Update uom for measurements

MSSQL/preparePCORnetOntology.sql

@@ -1,11 +1,16 @@
--- Modify the PCORnet ontology to be compatible with the new version of the OMOP transform, i2o 2020
--- Run this from your i2b2 database that has the mapped PCORnet ontology!
--- Jeff Klann PhD, April 2020
+--------------------------------------------------------------------------------------------------------
+-- Description: Prep the local PCORnet ontology for use in the OMOP transformation
+--				Run this from your i2b2 database that has the mapped PCORnet ontology!
+-- Authored By: Jeff Klann PhD, April 2020
+-- Updated on: 2020-12-07 by Kevin Embree 
+--              To include i_unit column to maintain compatibility with PHS specific logic
+--------------------------------------------------------------------------------------------------------
 
--- Set up the extra columns i_stdcode, i_stddomain for labs
+-- Set up the extra columns i_stdcode, i_stddomain, i_unit for labs
 ALTER TABLE [dbo].[pcornet_lab]
 	ADD [i_stdcode] varchar(50) NULL, 
-	[i_stddomain] varchar(25) NULL
+	[i_stddomain] varchar(25) NULL,
+	[i_unit] varchar(25) NULL
 GO
 CREATE NONCLUSTERED INDEX [pcornetlab_stdcode]
 	ON [dbo].[pcornet_lab]([i_stdcode])

MSSQL/preparePHSOntology.sql

@@ -0,0 +1,75 @@
+---------------------------------------------------------------------------------------------
+-- Mass General Brigham specific modifications 
+-- Description: i2o_transform works off the PCORNET ARCH ontologies, following script
+--              --Modifies the transformation to use i2b2 ontoloies in certain circumstances
+--              --Adds manual mappings specific to Mass General Brigham
+-- Authored by: Jeff Klann
+-- Updated by: Kevin Embree on 2020-12-07 to use units specified in the MGB i2b2 XML
+--             Added manual mappings for unit conversion
+--------------------------------------------------------------------------------------------
+--------------------------------------------------------------------------------------------
+-- When to run....
+-- After the initial install of the pcornet Ontology or updates to the preparePCORnetOntology.sql 
+--	   Run the new preparePCORnetOntology.sql
+-- Subsequent to preparePCORnetOntology.sql For Mass General Brigham users, after delivery of a new i2b2 datamart or updates to the PrepNewOMOPLoader_PHS.sql
+--	   Run this script, PrepNewOMOPLoader_PHS.sql
+--------------------------------------------------------------------------------------------
+
+-- Set up the extra columns i_stdcode, i_stddomain
+ALTER TABLE [dbo].[i2b2metadata]
+	ADD [i_stdcode] varchar(100) NULL, 
+	[i_stddomain] varchar(100) NULL,
+	[i_unit] varchar(100) NULL
+GO
+CREATE NONCLUSTERED INDEX [i2b2meta_stdcode]
+	ON [dbo].[i2b2metadata]([i_stdcode])
+GO
+
+-- Chris' approach, use a view
+drop view vw_labtests_reconstructed
+GO
+create view vw_LabTests_Reconstructed
+as
+with t as (
+select l.c_name,
+       l.c_basecode,
+       f.ENCOUNTER_NUM,
+       f.PATIENT_NUM,
+       f.VALTYPE_CD,
+       f.NVAL_NUM,
+       f.TVAL_CHAR,
+       f.VALUEFLAG_CD,
+       try_cast(l.c_metadataxml as xml) valuexml
+from i2b2metadata l
+       inner join observation_fact f on l.C_BASECODE = f.CONCEPT_CD
+where l.c_fullname like '\I2B2MetaData\LabTests\%')
+select c_name LabName,
+       C_BASECODE Concept_Cd,
+       ENCOUNTER_NUM Encounter_Num,
+       PATIENT_NUM Patient_Num,
+       VALTYPE_CD ValueType,
+       NVAL_NUM NumericValue,
+       TVAL_CHAR TextValue,
+       VALUEFLAG_CD ValueFlag,
+       valuexml,
+       valuexml.value('(/ValueMetadata/Loinc)[1]','VARCHAR(100)') Loinc,
+valuexml.value('(/ValueMetadata/LowofLowValue)[1]','VARCHAR(100)') RefLowofLow,
+valuexml.value('(/ValueMetadata/HighofLowValue)[1]','VARCHAR(100)') RefHighofLow,
+valuexml.value('(/ValueMetadata/LowofHighValue)[1]','VARCHAR(100)') RefLowofHigh,
+valuexml.value('(/ValueMetadata/HighofHighValue)[1]','VARCHAR(100)') RefHighofHigh,
+valuexml.value('(/ValueMetadata/UnitValues/NormalUnits)[1]','VARCHAR(100)') Units
+from t
+GO
+
+-- Update to set i_stddomain, i_stdcode and i_unit all at once from XML no need for vw_LabTests_Reconstructed
+update m set i_stddomain='LOINC',i_stdcode=try_cast(m.c_metadataxml as xml).value('(/ValueMetadata/Loinc)[1]','VARCHAR(50)'), i_unit = try_cast(m.c_metadataxml as xml).value('(/ValueMetadata/UnitValues/NormalUnits)[1]','VARCHAR(25)') from i2b2metadata m 
+ where m.C_FULLNAME like '%\I2B2MetaData\LabTests\%' 
+GO
+-- Create the new views - change COVID_Mart to your DB name
+IF  EXISTS (SELECT * FROM sys.views WHERE name = N'i2o_ontology_lab') DROP VIEW i2o_ontology_lab
+IF  EXISTS (SELECT * FROM sys.views WHERE name = N'i2o_ontology_drug') DROP VIEW i2o_ontology_drug
+GO
+create view i2o_ontology_lab as (select * from AllOfUs_Mart..i2b2metadata where i_stddomain='LOINC')
+GO
+create view i2o_ontology_drug as (select * from AllOfUs_Mart..pcornet_med where i_stddomain='RxNorm' or i_stddomain='NDC')
+GO