Merge pull request #68 from kind-lab/concept_map_documenting

Added valueset references for mimic valuesets that need concept mapping
kind-lab · May 26, 2022 · f958340 · f958340
2 parents 5aedb3a + 886faf5
commit f958340
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Showing 8 changed files with 11 additions and 7 deletions.
diff --git a/sql/codesystem/cs-admission-class.sql b/sql/codesystem/cs-admission-class.sql
@@ -1,5 +1,5 @@
 -- Admission class CodeSystem
--- Codes will need to be mapped to match US Core Act Encounter Code - http://terminology.hl7.org/CodeSystem/v3-ActCode
+-- Codes will need to be mapped to match US Core Act Encounter Code - http://terminology.hl7.org/ValueSet/v3-ActEncounterCode
 
 DROP TABLE IF EXISTS fhir_trm.cs_admission_class;
 CREATE TABLE fhir_trm.cs_admission_class(

diff --git a/sql/codesystem/cs-admission-type.sql b/sql/codesystem/cs-admission-type.sql
@@ -1,5 +1,5 @@
 -- Admission type CodeSystem
--- Codes will need to be mapped to match US Core Encounter Type -http://hl7.org/fhir/v3/ActPriority/vs.html
+-- Codes will need to be mapped to match US Core Encounter Type -http://hl7.org/fhir/ValueSet/encounter-type
 
 DROP TABLE IF EXISTS fhir_trm.cs_admission_type;
 CREATE TABLE fhir_trm.cs_admission_type(

diff --git a/sql/codesystem/cs-chartevents-d-items.sql b/sql/codesystem/cs-chartevents-d-items.sql
@@ -1,5 +1,5 @@
 -- Generate unique item codes for only the chartevents
--- This is pulled from the d-items CodeSystem
+-- This is pulled from the d-items CodeSystem, map to LOINC codes http://hl7.org/fhir/valueset-observation-codes.html
 
 
 DROP TABLE IF EXISTS fhir_trm.cs_chartevents_d_items;

diff --git a/sql/codesystem/cs-d-items.sql b/sql/codesystem/cs-d-items.sql
@@ -1,5 +1,6 @@
 -- Generate codesystem for icu item codes
--- Will be referenced by chartevents, datetimeevents, and outputevents
+-- Will be referenced by procedureevents, datetimeevents, and outputevents
+-- chartevents too large, an individual codesystem created for it
 
 DROP TABLE IF EXISTS fhir_trm.cs_d_items;
 CREATE TABLE fhir_trm.cs_d_items(
@@ -11,4 +12,5 @@ INSERT INTO fhir_trm.cs_d_items
 SELECT 
     DISTINCT itemid AS code
     , label AS display
-FROM mimic_icu.d_items di 
+FROM mimic_icu.d_items di 
+WHERE linksto IN ('procedureevents', 'datetimeevents', 'outputevents');
diff --git a/sql/codesystem/cs-lab-fluid.sql b/sql/codesystem/cs-lab-fluid.sql
@@ -1,5 +1,5 @@
 -- Lab fluid CodeSystem
--- Codes will need to be mapped to something like the Specimen type example-v2 - http://hl7.org/fhir/v2/0487/index.html
+-- Codes will need to be mapped to something like the Specimen type example-v2 - http://terminology.hl7.org/ValueSet/v2-0487
 
 DROP TABLE IF EXISTS fhir_trm.cs_lab_fluid;
 CREATE TABLE fhir_trm.cs_lab_fluid(

diff --git a/sql/codesystem/cs-medication-frequency.sql b/sql/codesystem/cs-medication-frequency.sql
@@ -1,4 +1,5 @@
 -- Medication Frequency CodeSystem
+-- Map the frequency values to http://hl7.org/fhir/ValueSet/timing-abbreviation
 
 DROP TABLE IF EXISTS fhir_trm.cs_medication_frequency;
 CREATE TABLE fhir_trm.cs_medication_frequency(

diff --git a/sql/codesystem/cs-observation-category.sql b/sql/codesystem/cs-observation-category.sql
@@ -1,4 +1,5 @@
 -- Observation Category CodeSystem
+-- Map values to http://hl7.org/fhir/valueset-observation-category.html
 
 DROP TABLE IF EXISTS fhir_trm.cs_observation_category;
 CREATE TABLE fhir_trm.cs_observation_category(

diff --git a/sql/codesystem/cs-spec-type-desc.sql b/sql/codesystem/cs-spec-type-desc.sql
@@ -1,5 +1,5 @@
 -- Specimen type labs CodeSystem
--- Codes will need to be mapped to something like the Specimen type example-v2 - http://hl7.org/fhir/v2/0487/index.html
+-- Codes will need to be mapped to something like the Specimen type example-v2 - http://terminology.hl7.org/ValueSet/v2-0487
 
 DROP TABLE IF EXISTS fhir_trm.cs_spec_type_desc;
 CREATE TABLE fhir_trm.cs_spec_type_desc(