Cerner specific: Observation Laboratory Result Codes are non-standard #13
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…se other codes for PCR tests, results, etc. (#12) * COVID Diagnosis formal ValueSet for ICD10 : U07.1 * COVID Diagnosis 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. * COVID PCR test LOINC test codes qualitiative and quantitative results. Requires associated "interpretation" of PCR result * Valusets for lab results POSITIVE or NEGATIVE. Includes synonyms like "identified", "presence", "weakly-reactive", etc. * covid_define.sql Diagnosis (DX) defers to covid_symptom__define_dx using 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. * removed any mention of Influenza, potentially confusing/distracting to anyone reading this repository. * BCH specific age is pediatric, other CDC pilot sites are general population 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 tests and results are now externalized to 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 * removed covid_symptom__define_pcr_result see instead negative and positive SQL definitions (seperate files now) * simplified covid_symptom__define_symptom_cui to select distinct cui,pref from covid_symptom__define_symptom * renamed : removed superfluous study prefix from filenaames, already in the correct folder. * covid_define.sql was deleted, partitioned into individual SQL files * covid_symptom__site_pcr is now found in define_pcr.sql * renamed covid_define.py to typesystem.py This file is depended on by other repos for COVID analysis. * renamed covid_define_symptom.* * site_define.sql is now deprecated, see instead each "define_***.sql" file. * count tables are not generated dynamically. * covid counts now generated dynamically. only the "table" of COVID data is prepared by hand to support study objectives. * updated manifest.toml to include new "define" SQL. updated pyproject.toml to include latest (core) "cumulus-library" * changed default to GENERAL population, not BCH specific pediatric #9 * comments only to reference ISSUES open as TODO * fixed missing comma "," * manifest.toml restored define_study_period.sql * removed 2016 retroactive period. use instead covid_symptom__define_period if modifications are needed to the covid study period. #11 * renamed covid_symptom__symptom_nlp removed "influenza" backdating in symptom comparison. * towards better support of PCR tests and results in different coding systems and EHR support. #8 #13 * renamed covid_symptom__define_dx_icd10 towards better support of PCR tests and results in different coding systems and EHR support. #8 #13 * define_ed_note.sql removed "ED Social Work" note type, only ED Note types are supported for COVID symptoms analysis. * "Observation Interpretation" added standard POS/NEG FHIR ValueSet * SNOMED or ICD10 can be used to build DX table_dx.sql * COVID study period can optionally be extended to before COVID ('before-covid', date('2016-06-01'), date('2020-02-29')), * MILESTONE: manifest.toml updated and "tested" by executing each SQL one at a time in Athena. table_prevalence_ed.sql now references renamed covid_symptom__symptom_nlp * define_ed_note.sql fixed column names AS t (from_system, from_code, from_display, system, code, display); * table_dx.sql covid_symptom__dx now contains c.recorded_month as cond_month, c.recorded_year as cond_year, * fixed minor issues in counts.py --> counts.sql * removed start_year counts query
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Cerner is supporting the TEST code but not the RESULT or INTERPRETATION
Observation.code
{coding=[{code=1148157467, display=Rapid SARS-CoV-2 PCR, Resp, QuaL, system=https://fhir.cerner.com/96976f07-eccb-424c-9825-e0d0b887148b/codeSet/72, userselected=true}, {code=94500-6, display=null, system=http://loinc.org/, userselected=false}], text=Rapid SARS-CoV-2 PCR, Resp, QuaL}
https://build.fhir.org/observation-definitions.html#Observation.value_x_
Observation.valuecodeableconcept
{coding=null, text=Negative}
Obseration.Interpreratation
[{coding=[{code=214, display=null, system=https://fhir.cerner.com/96976f07-eccb-424c-9825-e0d0b887148b/codeSet/52, userselected=true}], text=Normal}]
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