Merge pull request #277 from smart-on-fhir/mikix/covid-codes

feat(covid-symptom): add BCH/Cerner-specific ED codes
smart-on-fhir · Oct 3, 2023 · 0cdf86d · 0cdf86d
2 parents 31c2557 + 2e20fbf
commit 0cdf86d
Show file tree

Hide file tree

Showing 2 changed files with 32 additions and 12 deletions.
diff --git a/cumulus_etl/etl/studies/covid_symptom/covid_tasks.py b/cumulus_etl/etl/studies/covid_symptom/covid_tasks.py
@@ -14,18 +14,6 @@
 
 # List of recognized emergency department note types. We'll add more as we discover them in use.
 ED_CODES = {
-    "http://cumulus.smarthealthit.org/i2b2": {
-        "NOTE:3710480",
-        "NOTE:3807712",
-        "NOTE:149798455",
-        "NOTE:159552404",
-        "NOTE:189094576",
-        "NOTE:189094619",
-        "NOTE:189094644",
-        "NOTE:318198107",
-        "NOTE:318198110",
-        "NOTE:318198113",
-    },
     "http://loinc.org": {
         "18842-5",  # Discharge Summary
         "28568-4",  # Physician Emergency department Note
@@ -41,6 +29,33 @@
         "74187-6",  # InterRAI Emergency Screener for Psychiatry (ESP) Document
         "74211-4",  # Summary of episode note Emergency department+Hospital
     },
+    # The above _should_ be enough if everything is coded well.
+    # But sometimes not every document has a LOINC coding included.
+    # Below are some site-specific coding systems and their ED codes, to help fill in those gaps.
+    "http://cumulus.smarthealthit.org/i2b2": {  # BCH i2b2
+        "NOTE:3710480",  # ED Consultation
+        "NOTE:3807712",  # ED Note
+        "NOTE:149798455",  # Emergency MD
+        "NOTE:159552404",  # ED Note Scanned
+        "NOTE:189094576",  # ED Scanned
+        "NOTE:189094619",  # SANE Report
+        "NOTE:189094644",  # Emergency Dept Scanned Forms
+        "NOTE:318198107",  # ED Social Work Assessment
+        "NOTE:318198110",  # ED Social Work Brief Screening
+        "NOTE:318198113",  # ED Social Work
+    },
+    "https://fhir.cerner.com/96976f07-eccb-424c-9825-e0d0b887148b/codeSet/72": {  # BCH Cerner
+        "3710480",  # ED Consultation
+        "3807712",  # ED Note
+        "149798455",  # Emergency MD
+        "159552404",  # ED Note Scanned
+        "189094576",  # ED Scanned
+        "189094619",  # SANE Report
+        "189094644",  # Emergency Dept Scanned Forms
+        "318198107",  # ED Social Work Assessment
+        "318198110",  # ED Social Work Brief Screening
+        "318198113",  # ED Social Work
+    },
 }
 
 

diff --git a/tests/covid_symptom/test_nlp_results.py b/tests/covid_symptom/test_nlp_results.py
@@ -44,10 +44,15 @@ async def test_unknown_modifier_extensions_skipped_for_nlp_symptoms(self):
         # Invalid codes
         ([], False),
         ([{"system": "http://cumulus.smarthealthit.org/i2b2", "code": "NOTE:0"}], False),
+        ([{"system": "https://fhir.cerner.com/96976f07-eccb-424c-9825-e0d0b887148b/codeSet/72", "code": "0"}], False),
         ([{"system": "http://loinc.org", "code": "00000-0"}], False),
         ([{"system": "http://example.org", "code": "nope"}], False),
         # Valid codes
         ([{"system": "http://cumulus.smarthealthit.org/i2b2", "code": "NOTE:3710480"}], True),
+        (
+            [{"system": "https://fhir.cerner.com/96976f07-eccb-424c-9825-e0d0b887148b/codeSet/72", "code": "3710480"}],
+            True,
+        ),
         ([{"system": "http://loinc.org", "code": "57053-1"}], True),
         ([{"system": "nope", "code": "nope"}, {"system": "http://loinc.org", "code": "57053-1"}], True),
     )