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N3CCovid19Phenotypev1.4.cql
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N3CCovid19Phenotypev1.4.cql
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library "N3CCovid19Phenotype" version '1.4'
using QUICK
codesystem "ActCodes": 'http://hl7.org/fhir/v3/ActCode'
codesystem "LOINC": 'http://loinc.org'
codesystem "ICD-10": 'http://hl7.org/fhir/sid/icd-10'
codesystem "SNOMEDCT": 'http://snomed.info/sct'
codesystem "HCPCS": 'https://www.cms.gov/Medicare/Coding/HCPCS'
codesystem "CPT4": 'http://www.ama-assn.org/go/cpt '
/*
valueset "N3C Lab Concepts": '2.16.840.1.113883.3.N3C.labconcepts'
valueset "N3C "HCPCS"/CPT Procedure Codes": '2.16.840.1.113883.3.N3C.cptcodes'
valueset "N3C Strong Condition Codes": '2.16.840.1.113883.3.N3C.conditioncodes.strong'
valueset "N3C Weak Condition Codes": '2.16.840.1.113883.3.N3C.conditioncodes.weak'
*/
code "Inpatient Encounter": 'IMP' from "ActCodes"
code "Outpatient Encounter": 'AMB' from "ActCodes"
/*
N3C Lab Concepts
*/
code "94307-6" : '94307-6' from "LOINC" display '94307-6'
code "94308-4" : '94308-4' from "LOINC" display '94308-4'
code "94309-2" : '94309-2' from "LOINC" display '94309-2'
code "94310-0" : '94310-0' from "LOINC" display '94310-0'
code "94311-8" : '94311-8' from "LOINC" display '94311-8'
code "94312-6" : '94312-6' from "LOINC" display '94312-6'
code "94313-4" : '94313-4' from "LOINC" display '94313-4'
code "94314-2" : '94314-2' from "LOINC" display '94314-2'
code "94315-9" : '94315-9' from "LOINC" display '94315-9'
code "94316-7" : '94316-7' from "LOINC" display '94316-7'
code "94500-6" : '94500-6' from "LOINC" display '94500-6'
code "94502-2" : '94502-2' from "LOINC" display '94502-2'
code "94505-5" : '94505-5' from "LOINC" display '94505-5'
code "94506-3" : '94506-3' from "LOINC" display '94506-3'
code "94507-1" : '94507-1' from "LOINC" display '94507-1'
code "94508-9" : '94508-9' from "LOINC" display '94508-9'
code "94509-7" : '94509-7' from "LOINC" display '94509-7'
code "94510-5" : '94510-5' from "LOINC" display '94510-5'
code "94511-3" : '94511-3' from "LOINC" display '94511-3'
code "94532-9" : '94532-9' from "LOINC" display '94532-9'
code "94533-7" : '94533-7' from "LOINC" display '94533-7'
code "94534-5" : '94534-5' from "LOINC" display '94534-5'
code "94547-7" : '94547-7' from "LOINC" display '94547-7'
code "94558-4" : '94558-4' from "LOINC" display '94558-4'
code "94559-2" : '94559-2' from "LOINC" display '94559-2'
code "94562-6" : '94562-6' from "LOINC" display '94562-6'
code "94563-4" : '94563-4' from "LOINC" display '94563-4'
code "94564-2" : '94564-2' from "LOINC" display '94564-2'
code "94565-9" : '94565-9' from "LOINC" display '94565-9'
code "94639-2" : '94639-2' from "LOINC" display '94639-2'
code "94640-0" : '94640-0' from "LOINC" display '94640-0'
code "94641-8" : '94641-8' from "LOINC" display '94641-8'
code "94642-6" : '94642-6' from "LOINC" display '94642-6'
code "94643-4" : '94643-4' from "LOINC" display '94643-4'
code "94644-2" : '94644-2' from "LOINC" display '94644-2'
code "94645-9" : '94645-9' from "LOINC" display '94645-9'
code "94646-7" : '94646-7' from "LOINC" display '94646-7'
code "94647-5" : '94647-5' from "LOINC" display '94647-5'
code "94660-8" : '94660-8' from "LOINC" display '94660-8'
code "94661-6" : '94661-6' from "LOINC" display '94661-6'
code "94306-8" : '94306-8' from "LOINC" display '94306-8'
code "94503-0" : '94503-0' from "LOINC" display '94503-0'
code "94504-8" : '94504-8' from "LOINC" display '94504-8'
code "94531-1" : '94531-1' from "LOINC" display '94531-1'
code "94720-0" : '94720-0' from "LOINC" display '94720-0'
code "94758-0" : '94758-0' from "LOINC" display '94758-0'
code "94759-8" : '94759-8' from "LOINC" display '94759-8'
code "94760-6" : '94760-6' from "LOINC" display '94760-6'
code "94762-2" : '94762-2' from "LOINC" display '94762-2'
code "94763-0" : '94763-0' from "LOINC" display '94763-0'
code "94764-8" : '94764-8' from "LOINC" display '94764-8'
code "94765-5" : '94765-5' from "LOINC" display '94765-5'
code "94766-3" : '94766-3' from "LOINC" display '94766-3'
code "94767-1" : '94767-1' from "LOINC" display '94767-1'
code "94768-9" : '94768-9' from "LOINC" display '94768-9'
code "94769-7" : '94769-7' from "LOINC" display '94769-7'
code "94819-0" : '94819-0' from "LOINC" display '94819-0'
/*
N3C Procedure Codes
*/
code "U0001" : 'U0001' from "HCPCS" display 'U0001'
code "U0002" : 'U0002' from "HCPCS" display 'U0002'
code "87635" : '87635' from "CPT4" display '87635'
code "86318" : '86318' from "CPT4" display '86318'
code "86328" : '86328' from "CPT4" display '86328'
code "86769" : '86769' from "CPT4" display '86769'
/*
N3C Strong Condition Codes
*/
code "B97.21" : 'B97.21' from "ICD-10" display 'B97.21'
code "B97.29" : 'B97.29' from "ICD-10" display 'B97.29'
code "U07.1" : 'U07.1' from "ICD-10" display 'U07.1'
code "840539006" : '840539006' from "SNOMEDCT" display '840539006'
code "840544004" : '840544004' from "SNOMEDCT" display '840544004'
/*
N3C Weak Condition Codes
*/
code "Z20.828" : 'Z20.828' from "ICD-10" display 'Z20.828'
code "B34.2" : 'B34.2' from "ICD-10" display 'B34.2'
code "R50%" : 'R50%' from "ICD-10" display 'R50%'
code "R05%" : 'R05%' from "ICD-10" display 'R05%'
code "R06.0%" : 'R06.0%' from "ICD-10" display 'R06.0%'
code "J12%" : 'J12%' from "ICD-10" display 'J12%'
code "J18%" : 'J18%' from "ICD-10" display 'J18%'
code "J20%" : 'J20%' from "ICD-10" display 'J20%'
code "J40%" : 'J40%' from "ICD-10" display 'J40%'
code "J21%" : 'J21%' from "ICD-10" display 'J21%'
code "J96%" : 'J96%' from "ICD-10" display 'J96%'
code "J22%" : 'J22%' from "ICD-10" display 'J22%'
code "J06.9" : 'J06.9' from "ICD-10" display 'J06.9'
code "J98.8" : 'J98.8' from "ICD-10" display 'J98.8'
code "J80%" : 'J80%' from "ICD-10" display 'J80%'
code "R43.0" : 'R43.0' from "ICD-10" display 'R43.0'
code "R43.2" : 'R43.2' from "ICD-10" display 'R43.2'
code "R07.1" : 'R07.1' from "ICD-10" display 'R07.1'
code "R68.83" : 'R68.83' from "ICD-10" display 'R68.83'
code "840546002" : '840546002' from "SNOMEDCT" display '840546002'
code "103001002" : '103001002' from "SNOMEDCT" display '103001002'
code "11833005" : '11833005' from "SNOMEDCT" display '11833005'
code "267036007" : '267036007' from "SNOMEDCT" display '267036007'
code "28743005" : '28743005' from "SNOMEDCT" display '28743005'
code "36955009" : '36955009' from "SNOMEDCT" display '36955009'
code "426000000" : '426000000' from "SNOMEDCT" display '426000000'
code "44169009" : '44169009' from "SNOMEDCT" display '44169009'
code "49727002" : '49727002' from "SNOMEDCT" display '49727002'
code "135883003" : '135883003' from "SNOMEDCT" display '135883003'
code "161855003" : '161855003' from "SNOMEDCT" display '161855003'
code "161939006" : '161939006' from "SNOMEDCT" display '161939006'
code "161940008" : '161940008' from "SNOMEDCT" display '161940008'
code "161941007" : '161941007' from "SNOMEDCT" display '161941007'
code "2237002" : '2237002' from "SNOMEDCT" display '2237002'
code "23141003" : '23141003' from "SNOMEDCT" display '23141003'
code "247410004" : '247410004' from "SNOMEDCT" display '247410004'
code "274640006" : '274640006' from "SNOMEDCT" display '274640006'
code "274664007" : '274664007' from "SNOMEDCT" display '274664007'
code "284523002" : '284523002' from "SNOMEDCT" display '284523002'
code "386661006" : '386661006' from "SNOMEDCT" display '386661006'
code "409702008" : '409702008' from "SNOMEDCT" display '409702008'
code "426976009" : '426976009' from "SNOMEDCT" display '426976009'
code "43724002" : '43724002' from "SNOMEDCT" display '43724002'
code "60845006" : '60845006' from "SNOMEDCT" display '60845006'
code "75483001" : '75483001' from "SNOMEDCT" display '75483001'
parameter IndexDate default @2020-01-01
define "N3C Lab Tests Concept Union":
["DiagnosticReport": "94307-6" ] union
["DiagnosticReport": "94308-4" ] union
["DiagnosticReport": "94309-2" ] union
["DiagnosticReport": "94310-0" ] union
["DiagnosticReport": "94311-8" ] union
["DiagnosticReport": "94312-6" ] union
["DiagnosticReport": "94313-4" ] union
["DiagnosticReport": "94314-2" ] union
["DiagnosticReport": "94315-9" ] union
["DiagnosticReport": "94316-7" ] union
["DiagnosticReport": "94500-6" ] union
["DiagnosticReport": "94502-2" ] union
["DiagnosticReport": "94505-5" ] union
["DiagnosticReport": "94506-3" ] union
["DiagnosticReport": "94507-1" ] union
["DiagnosticReport": "94508-9" ] union
["DiagnosticReport": "94509-7" ] union
["DiagnosticReport": "94510-5" ] union
["DiagnosticReport": "94511-3" ] union
["DiagnosticReport": "94532-9" ] union
["DiagnosticReport": "94533-7" ] union
["DiagnosticReport": "94534-5" ] union
["DiagnosticReport": "94547-7" ] union
["DiagnosticReport": "94558-4" ] union
["DiagnosticReport": "94559-2" ] union
["DiagnosticReport": "94562-6" ] union
["DiagnosticReport": "94563-4" ] union
["DiagnosticReport": "94564-2" ] union
["DiagnosticReport": "94565-9" ] union
["DiagnosticReport": "94639-2" ] union
["DiagnosticReport": "94640-0" ] union
["DiagnosticReport": "94641-8" ] union
["DiagnosticReport": "94642-6" ] union
["DiagnosticReport": "94643-4" ] union
["DiagnosticReport": "94644-2" ] union
["DiagnosticReport": "94645-9" ] union
["DiagnosticReport": "94646-7" ] union
["DiagnosticReport": "94647-5" ] union
["DiagnosticReport": "94660-8" ] union
["DiagnosticReport": "94661-6" ] union
["DiagnosticReport": "94306-8" ] union
["DiagnosticReport": "94503-0" ] union
["DiagnosticReport": "94504-8" ] union
["DiagnosticReport": "94531-1" ] union
["DiagnosticReport": "94720-0" ] union
["DiagnosticReport": "94758-0" ] union
["DiagnosticReport": "94759-8" ] union
["DiagnosticReport": "94760-6" ] union
["DiagnosticReport": "94762-2" ] union
["DiagnosticReport": "94763-0" ] union
["DiagnosticReport": "94764-8" ] union
["DiagnosticReport": "94765-5" ] union
["DiagnosticReport": "94766-3" ] union
["DiagnosticReport": "94767-1" ] union
["DiagnosticReport": "94768-9" ] union
["DiagnosticReport": "94769-7" ] union
["DiagnosticReport": "94819-0" ]
define "N3C Procedure Code Union":
["Procedure": "U0001" ] union
["Procedure": "U0002" ] union
["Procedure": "87635" ] union
["Procedure": "86318" ] union
["Procedure": "86328" ] union
["Procedure": "86769" ]
define "N3C Strong Postive Condition Code Union":
["Condition": "B97.21" ] union
["Condition": "B97.29" ] union
["Condition": "U07.1" ] union
["Condition": "840539006" ] union
["Condition": "840544004" ]
define "N3C Weak Positive Condition Code Union":
["Condition": "Z20.828" ] union
["Condition": "B34.2" ] union
["Condition": "R50%" ] union
["Condition": "R05%" ] union
["Condition": "R06.0%" ] union
["Condition": "J12%" ] union
["Condition": "J18%" ] union
["Condition": "J20%" ] union
["Condition": "J40%" ] union
["Condition": "J21%" ] union
["Condition": "J96%" ] union
["Condition": "J22%" ] union
["Condition": "J06.9" ] union
["Condition": "J98.8" ] union
["Condition": "J80%" ] union
["Condition": "R43.0" ] union
["Condition": "R43.2" ] union
["Condition": "R07.1" ] union
["Condition": "R68.83" ] union
["Condition": "840546002" ] union
["Condition": "103001002" ] union
["Condition": "11833005" ] union
["Condition": "267036007" ] union
["Condition": "28743005" ] union
["Condition": "36955009" ] union
["Condition": "426000000" ] union
["Condition": "44169009" ] union
["Condition": "49727002" ] union
["Condition": "135883003" ] union
["Condition": "161855003" ] union
["Condition": "161939006" ] union
["Condition": "161940008" ] union
["Condition": "161941007" ] union
["Condition": "2237002" ] union
["Condition": "23141003" ] union
["Condition": "247410004" ] union
["Condition": "274640006" ] union
["Condition": "274664007" ] union
["Condition": "284523002" ] union
["Condition": "386661006" ] union
["Condition": "409702008" ] union
["Condition": "426976009" ] union
["Condition": "43724002" ] union
["Condition": "60845006" ] union
["Condition": "75483001" ]
define "Has N3C Lab Tests":
exists ("N3C Lab Tests Concept Union" lab
where lab.issued on or after IndexDate
)
define "Has N3C Procedures":
exists ("N3C Procedure Code Union" proc
where proc.performedDateTime on or after IndexDate
)
define "Has N3C Strong Positive Condition":
exists("N3C Strong Postive Condition Code Union" strong
where strong.onsetDateTime on or after IndexDate
)
define "Has N3C Weak Positive Condition":
exists ("N3C Weak Positive Condition Code Union" weak
where weak.onsetDateTime on or after IndexDate
)
define "Inpatient Encounters With Weak Condition":
[Encounter: "Inpatient Encounter"] E
with "N3C Weak Positive Condition Code Union" C
such that E.id = C.encounter
define "Outpatient Encounters With Weak Condition":
[Encounter: "Outpatient Encounter"] E
with "N3C Weak Positive Condition Code Union" C
such that E.id = C.encounter
define "Encounter Criteria With Weak Condition":
exists(Count("Inpatient Encounters With Weak Condition") >=2
or Count("Outpatient Encounters With Weak Condition") >= 2
)
define "N3C Cohort Cases":
"Has N3C Lab Tests"
or "Has N3C Procedures"
or "Has N3C Strong Positive Condition"
or ( "Has N3C Weak Positive Condition"
and "Encounter Criteria With Weak Condition")