COVID-19 Diagnostic Test in FHIR format - hl7-fhir

Question

I not really familiar with FHIR data format and need some help here. The story is, all the registered labs will sent the patient COVID-19 Diagnostic Test in our database. So the information they provide is
Basic patient information
Lab information (Lab name, contact and address) where the user take the test
Type of test (RNA, PCR, Antigen, or Antibody test)
Result of test (Positive or Negative)
I looking to follow this format from HERE. But I not sure which LOINC code I should use, and how to tell the result positive or negative.
{
"resourceType": "ValueSet",
"id": "Covid19Labs",
"text": {
"status": "generated",
"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>This value set includes codes based on the following rules:</p><ul><li>Import all the codes that are contained in http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1032.109</li><li>Include these codes as defined in <code>http://loinc.org</code><table class=\"none\"><tr><td style=\"white-space:nowrap\"><b>Code</b></td><td><b>Display</b></td></tr><tr><td>94307-6</td><td>SARS-CoV-2 (COVID-19) N gene [Presence] in Unspecified specimen by Nucleic acid amplification using CDC primer-probe set N1</td></tr><tr><td>94308-4</td><td>SARS-CoV-2 (COVID-19) N gene [Presence] in Unspecified specimen by Nucleic acid amplification using CDC primer-probe set N2</td></tr><tr><td>94309-2</td><td>SARS-CoV-2 (COVID-19) RNA [Presence] in Unspecified specimen by NAA with probe detection</td></tr><tr><td>94310-0</td><td>SARS-like coronavirus N gene [Presence] in Unspecified specimen by NAA with probe detection</td></tr><tr><td>94314-2</td><td>SARS-CoV-2 (COVID-19) RdRp gene [Presence] in Unspecified specimen by NAA with probe detection</td></tr><tr><td>94315-9</td><td>SARS-related coronavirus E gene [Presence] in Unspecified specimen by NAA with probe detection</td></tr><tr><td>94316-7</td><td>SARS-CoV-2 (COVID-19) N gene [Presence] in Unspecified specimen by NAA with probe detection</td></tr><tr><td>94500-6</td><td>SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory specimen by NAA with probe detection</td></tr><tr><td>94533-7</td><td>SARS-CoV-2 (COVID-19) N gene [Presence] in Respiratory specimen by NAA with probe detection</td></tr><tr><td>94534-5</td><td>SARS-CoV-2 (COVID-19) RdRp gene [Presence] in Respiratory specimen by NAA with probe detection</td></tr><tr><td>94559-2</td><td>SARS-CoV-2 (COVID-19) ORF1ab region [Presence] in Respiratory specimen by NAA with probe detection</td></tr><tr><td>94759-8</td><td>SARS-CoV-2 (COVID-19) RNA [Presence] in Nasopharynx by NAA with probe detection</td></tr><tr><td>94558-4</td><td>SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay</td></tr></table></li></ul></div>"
},
"url": "http://hl7.org/fhir/uv/saner/ValueSet/Covid19Labs",
"version": "0.1.0",
"name": "Covid19Labs",
"title": "COVID-19 Diagnostic Test",
"status": "active",
"date": "2021-06-09T20:53:59+00:00",
"publisher": "HL7 International Public Health Workgroup",
"contact": [
{
"telecom": [
{
"system": "url",
"value": "http://hl7.org/Special/committees/pher/index.cfm"
}
]
},
{
"telecom": [
{
"system": "email",
"value": "pher#lists.hl7.org"
}
]
},
{
"name": "HL7 Public Health Workgroup",
"telecom": [
{
"system": "url",
"value": "http://hl7.org/Special/committees/pher/index.cfm"
}
]
},
{
"name": "Keith W. Boone",
"telecom": [
{
"system": "email",
"value": "mailto:kboone#ainq.com"
}
]
}
],
"description": "Codes for COVID-19 Diagnostic Tests",
"jurisdiction": [
{
"coding": [
{
"system": "http://unstats.un.org/unsd/methods/m49/m49.htm",
"code": "001"
}
]
}
],
"copyright": "This material contains content from LOINC (http://loinc.org). LOINC is copyright © 1995-2020, Regenstrief Institute, Inc. and the Logical Observation Identifiers Names and Codes (LOINC) Committee and is available at no cost under the license at LOINC/license. LOINC® is a registered United States trademark of Regenstrief Institute, Inc",
"compose": {
"include": [
{
"valueSet": [
"http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1032.109"
]
},
{
"system": "http://loinc.org",
"concept": [
{
"code": "94307-6",
"display": "SARS-CoV-2 (COVID-19) N gene [Presence] in Unspecified specimen by Nucleic acid amplification using CDC primer-probe set N1"
},
{
"code": "94308-4",
"display": "SARS-CoV-2 (COVID-19) N gene [Presence] in Unspecified specimen by Nucleic acid amplification using CDC primer-probe set N2"
},
{
"code": "94309-2",
"display": "SARS-CoV-2 (COVID-19) RNA [Presence] in Unspecified specimen by NAA with probe detection"
},
{
"code": "94310-0",
"display": "SARS-like coronavirus N gene [Presence] in Unspecified specimen by NAA with probe detection"
},
{
"code": "94314-2",
"display": "SARS-CoV-2 (COVID-19) RdRp gene [Presence] in Unspecified specimen by NAA with probe detection"
},
{
"code": "94315-9",
"display": "SARS-related coronavirus E gene [Presence] in Unspecified specimen by NAA with probe detection"
},
{
"code": "94316-7",
"display": "SARS-CoV-2 (COVID-19) N gene [Presence] in Unspecified specimen by NAA with probe detection"
},
{
"code": "94500-6",
"display": "SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory specimen by NAA with probe detection"
},
{
"code": "94533-7",
"display": "SARS-CoV-2 (COVID-19) N gene [Presence] in Respiratory specimen by NAA with probe detection"
},
{
"code": "94534-5",
"display": "SARS-CoV-2 (COVID-19) RdRp gene [Presence] in Respiratory specimen by NAA with probe detection"
},
{
"code": "94559-2",
"display": "SARS-CoV-2 (COVID-19) ORF1ab region [Presence] in Respiratory specimen by NAA with probe detection"
},
{
"code": "94759-8",
"display": "SARS-CoV-2 (COVID-19) RNA [Presence] in Nasopharynx by NAA with probe detection"
},
{
"code": "94558-4",
"display": "SARS-CoV-2 (COVID-19) Ag [Presence] in Respiratory specimen by Rapid immunoassay"
}
]
}
]
}
}
Any idea how to do it? Thanks in advance

Answer 1

Azri,
Here's an example of what an instance of an Observation would look like for a SARS CoV 2 (the causative agent of COVID-19) lab test.
{
"resourceType" : "Observation",
"id" : "SARS_CoV2_example",
"meta" : {
"extension" : [
{
"url" : "http://hl7.org/fhir/StructureDefinition/instance-name",
"valueString" : "COVID-Example"
},
{
"url" : "http://hl7.org/fhir/StructureDefinition/instance-description",
"valueMarkdown" : "This is an example of a lab test for SARS CoV 2."
}
],
"versionId" : "1",
"lastUpdated" : "2021-06-22T15:29:57.818+00:00",
"profile" : [
"http://fhir.logicahealth.org/covid19/StructureDefinition/SARScoronavirus2AbIgGPlusIgMPrThrPtSerPlasOrdIALabObs"
]
},
"status" : "final",
"category" : [
{
"coding" : [
{
"system" : "http://terminology.hl7.org/CodeSystem/observation-
category",
"code" : "laboratory",
"display" : "Laboratory"
}
],
"text" : "Laboratory"
}
],
"code" : {
"coding" : [
{
"system" : "http://loinc.org",
"code" : "94547-7",
"display" : "SARS-CoV-2 (COVID-19) IgG+IgM Ab [Presence] in Serum or Plasma
by Immunoassay"
}
],
"text" : "SARS-CoV-2 (COVID-19) IgG+IgM Ab [Presence] in Serum or Plasma by
Immunoassay"
},
"subject" : {
"reference" : "Patient/1234",
},
"effectiveDateTime" : "2021-06-05",
"performer": "Organization/123",
"valueCodeableConcept" : {
"system" : "http://snomed.info/sct",
"value" : "10828004",
"display": "Positive (qualifier value)"
}
}
The patient information is a reference to an instance of the Patient resource. For this example it may look like:
{
"resourceType": "Patient",
"id": "1234",
"lastUpdated": "2021-06-22T15:29:57.818+00:00",
"identifier": [
{
"system": "http://example_hopsital.org/EHR",
"value": "143762_XYZ"
}
],
"name": [
{
"given": "example",
"family": "Patient"
}
],
"birthDate": "2003-02-14"
}
Likewise, the lab information is a reference to an instance of the Organization resource that may look like:
{
"resourceType": "Organization",
"id": "123",
"lastUpdated": "2021-06-22T15:29:57.818+00:00",
"identifier": [
{
"system": "http://HopsitalX.org/LIS",
"value": "543XCB_HospitalLab",
}
],
"name": "HospitalX-Lab"
}
The type of test (PCR, RNA, antibody, etc.) is defined by the LOINC code in the Observation.code element.
The code snippet you placed in your question is an instance of the ValueSet resource and defines a set of LOINC codes created for SARS CoV 2 testing. It's used as both a knowledge resource (helps you know what LOINC codes are for SARS CoV 2) and a validation tool (helps you determine if an Observation instance is one of the SARS CoV 2 LOINC tests).