GenomeX Data Exchange FHIR IG
0.2.0 - draft
GenomeX Data Exchange FHIR IG, published by MITRE. This guide is not an authorized publication; it is the continuous build for version 0.2.0 built by the FHIR (HL7® FHIR® Standard) CI Build. This version is based on the current content of https://github.com/CodeX-HL7-FHIR-Accelerator/GenomeX-DataExchange/ and changes regularly. See the Directory of published versions
{
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"meta" : {
"profile" : [
🔗 "http://mitre.org/gdx/StructureDefinition/gdx-genomics-somatic-bundle"
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"type" : "transaction",
"entry" : [
{
"fullUrl" : "urn:uuid:43e09316-c616-4b23-81df-e546d2b95c41",
"resource" : {
"resourceType" : "Patient",
"id" : "ct-cancer-patient-C3PO",
"meta" : {
"profile" : [
🔗 "http://mitre.org/gdx/StructureDefinition/gdx-patient"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Patient_ct-cancer-patient-C3PO\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Patient ct-cancer-patient-C3PO</b></p><a name=\"ct-cancer-patient-C3PO\"> </a><a name=\"hcct-cancer-patient-C3PO\"> </a><a name=\"ct-cancer-patient-C3PO-en-US\"> </a><p style=\"border: 1px #661aff solid; background-color: #e6e6ff; padding: 10px;\">C3P0 Test Male, DoB: 1950-01-01 ( Medical Record Number: 123456789)</p><hr/><table class=\"grid\"><tr><td style=\"background-color: #f3f5da\" title=\"Other Id (see the one above)\">Other Id:</td><td colspan=\"3\">Patient external identifier/0754aeb3-dd9c-458a-9b06-2da7d62ejh7k\u00a0(use:\u00a0usual,\u00a0)</td></tr><tr><td style=\"background-color: #f3f5da\" title=\"Ways to contact the Patient\">Contact Detail</td><td colspan=\"3\">987 Main St Anytown 12345 US </td></tr></table></div>"
},
"identifier" : [
{
"use" : "usual",
"type" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0203",
"code" : "PT",
"display" : "Patient external identifier"
}
]
},
"system" : "https://www.tempus.com",
"value" : "0754aeb3-dd9c-458a-9b06-2da7d62ejh7k"
},
{
"type" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0203",
"code" : "MR",
"display" : "Medical Record Number"
}
]
},
"system" : "http://hospital.example.org",
"value" : "123456789"
}
],
"name" : [
{
"family" : "Test",
"given" : [
"C3P0"
]
}
],
"gender" : "male",
"birthDate" : "1950-01-01",
"address" : [
{
"line" : [
"987 Main St"
],
"city" : "Anytown",
"postalCode" : "12345",
"country" : "US"
}
]
},
"request" : {
"method" : "POST",
"url" : "Patient"
}
},
{
"fullUrl" : "urn:uuid:d90e9857-574a-4fc6-98c6-6d61d6e024cd",
"resource" : {
"resourceType" : "DiagnosticReport",
"id" : "gx-genomics-report-C3PO",
"meta" : {
"profile" : [
🔗 "http://mitre.org/gdx/StructureDefinition/gdx-genomic-report"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"DiagnosticReport_gx-genomics-report-C3PO\"> </a><p class=\"res-header-id\"><b>Generated Narrative: DiagnosticReport gx-genomics-report-C3PO</b></p><a name=\"gx-genomics-report-C3PO\"> </a><a name=\"hcgx-genomics-report-C3PO\"> </a><a name=\"gx-genomics-report-C3PO-en-US\"> </a><h2><span title=\"Codes:{http://loinc.org 51969-4}\">Genetic analysis report</span> (<span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span>, <span title=\"Codes:\">DNA</span>, <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0074 GE}\">Genetics</span>) </h2><table class=\"grid\"><tr><td>Subject</td><td>Not done yet</td></tr><tr><td>When For</td><td>2022-02-15 19:28:58+0500</td></tr><tr><td>Performer</td><td> <a href=\"Bundle-ct-xG-bundle.html#urn-uuid-aeea668a-a035-4963-9e56-249d735916a5\">Bundle: type = transaction</a></td></tr><tr><td>Identifiers</td><td> Accession ID/TL-22-D3MTCAU4 Pipeline Version/3.9.3 Placer Identifier/d6eeedd1-92d3-45b9-bf33-6401e804425f</td></tr></table><p><b>Report Details</b></p><table class=\"grid\"><tr><td><b>Code</b></td><td><b>Value</b></td></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr><tr><td/><td/></tr></table></div>"
},
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-report-note",
"valueAnnotation" : {
"extension" : [
{
"url" : "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/annotation-code",
"valueCodeableConcept" : {
"coding" : [
{
"code" : "copyright"
}
]
}
}
],
"text" : "(c) Copyright Tempus 2022. All Rights Reserved."
}
}
],
"identifier" : [
{
"type" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0203",
"code" : "ACSN",
"display" : "Accession ID"
}
]
},
"system" : "https://www.tempus.com",
"value" : "TL-22-D3MTCAU4"
},
{
"type" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0203",
"code" : "RI",
"display" : "Pipeline Version"
}
]
},
"system" : "https://www.tempus.com",
"value" : "3.9.3"
},
{
"type" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0203",
"code" : "PLAC",
"display" : "Placer Identifier"
}
]
},
"system" : "https://www.tempus.com",
"value" : "d6eeedd1-92d3-45b9-bf33-6401e804425f"
}
],
"basedOn" : [
{
"reference" : "urn:uuid:150a3549-3114-4dea-bd1d-e24c036b2934"
}
],
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
}
]
},
{
"text" : "DNA"
},
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0074",
"code" : "GE"
}
]
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "51969-4",
"display" : "Genetic analysis report"
}
]
},
"subject" : {
"reference" : "urn:uuid:43e09316-c616-4b23-81df-e546d2b95c41"
},
"effectiveDateTime" : "2022-02-15T19:28:58+05:00",
"performer" : [
{
"reference" : "urn:uuid:aeea668a-a035-4963-9e56-249d735916a5"
}
],
"resultsInterpreter" : [
{
"reference" : "urn:uuid:26242dd9-b9c7-40cb-838c-7f5007fde86f"
}
],
"specimen" : [
{
"reference" : "urn:uuid:1a9edfe1-1620-4882-a81c-30c2f254f34f"
}
],
"result" : [
{
"reference" : "urn:uuid:6320918e-f5da-41fa-9481-6b75c2a0d712"
},
{
"reference" : "urn:uuid:92f37846-46db-41f2-b0f5-edd46b61880a"
},
{
"reference" : "urn:uuid:5a506248-dad9-441e-b898-6fd4be77974b"
},
{
"reference" : "urn:uuid:e44b5631-a39a-43c6-b189-de68720d66fa"
},
{
"reference" : "urn:uuid:33a4f8bb-eae5-4927-b20b-5915cbd862ab"
},
{
"reference" : "urn:uuid:82a8b9db-a68e-4e06-897e-77ed3ea5aced"
}
]
},
"request" : {
"method" : "POST",
"url" : "DiagnosticReport"
}
},
{
"fullUrl" : "urn:uuid:150a3549-3114-4dea-bd1d-e24c036b2934",
"resource" : {
"resourceType" : "ServiceRequest",
"id" : "ct-xG-ServiceRequest",
"meta" : {
"profile" : [
🔗 "http://mitre.org/gdx/StructureDefinition/gdx-service-request"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"ServiceRequest_ct-xG-ServiceRequest\"> </a><p class=\"res-header-id\"><b>Generated Narrative: ServiceRequest ct-xG-ServiceRequest</b></p><a name=\"ct-xG-ServiceRequest\"> </a><a name=\"hcct-xG-ServiceRequest\"> </a><a name=\"ct-xG-ServiceRequest-en-US\"> </a><p><b>identifier</b>: Filler Identifier/22hosvx</p><p><b>requisition</b>: Accession ID/TL-24-D3MTCAH8</p><p><b>status</b>: Completed</p><p><b>intent</b>: Order</p><p><b>code</b>: <span title=\"Codes:{https://www.tempus.com xG.V4}\">CancerNext</span></p><p><b>subject</b>: <a href=\"Bundle-ct-xG-bundle.html#urn-uuid-43e09316-c616-4b23-81df-e546d2b95c41\">Bundle: type = transaction</a></p><p><b>requester</b>: <a href=\"Bundle-ct-xG-bundle.html#urn-uuid-775af36d-3c44-4647-b120-5d5a6b490a1e\">Bundle: type = transaction</a></p><p><b>reasonCode</b>: <span title=\"Codes:{http://hl7.org/fhir/sid/icd-10-cm C24.0}\">^Malignant neoplasm of extrahepatic bile duct</span></p></div>"
},
"identifier" : [
{
"type" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0203",
"code" : "FILL",
"display" : "Filler Identifier"
}
]
},
"system" : "https://www.tempus.com",
"value" : "22hosvx"
}
],
"requisition" : {
"type" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0203",
"code" : "ACSN",
"display" : "Accession ID"
}
]
},
"system" : "https://www.tempus.com",
"value" : "TL-24-D3MTCAH8"
},
"status" : "completed",
"intent" : "order",
"code" : {
"coding" : [
{
"system" : "https://www.tempus.com",
"code" : "xG.V4",
"display" : "CancerNext"
}
]
},
"subject" : {
"reference" : "urn:uuid:43e09316-c616-4b23-81df-e546d2b95c41"
},
"requester" : {
"reference" : "urn:uuid:775af36d-3c44-4647-b120-5d5a6b490a1e"
},
"reasonCode" : [
{
"coding" : [
{
"system" : "http://hl7.org/fhir/sid/icd-10-cm",
"code" : "C24.0",
"display" : "^Malignant neoplasm of extrahepatic bile duct"
}
]
}
]
},
"request" : {
"method" : "POST",
"url" : "ServiceRequest"
}
},
{
"fullUrl" : "urn:uuid:775af36d-3c44-4647-b120-5d5a6b490a1e",
"resource" : {
"resourceType" : "Practitioner",
"id" : "ct-xG-practitioner",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Practitioner_ct-xG-practitioner\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Practitioner ct-xG-practitioner</b></p><a name=\"ct-xG-practitioner\"> </a><a name=\"hcct-xG-practitioner\"> </a><a name=\"ct-xG-practitioner-en-US\"> </a><p><b>identifier</b>: <a href=\"http://terminology.hl7.org/5.3.0/NamingSystem-npi.html\" title=\"National Provider Identifier\">United States National Provider Identifier</a>/9988776345</p><p><b>name</b>: Luke Skywalker </p><p><b>address</b>: 600 Chicago Drive Everywhere TX 16789 US (work)</p><p><b>gender</b>: Male</p><h3>Qualifications</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Code</b></td></tr><tr><td style=\"display: none\">*</td><td><span title=\"Codes:{http://terminology.hl7.org/CodeSystem/v2-0360 MD}\">Doctor of Medicine</span></td></tr></table></div>"
},
"identifier" : [
{
"system" : "http://hl7.org/fhir/sid/us-npi",
"value" : "9988776345"
}
],
"name" : [
{
"family" : "Skywalker",
"given" : [
"Luke"
]
}
],
"address" : [
{
"use" : "work",
"line" : [
"600 Chicago Drive"
],
"city" : "Everywhere",
"state" : "TX",
"postalCode" : "16789",
"country" : "US"
}
],
"gender" : "male",
"qualification" : [
{
"code" : {
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/v2-0360",
"version" : "2.7",
"code" : "MD"
}
]
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Practitioner"
}
},
{
"fullUrl" : "urn:uuid:eb4e82bd-2162-4b01-bfd7-19bac0828abe",
"resource" : {
"resourceType" : "PractitionerRole",
"id" : "ct-genomic-practitionerRole",
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"PractitionerRole_ct-genomic-practitionerRole\"> </a><p class=\"res-header-id\"><b>Generated Narrative: PractitionerRole ct-genomic-practitionerRole</b></p><a name=\"ct-genomic-practitionerRole\"> </a><a name=\"hcct-genomic-practitionerRole\"> </a><a name=\"ct-genomic-practitionerRole-en-US\"> </a><p><b>practitioner</b>: <a href=\"Bundle-ct-xG-bundle.html#urn-uuid-775af36d-3c44-4647-b120-5d5a6b490a1e\">Bundle: type = transaction</a></p><p><b>organization</b>: <a href=\"Bundle-ct-xG-bundle.html#urn-uuid-19fc189e-7287-4a4b-bf1c-1ab222bbfe3d\">Bundle: type = transaction</a></p></div>"
},
"practitioner" : {
"reference" : "urn:uuid:775af36d-3c44-4647-b120-5d5a6b490a1e"
},
"organization" : {
"reference" : "urn:uuid:19fc189e-7287-4a4b-bf1c-1ab222bbfe3d"
}
},
"request" : {
"method" : "POST",
"url" : "PractitionerRole"
}
},
{
"fullUrl" : "urn:uuid:19fc189e-7287-4a4b-bf1c-1ab222bbfe3d",
"resource" : {
"resourceType" : "Organization",
"id" : "ct-ordering-organization",
"meta" : {
"profile" : [
🔗 "http://mitre.org/gdx/StructureDefinition/gdx-lab-organization"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Organization_ct-ordering-organization\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Organization ct-ordering-organization</b></p><a name=\"ct-ordering-organization\"> </a><a name=\"hcct-ordering-organization\"> </a><a name=\"ct-ordering-organization-en-US\"> </a><p><b>identifier</b>: <code>http://example.emr.com/organization</code>/12345</p><p><b>active</b>: true</p><p><b>name</b>: TriHealth Cancer Institute - Cincinnati</p><p><b>address</b>: 1234 Brooks River Cincinnati OH 11111-1111 (work)</p><p><b>partOf</b>: Identifier: Oncology Group</p><h3>Contacts</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Name</b></td></tr><tr><td style=\"display: none\">*</td><td>Steve Jobs </td></tr></table></div>"
},
"identifier" : [
{
"system" : "http://example.emr.com/organization",
"value" : "12345"
}
],
"active" : true,
"name" : "TriHealth Cancer Institute - Cincinnati",
"address" : [
{
"use" : "work",
"line" : [
"1234 Brooks River"
],
"city" : "Cincinnati",
"state" : "OH",
"postalCode" : "11111-1111"
}
],
"partOf" : {
"identifier" : {
"value" : "Oncology Group"
}
},
"contact" : [
{
"name" : {
"family" : "Jobs",
"given" : [
"Steve"
]
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Organization"
}
},
{
"fullUrl" : "urn:uuid:aeea668a-a035-4963-9e56-249d735916a5",
"resource" : {
"resourceType" : "Organization",
"id" : "ct-organization-tempus-inc",
"meta" : {
"profile" : [
🔗 "http://mitre.org/gdx/StructureDefinition/gdx-lab-organization"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Organization_ct-organization-tempus-inc\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Organization ct-organization-tempus-inc</b></p><a name=\"ct-organization-tempus-inc\"> </a><a name=\"hcct-organization-tempus-inc\"> </a><a name=\"ct-organization-tempus-inc-en-US\"> </a><p><b>identifier</b>: <a href=\"http://terminology.hl7.org/5.3.0/NamingSystem-CLIA.html\" title=\""The Centers for Medicare & Medicaid Services (CMS) regulates all laboratory testing (except research) performed on humans in the U.S. through the Clinical Laboratory Improvement Amendments (CLIA). In total, CLIA covers approximately 330,000 laboratory entities. The Division of Clinical Laboratory Improvement & Quality, within the Quality, Safety & Oversight Group, under the Center for Clinical Standards and Quality (CCSQ) has the responsibility for implementing the CLIA Program.\r\n\r\nThe objective of the CLIA program is to ensure quality laboratory testing. Although all clinical laboratories must be properly certified to receive Medicare or Medicaid payments, CLIA has no direct Medicare or Medicaid program responsibilities."\r\n\r\nCMS CLIA certified laboratories will be assigned a10-digit alphanumeric CLIA identification number, with the "D" in the third position identifying the provider/supplier as a laboratory certified under CLIA."\r\n\r\nCLIA is maintained by CMS. It is in the public domain and free to use without restriction.\r\n\r\nSee http://cms.gov/regulations-and-guidance/legislation/clia.\">Clinical Laboratory Improvement Amendments</a>/14D2114007</p><p><b>active</b>: true</p><p><b>name</b>: Tempus Labs, Inc</p><p><b>telecom</b>: <a href=\"mailto:support@tempus.com\">support@tempus.com</a></p><p><b>address</b>: 600 W Chicago Avenue, Ste 510 Chicago IL 60654 USA </p><h3>Contacts</h3><table class=\"grid\"><tr><td style=\"display: none\">-</td><td><b>Name</b></td></tr><tr><td style=\"display: none\">*</td><td>Nike Beaubier, M,FCAP,MGAP</td></tr></table></div>"
},
"identifier" : [
{
"system" : "urn:oid:2.16.840.1.113883.4.7",
"value" : "14D2114007"
}
],
"active" : true,
"name" : "Tempus Labs, Inc",
"telecom" : [
{
"system" : "email",
"value" : "support@tempus.com"
}
],
"address" : [
{
"line" : [
"600 W Chicago Avenue, Ste 510"
],
"city" : "Chicago",
"state" : "IL",
"postalCode" : "60654",
"country" : "USA"
}
],
"contact" : [
{
"name" : {
"text" : "Nike Beaubier, M,FCAP,MGAP"
}
}
]
},
"request" : {
"method" : "POST",
"url" : "Organization"
}
},
{
"fullUrl" : "urn:uuid:26242dd9-b9c7-40cb-838c-7f5007fde86f",
"resource" : {
"resourceType" : "Practitioner",
"id" : "Inline-Instance-for-ct-xG-bundle-1",
"meta" : {
"lastUpdated" : "2023-10-02T07:03:06.120689+00:00",
"profile" : [
"http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner"
]
},
"text" : {
"status" : "generated",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Practitioner_Inline-Instance-for-ct-xG-bundle-1\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Practitioner Inline-Instance-for-ct-xG-bundle-1</b></p><a name=\"Inline-Instance-for-ct-xG-bundle-1\"> </a><a name=\"hcInline-Instance-for-ct-xG-bundle-1\"> </a><a name=\"Inline-Instance-for-ct-xG-bundle-1-en-US\"> </a><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\">Last updated: 2023-10-02 07:03:06+0000</p><p style=\"margin-bottom: 0px\">Profile: <code>http://hl7.org/fhir/us/core/StructureDefinition/us-core-practitioner</code></p></div><p><b>identifier</b>: <code>http://www.acme.com/identifiers/patient</code>/123456</p><p><b>name</b>: Test Pathologist </p></div>"
},
"identifier" : [
{
"system" : "http://www.acme.com/identifiers/patient",
"value" : "123456"
}
],
"name" : [
{
"family" : "Pathologist",
"given" : [
"Test"
]
}
]
},
"request" : {
"method" : "POST",
"url" : "Practitioner"
}
},
{
"fullUrl" : "urn:uuid:1a9edfe1-1620-4882-a81c-30c2f254f34f",
"resource" : {
"resourceType" : "Specimen",
"id" : "Inline-Instance-for-ct-xG-bundle-2",
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}
],
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},
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},
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}
]
},
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}
}
]
},
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"url" : "Observation"
}
},
{
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"id" : "ct-OverallInterp",
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},
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}
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}
},
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}
},
{
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"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-data-file"
]
},
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},
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"title" : "GeneList",
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}
}
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},
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}
},
{
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"resource" : {
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"meta" : {
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]
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"text" : {
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"performedDateTime" : "2023-02-02T01:01:10-06:00"
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}
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"id" : "ct-xT-genomicStudy-9",
"meta" : {
"profile" : [
🔗 "http://hl7.org/fhir/uv/genomics-reporting/StructureDefinition/genomic-study"
]
},
"text" : {
"status" : "extensions",
"div" : "<div xmlns=\"http://www.w3.org/1999/xhtml\"><a name=\"Procedure_ct-xT-genomicStudy-9\"> </a><p class=\"res-header-id\"><b>Generated Narrative: Procedure ct-xT-genomicStudy-9</b></p><a name=\"ct-xT-genomicStudy-9\"> </a><a name=\"hcct-xT-genomicStudy-9\"> </a><a name=\"ct-xT-genomicStudy-9-en-US\"> </a><p><b>Genomic Study Analysis Extension</b>: <a href=\"Bundle-ct-xG-bundle.html#urn-uuid-22263097-6033-41af-9f6a-d7b012e27bbb\">Bundle: type = transaction</a></p><p><b>basedOn</b>: <a href=\"Bundle-ct-xG-bundle.html#urn-uuid-150a3549-3114-4dea-bd1d-e24c036b2934\">Bundle: type = transaction</a></p><p><b>status</b>: Completed</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category laboratory}\">Laboratory</span></p><p><b>code</b>: <span title=\"Codes:\">xT panel</span></p><p><b>subject</b>: <a href=\"Bundle-ct-xG-bundle.html#urn-uuid-43e09316-c616-4b23-81df-e546d2b95c41\">Bundle: type = transaction</a></p><p><b>performed</b>: 2023-08-09</p></div>"
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},
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}
}
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