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
smart-on-fhir · Jun 15, 2023 · d159def · d159def
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diff --git a/...y_covid/covid_symptom/count_covid_pcr.sql → ...library_covid/covid_symptom/count_pcr.sql b/...y_covid/covid_symptom/count_covid_pcr.sql → ...library_covid/covid_symptom/count_pcr.sql
@@ -42,6 +42,9 @@ WHERE
         '10828004', 'Positive', 'POSITIVE'
     ));
 
+-- # TODO i2b2 specific lab result codes are hardcoded, should be covid_symptom__define_pcr
+-- https://github.com/smart-on-fhir/cumulus-etl/issues/231
+
 -- ############################################################################
 
 

diff --git a/cumulus_library_covid/covid_symptom/covid_define.sql b/cumulus_library_covid/covid_symptom/covid_define.sql
@@ -11,29 +11,6 @@
 -- https://www.nlm.nih.gov/vsac/support/usingvsac/covid19valuesets.html
 -- http://build.fhir.org/ig/HL7/fhir-COVID19Library-ig/ValueSet-covid19-pos-neg-inv-vs.html
 
--- ############################################################################
--- COVID19 PCR
-
-CREATE OR REPLACE VIEW covid_symptom__define_pcr AS
-SELECT
-    t.code_system,
-    t.code,
-    t.display
-FROM
-    (
-        VALUES
-        (
-            'http://loinc.org',
-            '94500-6',
-            'SARS-CoV-2 (COVID-19) RNA [Presence] in Respiratory specimen by NAA with probe detection' --noqa:LT05
-        ),
-        (
-            'http://loinc.org',
-            '95406-5',
-            'SARS-CoV-2 (COVID-19) RNA [Presence] in Nose by NAA with probe detection'
-        )
-    ) AS t (code_system, code, display);
-
 CREATE OR REPLACE VIEW covid_symptom__define_pcr_result AS
 SELECT
     t.code_system,
@@ -86,60 +63,3 @@ FROM (
     ('C0242429', 'Sore throat')
 )
 AS t (cui, pref);
-
-
--- ############################################################################
--- COVID19 Age Groups (primarily for Suicidality study)
-
-CREATE OR REPLACE VIEW covid_symptom__define_age AS
-SELECT
-    t.age,
-    t.age_group
-FROM
-    (
-        VALUES
-        (0, '<5'),
-        (1, '<5'),
-        (2, '<5'),
-        (3, '<5'),
-        (4, '<5'),
-        (5, '=>5'),
-        (6, '=>5'),
-        (7, '=>5'),
-        (8, '=>5'),
-        (9, '=>5'),
-        (10, '=>5'),
-        (11, '=>5'),
-        (12, '=>5'),
-        (13, '=>5'),
-        (14, '=>5'),
-        (15, '=>5'),
-        (16, '=>5'),
-        (17, '=>5'),
-        (18, '=>5'),
-        (19, '=>5'),
-        (20, '=>5'),
-        (21, '=>5')
-    ) AS t (age, age_group);
-
--- ############################################################################
--- COVID19 Study Period for Variant Eras
---
--- Variant eras are defined using COVID-19 data for Massachusetts from CoVariant [16].
--- Pre-Delta era was defined as March 1, 2020 to June 20, 2021
--- Delta era as June 21, 2021 to December 19, 2021
--- Omicron era as December 20, 2021 onwards.
-
-CREATE OR REPLACE VIEW covid_symptom__define_period AS
-SELECT
-    t.variant_era,
-    t.variant_start,
-    t.variant_end
-FROM (
-    VALUES
-    --  ('before-covid', date('2020-02-29'), date('2021-02-28'))
-    ('before-delta', date('2020-03-01'), date('2021-06-20')),
-    ('delta', date('2021-06-21'), date('2021-12-19')),
-    ('omicron', date('2021-12-20'), date('2022-06-01'))
-)
-AS t (variant_era, variant_start, variant_end);
diff --git a/..._covid/covid_symptom/define_pcr_loinc.sql → ...ibrary_covid/covid_symptom/define_pcr.sql b/..._covid/covid_symptom/define_pcr_loinc.sql → ...ibrary_covid/covid_symptom/define_pcr.sql
diff --git a/cumulus_library_covid/covid_symptom/define_pcr_negative.sql b/cumulus_library_covid/covid_symptom/define_pcr_negative.sql
@@ -0,0 +1,24 @@
+create or replace view covid_symptom__define_pcr_negative as select * from (values
+('http://snomed.info/sct', '131194007', 'Non-Reactive (qualifier value)')
+,('http://snomed.info/sct', '168230009', 'Sample direct microscopy no organism seen (finding)')
+,('http://snomed.info/sct', '17621005', 'Normal (qualifier value)')
+,('http://snomed.info/sct', '23506009', 'Normal flora (finding)')
+,('http://snomed.info/sct', '260385009', 'Negative (qualifier value)')
+,('http://snomed.info/sct', '260389003', 'No reaction (qualifier value)')
+,('http://snomed.info/sct', '260394003', 'Normal limits (qualifier value)')
+,('http://snomed.info/sct', '260395002', 'Normal range (qualifier value)')
+,('http://snomed.info/sct', '260415000', 'Not detected (qualifier value)')
+,('http://snomed.info/sct', '264868006', 'No growth (qualifier value)')
+,('http://snomed.info/sct', '264887000', 'Not isolated (qualifier value)')
+,('http://snomed.info/sct', '2667000', 'Absent (qualifier value)')
+,('http://snomed.info/sct', '272519000', 'Absence findings (qualifier value)')
+,('http://snomed.info/sct', '27863008', 'No organisms seen (finding)')
+,('http://snomed.info/sct', '280413001', 'Normal result (qualifier value)')
+,('http://snomed.info/sct', '281297005', 'Analyte not detected (qualifier value)')
+,('http://snomed.info/sct', '371928007', 'Not significant (qualifier value)')
+,('http://snomed.info/sct', '373067005', 'No (qualifier value)')
+,('http://snomed.info/sct', '435151000124100', 'No acid fast organisms seen (finding)')
+,('http://snomed.info/sct', '444991000124106', 'Repeatedly non-reactive (qualifier value)')
+,('http://snomed.info/sct', '449501000124109', 'Within defined limits (qualifier value)')
+,('http://snomed.info/sct', '47492008', 'Not seen (qualifier value)')
+) AS t (system, code, display) ;
diff --git a/cumulus_library_covid/covid_symptom/define_pcr_positive.sql b/cumulus_library_covid/covid_symptom/define_pcr_positive.sql
@@ -0,0 +1,32 @@
+create or replace view covid_symptom__define_pcr_positive as select * from (values
+('http://snomed.info/sct', '10828004', 'Positive (qualifier value)')
+,('http://snomed.info/sct', '11214006', 'Reactive (qualifier value)')
+,('http://snomed.info/sct', '117006002', 'Weakly-reactive (qualifier value)')
+,('http://snomed.info/sct', '260347006', 'Present + out of ++++ (qualifier value)')
+,('http://snomed.info/sct', '260348001', 'Present ++ out of ++++ (qualifier value)')
+,('http://snomed.info/sct', '260349009', 'Present +++ out of ++++ (qualifier value)')
+,('http://snomed.info/sct', '260350009', 'Present ++++ out of ++++ (qualifier value)')
+,('http://snomed.info/sct', '260351008', 'Just noticeable (qualifier value)')
+,('http://snomed.info/sct', '260373001', 'Detected (qualifier value)')
+,('http://snomed.info/sct', '260405006', 'Trace (qualifier value)')
+,('http://snomed.info/sct', '260408008', 'Weakly positive (qualifier value)')
+,('http://snomed.info/sct', '260411009', 'Presence findings (qualifier value)')
+,('http://snomed.info/sct', '263654008', 'Abnormal (qualifier value)')
+,('http://snomed.info/sct', '263776006', 'Heavy growth (qualifier value)')
+,('http://snomed.info/sct', '263812008', 'Moderate growth (qualifier value)')
+,('http://snomed.info/sct', '280415008', 'Abnormal result (qualifier value)')
+,('http://snomed.info/sct', '373066001', 'Yes (qualifier value)')
+,('http://snomed.info/sct', '410515003', 'Known present (qualifier value)')
+,('http://snomed.info/sct', '410591008', 'Definitely present (qualifier value)')
+,('http://snomed.info/sct', '410592001', 'Probably present (qualifier value)')
+,('http://snomed.info/sct', '410605003', 'Confirmed present (qualifier value)')
+,('http://snomed.info/sct', '43261007', 'Abnormal presence of (qualifier value)')
+,('http://snomed.info/sct', '441517005', 'Present two plus out of three plus (qualifier value)')
+,('http://snomed.info/sct', '441521003', 'Present three plus out of three plus (qualifier value)')
+,('http://snomed.info/sct', '441614007', 'Present one plus out of three plus (qualifier value)')
+,('http://snomed.info/sct', '46651001', 'Isolated (qualifier value)')
+,('http://snomed.info/sct', '52101004', 'Present (qualifier value)')
+,('http://snomed.info/sct', '61620004', 'True positive (qualifier value)')
+,('http://snomed.info/sct', '7882003', 'Identified (qualifier value)')
+,('http://snomed.info/sct', '89292003', 'Rare (qualifier value)')
+) AS t (system, code, display) ;
diff --git a/cumulus_library_covid/covid_symptom/manifest.toml b/cumulus_library_covid/covid_symptom/manifest.toml
@@ -2,15 +2,21 @@ study_prefix = "covid_symptom"
 
 [sql_config]
 file_names = [
-    "define_dx_icd10.sql",
-    "site_define.sql",
-    "covid_define_symptom.sql",
-    "covid_define.sql",
-    "count_covid_study_period.sql",
-    "count_covid_dx.sql",
-    "count_covid_pcr.sql",
-    "count_covid_symptom.sql",
-    "count_covid_prevalence_ed.sql",
+    "define_age_pediatric.sql",
+#     "define_age_general.sql", # Hospitals that are pediatric should use this instead !
+#    "define_study_period.sql",
+    "define_pcr.sql",
+    "define_pcr_positive.sql",
+    "define_pcr_negative.sql",
+#    "define_dx_icd10.sql",
+#    "site_define.sql",
+#    "covid_define_symptom.sql",
+#    "covid_define.sql",
+#    "count_covid_study_period.sql",
+#    "count_covid_dx.sql",
+#    "count_covid_pcr.sql",
+#    "count_covid_symptom.sql",
+#    "count_covid_prevalence_ed.sql",
 ]