FHIR ValueSet(s) should enable wider support for CDC Pilot sites to use other codes for PCR tests, results, etc. #12
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formal ValueSet for ICD10 : U07.1
optional support for SNOMED, in the rare case that ICD10 is not available. SNOMED also reports for *secondary morbidities caused by COVID*, such as PNA or resp infections, etc.
qualitiative and quantitative results. Requires associated "interpretation" of PCR result
Includes synonyms like "identified", "presence", "weakly-reactive", etc.
…ing define_dx_icd10.sql. Some sites may require instead using SNOMED, which is define_dx_snomed.sql. Note that this SNOMED is not the default because our papers are written with the billing ICD10 diagnosis of U07.1.
…o anyone reading this repository.
…lation age. Split age definitions into define_age_pediatric.sql define_age_general.sql to use one or the other, toggle the correct target in manifest.toml
define_pcr_negative.sql define_pcr_positive.sql todo: need to workaround "POSITIVE" vs "Positive" "NEGATIVE" vs "Negative" i2b2 specific observations that are not translated in transit by ETL smart-on-fhir/cumulus-etl#231
see instead negative and positive SQL definitions (seperate files now)
select distinct cui,pref from covid_symptom__define_symptom
…n the correct folder.
define_pcr.sql
This file is depended on by other repos for COVID analysis.
only the "table" of COVID data is prepared by hand to support study objectives.
updated pyproject.toml to include latest (core) "cumulus-library"
use instead covid_symptom__define_period if modifications are needed to the covid study period. #11
removed "influenza" backdating in symptom comparison.
…ypes are supported for COVID symptoms analysis.
added standard POS/NEG FHIR ValueSet
('before-covid', date('2016-06-01'), date('2020-02-29')),
…ne at a time in Athena. table_prevalence_ed.sql now references renamed covid_symptom__symptom_nlp
fixed column names AS t (from_system, from_code, from_display, system, code, display);
covid_symptom__dx now contains
c.recorded_month as cond_month,
c.recorded_year as cond_year,
dogversioning
approved these changes
Jun 29, 2023
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FIX pediatric age criteria
Examine criteria of "age at visit" : covid_symptom__define_age #9
Improvement **PCR nucleic acid amplication test codes and results ** (wider support via FHIR ValueSet)
COVID diagnosis and DNA/RNA testing: Support VSAC Valueset definitions #8
Improvement: COUNT SQL is now dynamically created via cumulus library.
Refactoring: define, tables, and counts now clearly separated into each file with the corresponding name.
Refactoring: study_prefix (covid_symptom__) now assumed in filepath, renamed files as this would be redundant.
TODO: need fix "ED note" codes are inherited from CORE library
ED Note definition lives in core, not covid symptom (core__ed_note) #10