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
{
"resourceType" : "Bundle",
"id" : "PhenopacketsBundleExample01",
"meta" : {
"lastUpdated" : "2022-02-02T22:22:22Z"
},
"identifier" : {
"system" : "urn:ietf:rfc:3986",
"value" : "urn:uuid:1111-1111-1111-1111"
},
"type" : "document",
"timestamp" : "2022-02-02T22:22:22Z",
"entry" : [
{
"fullUrl" : "http://phenopackets.org/fhir/Composition/PhenopacketCompositionExample01",
"resource" : {
"resourceType" : "Composition",
"id" : "PhenopacketCompositionExample01",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Phenopacket"
]
},
"text" : {
"status" : "generated",
"div" : "<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 \r\n\r\nThis 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: \r\n\r\nNote 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.\r\n\r\nThis 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>"
},
"identifier" : {
"system" : "urn:ietf:rfc:3986",
"value" : "urn:uuid:1111-1111-1111-1112"
},
"status" : "preliminary",
"type" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "11503-0",
"display" : "Medical records"
}
]
},
"subject" : {
🔗 "reference" : "Patient/example-patient",
"display" : "Anyname A. Anyperson"
},
"date" : "2022-02-02",
"author" : [
{
🔗 "reference" : "Practitioner/PhenopacketPractitionerExample01",
"display" : "John T. Practitioner"
}
],
"title" : "This is an example of a composition resource that represents some of the Phenopackets data elements",
"section" : [
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type",
"code" : "phenotypic_features"
}
]
},
"entry" : [
{
🔗 "reference" : "Observation/CHF-with-severity",
"display" : "Congestive heart failure"
}
]
},
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type",
"code" : "measurements"
}
]
},
"entry" : [
{
🔗 "reference" : "Observation/thrombocytopenia",
"display" : "Thrombocytopenia"
}
]
},
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type",
"code" : "biosamples"
}
]
},
"entry" : [
{
🔗 "reference" : "Specimen/bladderCarcinoma",
"display" : "Bladder Carcinoma"
}
]
},
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type",
"code" : "interpretations"
}
]
},
"entry" : [
{
🔗 "reference" : "DiagnosticReport/PhenopacketsGenomicInterpretationExample02",
"display" : "Obesity due to centrosomal protein 19 deficiency (disorder)"
}
]
},
{
"code" : {
"coding" : [
{
"system" : "http://hl7.org/fhir/uv/phenomics-exchange/CodeSystem/section-type",
"code" : "diseases"
}
]
},
"entry" : [
{
🔗 "reference" : "Condition/CHF-stageIII",
"display" : "CHF-stageIII"
}
]
}
]
}
},
{
"fullUrl" : "http://phenopackets.org/fhir/Patient/example-patient",
"resource" : {
"resourceType" : "Patient",
"id" : "example-patient",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Individual"
]
},
"text" : {
"status" : "generated",
"div" : "<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\u00a0(use:\u00a0usual)</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>"
},
"identifier" : [
{
"use" : "usual",
"type" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0203",
"code" : "MR",
"display" : "Medical Record Number"
}
]
},
"system" : "http://hospital.example.org",
"value" : "m123"
}
],
"name" : [
{
"family" : "Anyperson",
"given" : [
"Anyname",
"A."
]
}
],
"gender" : "male",
"birthDate" : "2001-01-20",
"address" : [
{
"line" : [
"123 Any St"
],
"city" : "Anytown",
"postalCode" : "12345",
"country" : "US"
}
],
"contact" : [
{
"telecom" : [
{
"system" : "phone",
"value" : "777-444-2222",
"use" : "home"
},
{
"system" : "email",
"value" : "anyname.anyperson@example.com"
}
]
}
],
"communication" : [
{
"language" : {
"coding" : [
{
"system" : "urn:ietf:bcp:47",
"code" : "en-US",
"display" : "English (Region=United States)"
}
],
"text" : "English"
}
}
]
}
},
{
"fullUrl" : "http://phenopackets.org/fhir/Practitioner/PhenopacketPractitionerExample01",
"resource" : {
"resourceType" : "Practitioner",
"id" : "PhenopacketPractitionerExample01",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\">This is an incomplete example that used as a placeholder for a curated Practitioner example</div>"
},
"identifier" : [
{
"use" : "temp",
"value" : "03"
}
],
"name" : [
{
"text" : "John T. Practitioner"
}
]
}
},
{
"fullUrl" : "http://phenopackets.org/fhir/Observation/CHF-with-severity",
"resource" : {
"resourceType" : "Observation",
"id" : "CHF-with-severity",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PhenotypicFeature"
]
},
"text" : {
"status" : "generated",
"div" : "<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>"
},
"status" : "final",
"code" : {
"coding" : [
{
"system" : "http://human-phenotype-ontology.org",
"code" : "HP:0009805",
"display" : "Low-output congestive heart failure"
}
]
},
"subject" : {
🔗 "reference" : "Patient/example-patient"
},
"effectiveDateTime" : "2018-03-06",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "LA9633-4",
"display" : "Present"
}
]
},
"component" : [
{
"code" : {
"coding" : [
{
"system" : "http://human-phenotype-ontology.org",
"code" : "HP:0012824",
"display" : "Severity"
}
]
},
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://human-phenotype-ontology.org",
"code" : "HP:0012828",
"display" : "Severe"
}
]
}
}
]
}
},
{
"fullUrl" : "http://phenopackets.org/fhir/Observation/thrombocytopenia",
"resource" : {
"resourceType" : "Observation",
"id" : "thrombocytopenia",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Measurement"
]
},
"text" : {
"status" : "generated",
"div" : "<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>"
},
"status" : "final",
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "26515-7",
"display" : "Platelets [#/volume] in Blood"
}
]
},
"effectiveDateTime" : "2018-03-06",
"valueQuantity" : {
"value" : 20,
"unit" : "10^12/L",
"system" : "http://unitsofmeasure.org"
},
"referenceRange" : [
{
"low" : {
"value" : 150000,
"unit" : "10^12/L",
"system" : "http://unitsofmeasure.org"
},
"high" : {
"value" : 450000,
"unit" : "10^12/L",
"system" : "http://unitsofmeasure.org"
}
}
]
}
},
{
"fullUrl" : "http://phenopackets.org/fhir/Condition/CHF-stageIII",
"resource" : {
"resourceType" : "Condition",
"id" : "CHF-stageIII",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Disease"
]
},
"text" : {
"status" : "generated",
"div" : "<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>"
},
"clinicalStatus" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/condition-clinical",
"code" : "active",
"display" : "Active"
}
]
},
"code" : {
"coding" : [
{
"system" : "http://purl.obolibrary.org/obo/mondo.owl",
"code" : "MONDO_0005009",
"display" : "congestive heart failure"
}
]
},
"subject" : {
🔗 "reference" : "Patient/example-patient"
},
"stage" : [
{
"summary" : {
"coding" : [
{
"system" : "http://github.com/EBISPOT/efo",
"code" : "EFO:0003148",
"display" : "moderate heart failure"
}
]
},
"type" : {
"coding" : [
{
"system" : "http://snomed.info/sct",
"code" : "260998006",
"display" : "Clinical staging"
}
]
}
}
]
}
},
{
"fullUrl" : "http://phenopackets.org/fhir/Specimen/bladderCarcinoma",
"resource" : {
"resourceType" : "Specimen",
"id" : "bladderCarcinoma",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/Biosample"
]
},
"text" : {
"status" : "extensions",
"div" : "<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>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/HistologicalDiagnosis",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl",
"code" : "NCIT_C39853",
"display" : "Infiltrating Urothelial Carcinoma"
}
]
}
},
{
"url" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/TumorProgression",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl",
"code" : "NCIT_C84509",
"display" : "Primary Malignant Neoplasm"
}
]
}
},
{
"url" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/TumorGrade",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl",
"code" : "NCIT_C36136",
"display" : "Grade 2 Lesion"
}
]
}
},
{
"url" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PathologicalStage",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl",
"code" : "NCIT_C28054",
"display" : "Stage II"
}
]
}
},
{
"url" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/PathologicalTnmFinding",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl",
"code" : "NCIT_C48699",
"display" : "M0 Stage Finding"
}
]
}
},
{
"url" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/MaterialSample",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://github.com/EBISPOT/efo",
"code" : "EFO_0009655",
"display" : "abnormal sample"
}
]
}
}
],
"identifier" : [
{
"value" : "arbitrary identifier"
}
],
"type" : {
"coding" : [
{
"system" : "http://github.com/EBISPOT/efo",
"code" : "EFO_0010942",
"display" : "primary tumor sample"
}
]
},
"subject" : {
🔗 "reference" : "Patient/example-patient"
},
"collection" : {
"collectedDateTime" : "2021-01-20",
"bodySite" : {
"coding" : [
{
"system" : "http://github.com/obophenotype/uberon",
"code" : "UBERON_0001256",
"display" : "wall of urinary bladder"
}
]
}
},
"processing" : [
{
"procedure" : {
"coding" : [
{
"system" : "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl",
"code" : "NCIT_C5189",
"display" : "Radical Cystoprostatectomy"
}
]
}
}
]
}
},
{
"fullUrl" : "http://phenopackets.org/fhir/DiagnosticReport/PhenopacketsGenomicInterpretationExample02",
"resource" : {
"resourceType" : "DiagnosticReport",
"id" : "PhenopacketsGenomicInterpretationExample02",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/phenopackets-genomic-interpretation"
]
},
"text" : {
"status" : "generated",
"div" : "<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>"
},
"modifierExtension" : [
{
"url" : "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/interpretation-status",
"valueCodeableConcept" : {
"coding" : [
{
"system" : "http://phenopacket-schema.readthedocs.io/en/v2/genomic-interpretation.html#interpretationstatus",
"code" : "0",
"display" : "UNKNOWN_STATUS"
}
]
}
}
],
"identifier" : [
{
"value" : "02"
}
],
"status" : "unknown",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE",
"display" : "Genetics"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc",
"code" : "123",
"display" : "some loinc code"
}
]
},
"subject" : {
🔗 "reference" : "Patient/phenopacketPatientExample01"
},
"specimen" : [
{
🔗 "reference" : "Specimen/phenopacketSpecimenExample01"
}
],
"result" : [
{
🔗 "reference" : "Observation/PhenopacketsVariantExample01"
}
],
"conclusion" : "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" : "http://snomed.info/sct",
"code" : "783549006",
"display" : "Obesity due to centrosomal protein 19 deficiency (disorder)"
}
]
}
]
}
},
{
"fullUrl" : "http://phenopackets.org/fhir/Observation/PhenopacketsVariantExample01",
"resource" : {
"resourceType" : "Observation",
"id" : "PhenopacketsVariantExample01",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/phenomics-exchange/StructureDefinition/phenopackets-variant"
]
},
"text" : {
"status" : "generated",
"div" : "<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>"
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-category",
"code" : "laboratory"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "69548-6"
}
]
}
}
}
]
}
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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