output congestive heart failure"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/example-patient"/>
</subject>
<effectiveDateTime value="2018-03-06"/>
<valueCodeableConcept>
<coding>
<system value="http://loinc.org"/>
<code value="LA9633-4"/>
<display value="Present"/>
</coding>
</valueCodeableConcept>
<component>
<code>
<coding>
<system value="http://human-phenotype-ontology.org"/>
<code value="HP:0012824"/>
<display value="Severity"/>
</coding>
</code>
<valueCodeableConcept>
<coding>
<system value="http://human-phenotype-ontology.org"/>
<code value="HP:0012828"/>
<display value="Severe"/>
</coding>
</valueCodeableConcept>
</component>
</Observation>
</resource>
</entry>
<entry>
<fullUrl
value="http://phenopackets.org/fhir/Observation/thrombocytopenia"/>
<resource>
<Observation>
<id value="thrombocytopenia"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Measurement"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_thrombocytopenia"> </a><p><b>Generated Narrative: Observation </b><a name="thrombocytopenia"> </a><a name="hcthrombocytopenia"> </a></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">ResourceObservation "thrombocytopenia" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-Measurement.html">Measurement</a></p></div><p><b>status</b>: final</p><p><b>code</b>: Platelets [#/volume] in Blood <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#26515-7)</span></p><p><b>effective</b>: 2018-03-06</p><p><b>value</b>: 20 10^12/L</p><h3>ReferenceRanges</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Low</b></td><td><b>High</b></td></tr><tr><td style="display: none">*</td><td>150000 10^12/L</td><td>450000 10^12/L</td></tr></table></div>
</text>
<status value="final"/>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="26515-7"/>
<display value="Platelets [#/volume] in Blood"/>
</coding>
</code>
<effectiveDateTime value="2018-03-06"/>
<valueQuantity>
<value value="20"/>
<unit value="10^12/L"/>
<system value="http://unitsofmeasure.org"/>
</valueQuantity>
<referenceRange>
<low>
<value value="150000"/>
<unit value="10^12/L"/>
<system value="http://unitsofmeasure.org"/>
</low>
<high>
<value value="450000"/>
<unit value="10^12/L"/>
<system value="http://unitsofmeasure.org"/>
</high>
</referenceRange>
</Observation>
</resource>
</entry>
<entry>
<fullUrl value="http://phenopackets.org/fhir/Condition/CHF-stageIII"/>
<resource>
<Condition>
<id value="CHF-stageIII"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Disease"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Condition_CHF-stageIII"> </a><p><b>Generated Narrative: Condition </b><a name="CHF-stageIII"> </a><a name="hcCHF-stageIII"> </a></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">ResourceCondition "CHF-stageIII" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-Disease.html">Disease profile</a></p></div><p><b>clinicalStatus</b>: Active <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-condition-clinical.html">Condition Clinical Status Codes</a>#active)</span></p><p><b>code</b>: congestive heart failure <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-MONDO.html">Mondo Disease Ontology</a>#MONDO_0005009)</span></p><p><b>subject</b>: See on this page: Patient/example-patient</p><h3>Stages</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Summary</b></td><td><b>Type</b></td></tr><tr><td style="display: none">*</td><td>moderate heart failure <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (efo#EFO:0003148)</span></td><td>Clinical staging <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://browser.ihtsdotools.org/">SNOMED CT</a>#260998006)</span></td></tr></table></div>
</text>
<clinicalStatus>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/condition-clinical"/>
<code value="active"/>
<display value="Active"/>
</coding>
</clinicalStatus>
<code>
<coding>
<system value="http://purl.obolibrary.org/obo/mondo.owl"/>
<code value="MONDO_0005009"/>
<display value="congestive heart failure"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/example-patient"/>
</subject>
<stage>
<summary>
<coding>
<system value="http://github.com/EBISPOT/efo"/>
<code value="EFO:0003148"/>
<display value="moderate heart failure"/>
</coding>
</summary>
<type>
<coding>
<system value="http://snomed.info/sct"/>
<code value="260998006"/>
<display value="Clinical staging"/>
</coding>
</type>
</stage>
</Condition>
</resource>
</entry>
<entry>
<fullUrl value="http://phenopackets.org/fhir/Specimen/bladderCarcinoma"/>
<resource>
<Specimen>
<id value="bladderCarcinoma"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Biosample"/>
</meta>
<text>
<status value="extensions"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Specimen_bladderCarcinoma"> </a><p><b>Generated Narrative: Specimen </b><a name="bladderCarcinoma"> </a><a name="hcbladderCarcinoma"> </a></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">ResourceSpecimen "bladderCarcinoma" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-Biosample.html">Biosample</a></p></div><p><b>Histological Diagnosis</b>: Infiltrating Urothelial Carcinoma <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-v3-nciThesaurus.html">NCI Thesaurus</a>#NCIT_C39853)</span></p><p><b>Tumor Progression</b>: Primary Malignant Neoplasm <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-v3-nciThesaurus.html">NCI Thesaurus</a>#NCIT_C84509)</span></p><p><b>Tumor Grade</b>: Grade 2 Lesion <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-v3-nciThesaurus.html">NCI Thesaurus</a>#NCIT_C36136)</span></p><p><b>Pathological Tumor Stage</b>: Stage II <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-v3-nciThesaurus.html">NCI Thesaurus</a>#NCIT_C28054)</span></p><p><b>Pathological TNM Finding</b>: M0 Stage Finding <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-v3-nciThesaurus.html">NCI Thesaurus</a>#NCIT_C48699)</span></p><p><b>Material Sample</b>: abnormal sample <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (efo#EFO_0009655)</span></p><p><b>identifier</b>: arbitrary identifier</p><p><b>type</b>: primary tumor sample <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (efo#EFO_0010942)</span></p><p><b>subject</b>: See on this page: Patient/example-patient</p><h3>Collections</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Collected[x]</b></td><td><b>BodySite</b></td></tr><tr><td style="display: none">*</td><td>2021-01-20</td><td>wall of urinary bladder <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (uberon#UBERON_0001256)</span></td></tr></table><h3>Processings</h3><table class="grid"><tr><td style="display: none">-</td><td><b>Procedure</b></td></tr><tr><td style="display: none">*</td><td>Radical Cystoprostatectomy <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-v3-nciThesaurus.html">NCI Thesaurus</a>#NCIT_C5189)</span></td></tr></table></div>
</text>
<extension
url="http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/HistologicalDiagnosis">
<valueCodeableConcept>
<coding>
<system
value="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl"/>
<code value="NCIT_C39853"/>
<display value="Infiltrating Urothelial Carcinoma"/>
</coding>
</valueCodeableConcept>
</extension>
<extension
url="http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/TumorProgression">
<valueCodeableConcept>
<coding>
<system
value="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl"/>
<code value="NCIT_C84509"/>
<display value="Primary Malignant Neoplasm"/>
</coding>
</valueCodeableConcept>
</extension>
<extension
url="http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/TumorGrade">
<valueCodeableConcept>
<coding>
<system
value="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl"/>
<code value="NCIT_C36136"/>
<display value="Grade 2 Lesion"/>
</coding>
</valueCodeableConcept>
</extension>
<extension
url="http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PathologicalStage">
<valueCodeableConcept>
<coding>
<system
value="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl"/>
<code value="NCIT_C28054"/>
<display value="Stage II"/>
</coding>
</valueCodeableConcept>
</extension>
<extension
url="http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PathologicalTnmFinding">
<valueCodeableConcept>
<coding>
<system
value="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl"/>
<code value="NCIT_C48699"/>
<display value="M0 Stage Finding"/>
</coding>
</valueCodeableConcept>
</extension>
<extension
url="http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/MaterialSample">
<valueCodeableConcept>
<coding>
<system value="http://github.com/EBISPOT/efo"/>
<code value="EFO_0009655"/>
<display value="abnormal sample"/>
</coding>
</valueCodeableConcept>
</extension>
<identifier>
<value value="arbitrary identifier"/>
</identifier>
<type>
<coding>
<system value="http://github.com/EBISPOT/efo"/>
<code value="EFO_0010942"/>
<display value="primary tumor sample"/>
</coding>
</type>
<subject>🔗
<reference value="Patient/example-patient"/>
</subject>
<collection>
<collectedDateTime value="2021-01-20"/>
<bodySite>
<coding>
<system value="http://github.com/obophenotype/uberon"/>
<code value="UBERON_0001256"/>
<display value="wall of urinary bladder"/>
</coding>
</bodySite>
</collection>
<processing>
<procedure>
<coding>
<system
value="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl"/>
<code value="NCIT_C5189"/>
<display value="Radical Cystoprostatectomy"/>
</coding>
</procedure>
</processing>
</Specimen>
</resource>
</entry>
<entry>
<fullUrl
value="http://phenopackets.org/fhir/DiagnosticReport/PhenopacketsGenomicInterpretationExample02"/>
<resource>
<DiagnosticReport>
<id value="PhenopacketsGenomicInterpretationExample02"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/phenopackets-genomic-interpretation"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="DiagnosticReport_PhenopacketsGenomicInterpretationExample02"> </a><p><b>Generated Narrative: DiagnosticReport </b><a name="PhenopacketsGenomicInterpretationExample02"> </a><a name="hcPhenopacketsGenomicInterpretationExample02"> </a></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">ResourceDiagnosticReport "PhenopacketsGenomicInterpretationExample02" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-phenopackets-genomic-interpretation.html">Phenopackets Genomic Interpretation</a></p></div><blockquote><p><b>modifierExtension[http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/interpretation-status]</b></p></blockquote><p><b>identifier</b>: 02</p><p><b>status</b>: unknown</p><p><b>category</b>: Genetics <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-v2-0074.html">diagnosticServiceSectionId</a>#GE)</span></p><p><b>code</b>: some loinc code <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (loinc#123)</span></p><p><b>subject</b>: <a href="Patient-phenopacketPatientExample01.html">Patient/phenopacketPatientExample01</a> " DOE"</p><p><b>specimen</b>: <a href="Specimen-phenopacketSpecimenExample01.html">Specimen/phenopacketSpecimenExample01</a></p><p><b>result</b>: See on this page: Observation/PhenopacketsVariantExample01</p><p><b>conclusion</b>: A rare genetic form of obesity characterized by morbid obesity, hypertension, type 2 diabetes mellitus and dyslipidemia leading to early coronary disease, myocardial infarction and congestive heart failure. Intellectual disability and decreased sperm counts or azoospermia have also been reported.</p><p><b>conclusionCode</b>: Obesity due to centrosomal protein 19 deficiency (disorder) <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://browser.ihtsdotools.org/">SNOMED CT</a>#783549006)</span></p></div>
</text>
<modifierExtension
url="http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/interpretation-status">
<valueCodeableConcept>
<coding>
<system
value="http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus"/>
<code value="0"/>
<display value="UNKNOWN_STATUS"/>
</coding>
</valueCodeableConcept>
</modifierExtension>
<identifier>
<value value="02"/>
</identifier>
<status value="unknown"/>
<category>
<coding>
<system value="http://terminology.hl7.org/CodeSystem/v2-0074"/>
<code value="GE"/>
<display value="Genetics"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc"/>
<code value="123"/>
<display value="some loinc code"/>
</coding>
</code>
<subject>🔗
<reference value="Patient/phenopacketPatientExample01"/>
</subject>
<specimen>🔗
<reference value="Specimen/phenopacketSpecimenExample01"/>
</specimen>
<result>🔗
<reference value="Observation/PhenopacketsVariantExample01"/>
</result>
<conclusion
value="A rare genetic form of obesity characterized by morbid obesity, hypertension, type 2 diabetes mellitus and dyslipidemia leading to early coronary disease, myocardial infarction and congestive heart failure. Intellectual disability and decreased sperm counts or azoospermia have also been reported."/>
<conclusionCode>
<coding>
<system value="http://snomed.info/sct"/>
<code value="783549006"/>
<display
value="Obesity due to centrosomal protein 19 deficiency (disorder)"/>
</coding>
</conclusionCode>
</DiagnosticReport>
</resource>
</entry>
<entry>
<fullUrl
value="http://phenopackets.org/fhir/Observation/PhenopacketsVariantExample01"/>
<resource>
<Observation>
<id value="PhenopacketsVariantExample01"/>
<meta>
<profile
value="http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/phenopackets-variant"/>
</meta>
<text>
<status value="generated"/>
<div xmlns="http://www.w3.org/1999/xhtml"><a name="Observation_PhenopacketsVariantExample01"> </a><p><b>Generated Narrative: Observation </b><a name="PhenopacketsVariantExample01"> </a><a name="hcPhenopacketsVariantExample01"> </a></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">ResourceObservation "PhenopacketsVariantExample01" </p><p style="margin-bottom: 0px">Profile: <a href="StructureDefinition-phenopackets-variant.html">Phenopackets Variant</a></p></div><p><b>status</b>: final</p><p><b>category</b>: Laboratory <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="http://terminology.hl7.org/5.5.0/CodeSystem-observation-category.html">Observation Category Codes</a>#laboratory)</span></p><p><b>code</b>: Genetic variant assessment <span style="background: LightGoldenRodYellow; margin: 4px; border: 1px solid khaki"> (<a href="https://loinc.org/">LOINC</a>#69548-6)</span></p></div>
</text>
<status value="final"/>
<category>
<coding>
<system
value="http://terminology.hl7.org/CodeSystem/observation-category"/>
<code value="laboratory"/>
</coding>
</category>
<code>
<coding>
<system value="http://loinc.org"/>
<code value="69548-6"/>
</coding>
</code>
</Observation>
</resource>
</entry>
</Bundle>
IG © 2021+ HL7 International / Clinical Interoperability Council. Package hl7.fhir.uv.phenomics-exchange#0.1.0 based on FHIR 4.0.1. Generated 2024-06-18
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