OMOP Common Data Model

* initial update for OMOP CDM version

amsterdamumcdb/connections.py

@@ -58,7 +58,8 @@ def connect_pg(config_file='config.ini'):
     pg_con.set_session(autocommit=True)
 
     cursor = pg_con.cursor()
-    cursor.execute('SET SCHEMA \'amsterdamumcdb\'');  # set search_path to amsterdamumcdb schema
+    schema = config['psycopg2']['schema']
+    cursor.execute(f'SET SCHEMA \'{schema}\';')  # set search_path to amsterdamumcdb schema
 
     # create SQLAlchemy engine for official pandas database support
     engine = sqlalchemy.create_engine('postgresql+psycopg2://', creator=lambda: pg_con)

amsterdamumcdb/sql/diagnosis/cardiac_arrest.sql

@@ -0,0 +1,33 @@
+SELECT
+    condition_occurrence_id,
+    person_id,
+    visit_occurrence_id,
+    condition_concept_id,
+    c_condition.concept_name AS condition_concept_name,
+    condition_start_datetime,
+    condition_status_concept_id,
+    c_status.concept_name    AS status_concept_name
+FROM
+    condition_occurrence c_o
+    LEFT JOIN concept c_condition ON
+        c_condition.concept_id = c_o.condition_concept_id
+    LEFT JOIN concept c_status ON
+        c_status.concept_id = c_o.condition_status_concept_id
+WHERE
+    condition_status_concept_id IN
+    (
+     32901, --Primary admission diagnosis
+     32907 --Secondary admission diagnosis
+        )
+    AND condition_concept_id IN
+        (SELECT
+             descendant_concept_id
+         FROM
+             concept_ancestor
+         WHERE
+             ancestor_concept_id IN
+             (
+                 4256374 -- Cardiorespiratory arrest
+                 ))
+ORDER BY
+    person_id, visit_occurrence_id

amsterdamumcdb/sql/diagnosis/cardiac_surgery.sql

@@ -0,0 +1,38 @@
+SELECT
+    procedure_occurrence_id,
+    po.person_id,
+    po.visit_occurrence_id,
+    procedure_concept_id,
+    c.concept_name AS procedure_concept_name,
+    procedure_datetime
+FROM
+    procedure_occurrence po
+    LEFT JOIN visit_occurrence visit ON
+        visit.visit_occurrence_id = po.visit_occurrence_id
+    LEFT JOIN concept c ON
+        c.concept_id = po.procedure_concept_id
+    LEFT JOIN provider p ON
+        p.provider_id = visit.provider_id
+WHERE
+    procedure_datetime < visit.visit_start_datetime
+    AND procedure_datetime >= visit.visit_start_datetime - INTERVAL '8 HOUR'
+    AND (p.specialty_concept_id = 38004497 -- Cardiac Surgery
+        OR procedure_concept_id IN
+           (SELECT
+                descendant_concept_id
+            FROM
+                concept_ancestor
+            WHERE
+                ancestor_concept_id IN
+                (
+                 4275564, -- Cardiac surgery procedure
+                 44783222, -- Aortic arch replacement
+                 4049406, -- Operation on the pulmonary trunk and arteries
+                 44782479, -- Repair of ascending aorta
+                 4339824, -- Aortic valve replacement and replacement of ascending aorta
+                 4049406, -- Operation on the pulmonary trunk and arteries
+                 44783314 -- Repair of dissection of proximal thoracic aorta
+                    ))
+        )
+    AND NOT po.provider_id IS NULL
+

amsterdamumcdb/sql/diagnosis/gastro_intestinal_surgery.sql

@@ -0,0 +1,46 @@
+SELECT
+    procedure_occurrence_id,
+    po.person_id,
+    po.visit_occurrence_id,
+    procedure_concept_id,
+    c.concept_name AS procedure_concept_name,
+    procedure_datetime
+FROM
+    procedure_occurrence po
+    LEFT JOIN visit_occurrence visit ON
+        visit.visit_occurrence_id = po.visit_occurrence_id
+    LEFT JOIN concept c ON
+        c.concept_id = po.procedure_concept_id
+    LEFT JOIN provider p ON
+        p.provider_id = visit.provider_id
+WHERE
+    procedure_datetime < visit.visit_start_datetime
+    AND procedure_datetime >= visit.visit_start_datetime - INTERVAL '8 HOUR'
+    AND (p.specialty_concept_id = 38004447 -- General Surgery
+        OR procedure_concept_id IN
+           (SELECT
+                descendant_concept_id
+            FROM
+                concept_ancestor
+            WHERE
+                ancestor_concept_id IN
+                (
+                    --4314251, -- Laparotomy
+                    4293032 --Procedure on gastrointestinal tract
+                    ))
+        )
+    AND NOT procedure_concept_id IN
+            (SELECT
+                 descendant_concept_id
+             FROM
+                 concept_ancestor
+             WHERE
+                 ancestor_concept_id IN
+                 (
+                  4042641, --Procedure on cardiovascular system
+                  4030781 --Operative procedure on male genitourinary system (procedure)
+                     ))
+    AND NOT po.provider_id IS NULL
+
+
+

amsterdamumcdb/sql/diagnosis/infection.sql

@@ -0,0 +1,33 @@
+SELECT
+    condition_occurrence_id,
+    person_id,
+    visit_occurrence_id,
+    condition_concept_id,
+    c_condition.concept_name AS condition_concept_name,
+    condition_start_datetime,
+    condition_status_concept_id,
+    c_status.concept_name    AS status_concept_name
+FROM
+    condition_occurrence c_o
+    LEFT JOIN concept c_condition ON
+        c_condition.concept_id = c_o.condition_concept_id
+    LEFT JOIN concept c_status ON
+        c_status.concept_id = c_o.condition_status_concept_id
+WHERE
+    condition_status_concept_id IN
+    (
+     32901, --Primary admission diagnosis
+     32907 --Secondary admission diagnosis
+        )
+    AND condition_concept_id IN
+        (SELECT
+             descendant_concept_id
+         FROM
+             concept_ancestor
+         WHERE
+             ancestor_concept_id IN
+             (
+                 4181063 --Inflammation of specific body organs (disorder)
+                 ))
+ORDER BY
+    person_id, visit_occurrence_id