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Unwanted conditions to notes schema #15764

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Original file line number Diff line number Diff line change
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# $schema: ./../../../../../../../../metadata/json_schema/fhir/fhir-to-hl7-mapping.json

constants:
commentCondition: '%resource.code.coding.code.exists() and %resource.code.text.exists()'

elements:
- name: note-id
value: [ '%noteIndex + 1' ]
hl7Spec: [ '%{hl7NotePath}/NTE(%{noteIndex})-1' ]

- name: note-source
value: [ '%resource.extension(%`rsext-note-source`).value' ]
hl7Spec: [ '%{hl7NotePath}/NTE(%{noteIndex})-2' ]

- name: unwanted-condition-source
condition: '%commentCondition'
value: ['"0"']
hl7Spec: [ '%{hl7NotePath}/NTE(%{noteIndex})-2' ]

- name: unwanted-condition-comment-string
condition: '%commentCondition'
value: [ '"OBX filtered for identifier = " + %resource.code.coding.code + " - " + %resource.code.text + "; value = " + %resource.value.coding.code + " - " + %resource.value.coding.display + ". OBX was removed due to your jurisdictional reporting rules indicating this result is not reportable."' ]
hl7Spec: [ '%{hl7NotePath}/NTE(%{noteIndex})-3' ]

- name: note-comment
condition: '%context.author.exists().not() or (%context.author.exists() and %context.author.is(string).not())'
resource: '%resource.text.union(%resource.extension(%`rsext-note-comment`).tail().value)'
resourceIndex: stIndex
constants:
stField: '%{hl7NotePath}/NTE(%{noteIndex})-3(%{stIndex})'
schema: classpath:/metadata/hl7_mapping/datatypes/annotation/ST.yml

- name: note-comment-author-string
condition: '%resource.author.exists() and %resource.author.is(string)'
value: [ '%resource.text + " Authored by: " + %resource.author' ]
hl7Spec: [ '%{hl7NotePath}/NTE(%{noteIndex})-3' ]

- name: note-comment-type-identifier
resource: '%resource.extension(%`rsext-note-type`).value'
constants:
cweField: '%{hl7NotePath}/NTE(%{noteIndex})-4'
schema: classpath:/metadata/hl7_mapping/datatypes/codeableConcept/CWE.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
hl7Class: ca.uhn.hl7v2.model.v251.message.ORU_R01

extends: classpath:/metadata/hl7_mapping/ORU_R01/ORU_R01-base.yml

elements:

- name: observation-result-with-aoe
resource: "%resource.result.resolve().where(code.coding.extension('https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code').value.where(code in ('55735004' | '840539006'))) | %resource.basedOn.resolve().supportingInfo.resolve()"

- name: order-note
resource: "%resource.basedOn.resolve().note | %resource.result.resolve().where(code.coding.extension('https://reportstream.cdc.gov/fhir/StructureDefinition/condition-code').value.where(code in ('55735004' | '840539006')).exists().not())"
schema: classpath:/metadata/hl7_mapping/receivers/Common/observation-to-nte/unwanted-conditions-to-notes.yml



Original file line number Diff line number Diff line change
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{"resourceType":"Bundle","identifier":{"value":"bfe0d734-06a8-472e-bf6a-cad808150c4e"},"type":"message","timestamp":"2024-08-28T17:42:09.958Z","entry":[{"fullUrl":"MessageHeader/98e7dcc8-11ff-4213-a9a7-c5373b4051a8","resource":{"resourceType":"MessageHeader","id":"98e7dcc8-11ff-4213-a9a7-c5373b4051a8","meta":{"tag":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0103","code":"P","display":"Production"}]},"eventCoding":{"system":"http://terminology.hl7.org/CodeSystem/v2-0003","code":"R01","display":"ORU/ACK - Unsolicited transmission of an observation message"},"destination":[{"name":"PRIME ReportStream","endpoint":"https://prime.cdc.gov/api/reports?option=SkipInvalidItems"}],"sender":{"reference":"Organization/719ec8ad-cf59-405a-9832-c4065945c130"},"source":{"extension":[{"url":"https://reportstream.cdc.gov/fhir/StructureDefinition/software-binary-id","valueString":"453dc84"},{"url":"https://reportstream.cdc.gov/fhir/StructureDefinition/software-install-date","valueInstant":"2024-08-27T20:59:08Z"},{"url":"https://reportstream.cdc.gov/fhir/StructureDefinition/software-vendor-org","valueReference":{"reference":"Organization/07640c5d-87cd-488b-9343-a226c5166539"}}],"software":"PRIME SimpleReport","version":"453dc84","endpoint":"https://simplereport.gov"},"focus":[{"reference":"Provenance/71a34b40-194e-428c-8995-fdb6e4401007"},{"reference":"DiagnosticReport/bfe0d734-06a8-472e-bf6a-cad808150c4e"}]}},{"fullUrl":"Provenance/71a34b40-194e-428c-8995-fdb6e4401007","resource":{"resourceType":"Provenance","id":"71a34b40-194e-428c-8995-fdb6e4401007","recorded":"2024-08-28T17:42:09.958Z","activity":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0003","code":"R01","display":"ORU/ACK - Unsolicited transmission of an observation message"}]},"agent":[{"who":{"reference":"Organization/719ec8ad-cf59-405a-9832-c4065945c130"}}]}},{"fullUrl":"DiagnosticReport/bfe0d734-06a8-472e-bf6a-cad808150c4e","resource":{"resourceType":"DiagnosticReport","id":"bfe0d734-06a8-472e-bf6a-cad808150c4e","identifier":[{"value":"bfe0d734-06a8-472e-bf6a-cad808150c4e"}],"basedOn":[{"reference":"ServiceRequest/18d22920-86e5-4d7a-bca7-5db7a2f969bb"}],"status":"final","code":{"coding":[{"system":"http://loinc.org","code":"96123-5"}]},"subject":{"reference":"Patient/4a48b374-1aec-4b71-a595-41aa031ef42f"},"effectiveDateTime":"2024-08-28T17:27:09+00:00","issued":"2024-08-28T17:42:09+00:00","specimen":[{"reference":"Specimen/66f0d890-8a9e-4d5c-8a6a-20bdf7f5da05"}],"result":[{"reference":"Observation/93817f53-df96-45ac-aa7a-05aa701094c7"}]}},{"fullUrl":"Patient/4a48b374-1aec-4b71-a595-41aa031ef42f","resource":{"resourceType":"Patient","id":"4a48b374-1aec-4b71-a595-41aa031ef42f","extension":[{"url":"http://ibm.com/fhir/cdm/StructureDefinition/local-race-cd","valueCodeableConcept":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v3-Race","code":"2106-3"}],"text":"white"}},{"url":"https://reportstream.cdc.gov/fhir/StructureDefinition/ethnic-group","valueCodeableConcept":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0189","code":"N","display":"Not Hispanic or Latino"}],"text":"Not Hispanic or Latino"}}],"identifier":[{"value":"4a48b374-1aec-4b71-a595-41aa031ef42f"}],"name":[{"family":"Davar","given":["Shallan"]}],"telecom":[{"system":"phone","value":"(540) 867 5309","use":"mobile"}],"gender":"female","birthDate":"2006-01-03","address":[{"line":["10 Pattern Way"],"city":"Newport","state":"RI","postalCode":"02840","country":"USA"}],"managingOrganization":{"reference":"Organization/719ec8ad-cf59-405a-9832-c4065945c130"}}},{"fullUrl":"Organization/719ec8ad-cf59-405a-9832-c4065945c130","resource":{"resourceType":"Organization","id":"719ec8ad-cf59-405a-9832-c4065945c130","identifier":[{"use":"official","type":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0301","code":"CLIA"}]},"value":"12D4567890"}],"name":"Testing Lab","telecom":[{"system":"phone","value":"(530) 867 5309","use":"work"}],"address":[{"line":["123 Beach Way"],"city":"Denver","state":"CO","postalCode":"80210","country":"USA"}]}},{"fullUrl":"Practitioner/ee29ccf5-631d-4b35-a6d4-30a61c0eb8d9","resource":{"resourceType":"Practitioner","id":"ee29ccf5-631d-4b35-a6d4-30a61c0eb8d9","identifier":[{"system":"http://hl7.org/fhir/sid/us-npi","value":"1245319599"}],"name":[{"family":"McTester","given":["Phil"]}],"telecom":[{"system":"phone","value":"(530) 867 5309","use":"work"}],"address":[{"line":["321 Ocean Drive"],"city":"Denver","state":"CO","postalCode":"80210","country":"USA"}]}},{"fullUrl":"Specimen/66f0d890-8a9e-4d5c-8a6a-20bdf7f5da05","resource":{"resourceType":"Specimen","id":"66f0d890-8a9e-4d5c-8a6a-20bdf7f5da05","identifier":[{"value":"d0f0ddd1-bef3-4fe1-8642-d4f3270e76e7"}],"type":{"coding":[{"system":"http://snomed.info/sct","code":"697989009"}],"text":"Anterior nares swab"},"subject":{"reference":"Patient/4a48b374-1aec-4b71-a595-41aa031ef42f"},"receivedTime":"2024-08-28T17:27:09+00:00","collection":{"collectedDateTime":"2024-08-28T17:27:09+00:00","bodySite":{"coding":[{"system":"http://snomed.info/sct","code":"87100004"}],"text":"Topography unknown (body structure)"}}}},{"fullUrl":"ServiceRequest/18d22920-86e5-4d7a-bca7-5db7a2f969bb","resource":{"resourceType":"ServiceRequest","id":"18d22920-86e5-4d7a-bca7-5db7a2f969bb","extension":[{"url":"https://reportstream.cdc.gov/fhir/StructureDefinition/order-control","valueCodeableConcept":{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0119","code":"RE"}]}},{"url":"https://reportstream.cdc.gov/fhir/StructureDefinition/order-effective-date","valueDateTime":"2024-08-28T17:42:09+00:00"}],"status":"completed","intent":"order","code":{"coding":[{"system":"http://loinc.org","code":"96123-5"}]},"subject":{"reference":"Patient/4a48b374-1aec-4b71-a595-41aa031ef42f"},"requester":{"reference":"PractitionerRole/464f3137-27b5-4d6f-b3ba-f6e0810e3682"},"performer":[{"reference":"Organization/719ec8ad-cf59-405a-9832-c4065945c130"}],"supportingInfo":[{"reference":"Observation/dd88e296-6100-3dbe-9a2c-8eebe44cddcf"},{"reference":"Observation/7a6852e6-66bd-36cb-92b6-74d7a29493c3"},{"reference":"Observation/f0b7c135-d14b-31dc-bd6b-61d5d6429197"},{"reference":"Observation/885eb9e0-b499-3c67-9f80-51f78b30e161"},{"reference":"Observation/f9078615-63ba-3f61-8327-88a4c974987d"},{"reference":"Observation/090f3c87-6bed-3fec-a898-2a3e3058a4b0"}],"note":[{"extension":[{"url":"https://reportstream.cdc.gov/fhir/StructureDefinition/note-type","valueCodeableConcept":{"coding":[{"extension":[{"url":"https://reportstream.cdc.gov/fhir/StructureDefinition/code-index-name","valueString":"identifier"}],"system":"HL70364","version":"2.5.1","code":"RE","display":"Remark"}]}}],"text":"This is a note"}]}},{"fullUrl":"Device/237e9daf-1293-45c0-90fb-927b14cabdf8","resource":{"resourceType":"Device","id":"237e9daf-1293-45c0-90fb-927b14cabdf8","identifier":[{"value":"00811877010616"},{"type":{"coding":[{"code":"DII"}]}}],"manufacturer":"Abbott Diagnostics Scarborough, Inc.","deviceName":[{"name":"ID NOW COVID-19 2.0","type":"model-name"}]}},{"fullUrl":"PractitionerRole/464f3137-27b5-4d6f-b3ba-f6e0810e3682","resource":{"resourceType":"PractitionerRole","id":"464f3137-27b5-4d6f-b3ba-f6e0810e3682","practitioner":{"reference":"Practitioner/ee29ccf5-631d-4b35-a6d4-30a61c0eb8d9"},"organization":{"reference":"Organization/719ec8ad-cf59-405a-9832-c4065945c130"}}},{"fullUrl":"Organization/07640c5d-87cd-488b-9343-a226c5166539","resource":{"resourceType":"Organization","id":"07640c5d-87cd-488b-9343-a226c5166539","name":"SimpleReport"}},{"fullUrl":"Observation/93817f53-df96-45ac-aa7a-05aa701094c7","resource":{"resourceType":"Observation","id":"93817f53-df96-45ac-aa7a-05aa701094c7","status":"final","code":{"coding":[{"system":"http://loinc.org","code":"96123-5"}],"text":"COVID-19"},"subject":{"reference":"Patient/4a48b374-1aec-4b71-a595-41aa031ef42f"},"issued":"2024-08-28T17:42:09.803Z","performer":[{"reference":"Organization/719ec8ad-cf59-405a-9832-c4065945c130"}],"valueCodeableConcept":{"coding":[{"system":"http://snomed.info/sct","code":"260373001","display":"Detected"}]},"interpretation":[{"coding":[{"system":"http://terminology.hl7.org/CodeSystem/v2-0078","code":"A","display":"Abnormal"}]}],"method":{"extension":[{"url":"https://reportstream.cdc.gov/fhir/StructureDefinition/testkit-name-id","valueCoding":{"code":"ID NOW COVID-19 2.0_Abbott Diagnostics Scarborough, Inc."}}],"coding":[{"display":"ID NOW COVID-19 2.0"}]},"specimen":{"reference":"Specimen/66f0d890-8a9e-4d5c-8a6a-20bdf7f5da05"},"device":{"reference":"Device/237e9daf-1293-45c0-90fb-927b14cabdf8"}}},{"fullUrl":"Observation/dd88e296-6100-3dbe-9a2c-8eebe44cddcf","resource":{"resourceType":"Observation","id":"dd88e296-6100-3dbe-9a2c-8eebe44cddcf","identifier":[{"use":"official","type":{"coding":[{"system":"http://loinc.org","code":"81959-9","display":"Public health laboratory ask at order entry panel"}]}}],"status":"final","code":{"coding":[{"system":"http://loinc.org","code":"95419-8","display":"Has symptoms related to condition of interest"}],"text":"Has symptoms related to condition of interest"},"subject":{"reference":"Patient/4a48b374-1aec-4b71-a595-41aa031ef42f"},"valueCodeableConcept":{"coding":[{"system":"http://terminology.hl7.org/ValueSet/v2-0136","code":"Y","display":"Yes"}]}}},{"fullUrl":"Observation/7a6852e6-66bd-36cb-92b6-74d7a29493c3","resource":{"resourceType":"Observation","id":"7a6852e6-66bd-36cb-92b6-74d7a29493c3","identifier":[{"use":"official","type":{"coding":[{"system":"http://loinc.org","code":"81959-9","display":"Public health laboratory ask at order entry panel"}]}}],"status":"final","code":{"coding":[{"system":"http://loinc.org","code":"11368-8","display":"Illness or injury onset date and time"}],"text":"Illness or injury onset date and time"},"subject":{"reference":"Patient/4a48b374-1aec-4b71-a595-41aa031ef42f"},"valueDateTime":"2024-08-01"}},{"fullUrl":"Observation/f0b7c135-d14b-31dc-bd6b-61d5d6429197","resource":{"resourceType":"Observation","id":"f0b7c135-d14b-31dc-bd6b-61d5d6429197","identifier":[{"use":"official","type":{"coding":[{"system":"http://loinc.org","code":"81959-9","display":"Public health laboratory ask at order entry panel"}]}}],"status":"final","code":{"coding":[{"system":"http://loinc.org","code":"82810-3","display":"Pregnancy status"}],"text":"Pregnancy status"},"subject":{"reference":"Patient/4a48b374-1aec-4b71-a595-41aa031ef42f"},"valueCodeableConcept":{"coding":[{"system":"http://snomed.info/sct","code":"60001007","display":"Not pregnant"}]}}},{"fullUrl":"Observation/885eb9e0-b499-3c67-9f80-51f78b30e161","resource":{"resourceType":"Observation","id":"885eb9e0-b499-3c67-9f80-51f78b30e161","identifier":[{"use":"official","type":{"coding":[{"system":"http://loinc.org","code":"81959-9","display":"Public health laboratory ask at order entry panel"}]}}],"status":"final","code":{"coding":[{"system":"http://loinc.org","code":"95418-0","display":"Employed in a healthcare setting"}],"text":"Employed in a healthcare setting"},"subject":{"reference":"Patient/4a48b374-1aec-4b71-a595-41aa031ef42f"},"valueCodeableConcept":{"coding":[{"system":"http://terminology.hl7.org/ValueSet/v2-0136","code":"N","display":"No"}]}}},{"fullUrl":"Observation/f9078615-63ba-3f61-8327-88a4c974987d","resource":{"resourceType":"Observation","id":"f9078615-63ba-3f61-8327-88a4c974987d","identifier":[{"use":"official","type":{"coding":[{"system":"http://loinc.org","code":"81959-9","display":"Public health laboratory ask at order entry panel"}]}}],"status":"final","code":{"coding":[{"system":"http://loinc.org","code":"95421-4","display":"Resides in a congregate care setting"}],"text":"Resides in a congregate care setting"},"subject":{"reference":"Patient/4a48b374-1aec-4b71-a595-41aa031ef42f"},"valueCodeableConcept":{"coding":[{"system":"http://terminology.hl7.org/ValueSet/v2-0136","code":"N","display":"No"}]}}},{"fullUrl":"Observation/090f3c87-6bed-3fec-a898-2a3e3058a4b0","resource":{"resourceType":"Observation","id":"090f3c87-6bed-3fec-a898-2a3e3058a4b0","identifier":[{"use":"official","type":{"coding":[{"system":"http://loinc.org","code":"81959-9","display":"Public health laboratory ask at order entry panel"}]}}],"status":"final","code":{"coding":[{"system":"http://loinc.org","code":"76691-5","display":"Gender identity"}],"text":"Gender identity"},"subject":{"reference":"Patient/4a48b374-1aec-4b71-a595-41aa031ef42f"},"valueCodeableConcept":{"coding":[{"system":"http://terminology.hl7.org/5.0.0/CodeSystem-data-absent-reason.html","code":"asked-declined","display":"Asked But Declined"}]}}}]}
Original file line number Diff line number Diff line change
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MSH|^~\&|CDC PRIME - Atlanta^2.16.840.1.114222.4.1.237821^ISO|Testing Lab^12D4567890^CLIA|||20240828174209+0000||ORU^R01^ORU_R01|bfe0d734-06a8-472e-bf6a-cad808150c4e|P|2.5.1|||NE|NE|USA|UNICODE UTF-8|ENG^English^ISO||PHLabReport-NoAck^ELR_Receiver^2.16.840.1.113883.9.11^ISO
SFT|Centers for Disease Control and Prevention|0.2-SNAPSHOT|PRIME ReportStream|0.2-SNAPSHOT||20240827205908+0000
PID|1||4a48b374-1aec-4b71-a595-41aa031ef42f^^^Testing Lab&12D4567890&CLIA^PI^Testing Lab&12D4567890&CLIA||Davar^Shallan^^^^^L||20060103|F||2106-3^white^^^^^2.5.1^^white|10 Pattern Way^^Newport^RI^02840^USA||(540) 867 5309^PRS^CP^^1^540^8675309^^^^^(540) 867 5309|||||||||N^Not Hispanic or Latino^HL70189^^^^2.9^^Not Hispanic or Latino||||||||N
ORC|RE|bfe0d734-06a8-472e-bf6a-cad808150c4e^Testing Lab^12D4567890^CLIA|bfe0d734-06a8-472e-bf6a-cad808150c4e^Testing Lab^12D4567890^CLIA|||||||||1245319599^McTester^Phil^^^^^^NPI&2.16.840.1.113883.4.6&ISO^L^^^NPI||(530) 867 5309^WPN^PH^^1^530^8675309^^^^^(530) 867 5309|20240828174209+0000||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA|(530) 867 5309^WPN^PH^^1^530^8675309^^^^^(530) 867 5309|321 Ocean Drive^^Denver^CO^80210^USA
OBR|1|bfe0d734-06a8-472e-bf6a-cad808150c4e^Testing Lab^12D4567890^CLIA|bfe0d734-06a8-472e-bf6a-cad808150c4e^Testing Lab^12D4567890^CLIA|96123-5^SARS-CoV-2 (COVID-19) RdRp gene [Presence] in Upper respiratory specimen by NAA with probe detection^LN|||20240828172709+0000|||||||||1245319599^McTester^Phil^^^^^^NPI&2.16.840.1.113883.4.6&ISO^L^^^NPI|(530) 867 5309^WPN^PH^^1^530^8675309^^^^^(530) 867 5309|||||20240828174209+0000|||F
NTE|1||This is a note
NTE|2|0|OBX filtered for identifier = 96123-5 - COVID-19; value = 260373001 - Detected. OBX was removed due to your jurisdictional reporting rules indicating this result is not reportable.
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@GilmoreA6 GilmoreA6 Sep 5, 2024

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This value in NTE-2 should not be numeric, This should be one of the values in table HL70105 "O", "L" or "P"

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Can we also add a test where multiple observations are converted to notes?

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Ah, nice catch, thanks. Also added test with Flu A, Flu B, and COVID.

OBX|1|CWE|95419-8^Has symptoms related to condition of interest^LN^^^^2.69^^Has symptoms related to condition of interest||Y^Yes^HL70136||||||F|||20240828172709+0000|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA|||||QST
OBX|2|DT|11368-8^Illness or injury onset date and time^LN^^^^^^Illness or injury onset date and time||20240801000000+0000||||||F|||20240828172709+0000|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA|||||QST
OBX|3|CWE|82810-3^Pregnancy status^LN^^^^2.68^^Pregnancy status||60001007^Not pregnant^SCT||||||F|||20240828172709+0000|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA|||||QST
OBX|4|CWE|95418-0^Employed in a healthcare setting^LN^^^^2.69^^Employed in a healthcare setting||N^No^HL70136||||||F|||20240828172709+0000|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA|||||QST
OBX|5|CWE|95421-4^Resides in a congregate care setting^LN^^^^2.69^^Resides in a congregate care setting||N^No^HL70136||||||F|||20240828172709+0000|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA|||||QST
OBX|6|CWE|76691-5^Gender identity^LN^^^^^^Gender identity||asked-declined^Asked But Declined||||||F|||20240828172709+0000|12D4567890^Testing Lab^CLIA||||||||Testing Lab^L^^^^CLIA&2.16.840.1.113883.4.7&ISO^XX^^^12D4567890|123 Beach Way^^Denver^CO^80210^USA|||||QST
SPM|1|bfe0d734-06a8-472e-bf6a-cad808150c4e&Testing Lab&12D4567890&CLIA^bfe0d734-06a8-472e-bf6a-cad808150c4e&Testing Lab&12D4567890&CLIA||697989009^Anterior nares swab^SCT^^^^2.67^^Anterior nares swab||||87100004^Topography unknown (body structure)^SCT^^^^^^Topography unknown (body structure)|||||||||20240828172709+0000|20240828172709+0000
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