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modified OMOP loader to refer to OMOP instead of PCORNET,
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and modified demographic proc to refer to person table and
OMOP_BASECODE
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@matthewjoss
matthewjoss committed Jan 5, 2017
1 parent 0f4088e commit 9a3f78f
Showing 1 changed file with 65 additions and 66 deletions.
131 changes: 65 additions & 66 deletions MSSQL/OMOPLoader.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -207,24 +207,23 @@ GO
----------------------------------------------------------------------------------------------------------------------------------------
----------------------------------------------------------------------------------------------------------------------------------------
-- 1. Demographics - v4.1 by Aaron Abend
-- Modified by Matthew Joss to support biobank flags
----------------------------------------------------------------------------------------------------------------------------------------
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'PCORNetDemographics') AND type in (N'P', N'PC')) DROP PROCEDURE PCORNetDemographics
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'OMOPdemographics') AND type in (N'P', N'PC')) DROP PROCEDURE OMOPdemographics
go

create procedure PCORNetDemographics as
create procedure OMOPdemographics as

DECLARE @sqltext NVARCHAR(4000);
DECLARE @batchid numeric
declare getsql cursor local for
--1 -- S,R,NH
select 'insert into PMNDEMOGRAPHIC(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HISPANIC, RACE) '+
select 'insert into person(gender_source_value,person_id,year_of_birth,time_of_birth,gender_concept_id,ethnicity_source_value,race_source_value) '+ --person(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HISPANIC, RACE)
' select ''1'',patient_num, '+
' birth_date, '+
' substring(convert(varchar,birth_date,20),12,5), '+
''''+sex.pcori_basecode+''','+
''''+sex.omop_basecode+''','+
'''NI'','+
''''+race.pcori_basecode+''''+
''''+race.omop_basecode+''''+
' from i2b2patient p '+
' where lower(p.sex_cd) in ('+lower(sex.c_dimcode)+') '+
' and lower(p.race_cd) in ('+lower(race.c_dimcode)+') '+
Expand All @@ -235,13 +234,13 @@ declare getsql cursor local for
and sex.c_fullname like '\PCORI\DEMOGRAPHIC\SEX%'
and sex.c_visualattributes like 'L%'
union -- A - S,R,H
select 'insert into PMNDEMOGRAPHIC(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HISPANIC, RACE) '+
select 'insert into person(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HISPANIC, RACE) '+
' select ''A'',patient_num, '+
' birth_date, '+
' substring(convert(varchar,birth_date,20),12,5), '+
''''+sex.pcori_basecode+''','+
''''+hisp.pcori_basecode+''','+
''''+race.pcori_basecode+''''+
''''+sex.omop_basecode+''','+
''''+hisp.omop_basecode+''','+
''''+race.omop_basecode+''''+
' from i2b2patient p '+
' where lower(p.sex_cd) in ('+lower(sex.c_dimcode)+') '+
' and lower(p.race_cd) in ('+lower(race.c_dimcode)+') '+
Expand All @@ -255,11 +254,11 @@ select 'insert into PMNDEMOGRAPHIC(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HI
and sex.c_fullname like '\PCORI\DEMOGRAPHIC\SEX%'
and sex.c_visualattributes like 'L%'
union --2 S, nR, nH
select 'insert into PMNDEMOGRAPHIC(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HISPANIC, RACE) '+
select 'insert into person(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HISPANIC, RACE) '+
' select ''2'',patient_num, '+
' birth_date, '+
' substring(convert(varchar,birth_date,20),12,5), '+
''''+sex.pcori_basecode+''','+
''''+sex.omop_basecode+''','+
'''NI'','+
'''NI'''+
' from i2b2patient p '+
Expand All @@ -270,13 +269,13 @@ union --2 S, nR, nH
where sex.c_fullname like '\PCORI\DEMOGRAPHIC\SEX%'
and sex.c_visualattributes like 'L%'
union --3 -- nS,R, NH
select 'insert into PMNDEMOGRAPHIC(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HISPANIC, RACE) '+
select 'insert into person(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HISPANIC, RACE) '+
' select ''3'',patient_num, '+
' birth_date, '+
' substring(convert(varchar,birth_date,20),12,5), '+
'''NI'','+
'''NI'','+
''''+race.pcori_basecode+''''+
''''+race.omop_basecode+''''+
' from i2b2patient p '+
' where lower(isnull(p.sex_cd,''xx'')) not in (select lower(code) from omop_codelist where codetype=''SEX'') '+
' and lower(p.race_cd) in ('+lower(race.c_dimcode)+') '+
Expand All @@ -285,13 +284,13 @@ union --3 -- nS,R, NH
where race.c_fullname like '\PCORI\DEMOGRAPHIC\RACE%'
and race.c_visualattributes like 'L%'
union --B -- nS,R, H
select 'insert into PMNDEMOGRAPHIC(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HISPANIC, RACE) '+
select 'insert into person(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HISPANIC, RACE) '+
' select ''B'',patient_num, '+
' birth_date, '+
' substring(convert(varchar,birth_date,20),12,5), '+
'''NI'','+
''''+hisp.pcori_basecode+''','+
''''+race.pcori_basecode+''''+
''''+hisp.omop_basecode+''','+
''''+race.omop_basecode+''''+
' from i2b2patient p '+
' where lower(isnull(p.sex_cd,''xx'')) not in (select lower(code) from omop_codelist where codetype=''SEX'') '+
' and lower(p.race_cd) in ('+lower(race.c_dimcode)+') '+
Expand All @@ -303,11 +302,11 @@ union --B -- nS,R, H
and hisp.c_fullname like '\PCORI\DEMOGRAPHIC\HISPANIC\Y%'
and hisp.c_visualattributes like 'L%'
union --4 -- S, NR, H
select 'insert into PMNDEMOGRAPHIC(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HISPANIC, RACE) '+
select 'insert into person(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HISPANIC, RACE) '+
' select ''4'',patient_num, '+
' birth_date, '+
' substring(convert(varchar,birth_date,20),12,5), '+
''''+sex.pcori_basecode+''','+
''''+sex.omop_basecode+''','+
'''Y'','+
'''NI'''+
' from i2b2patient p '+
Expand All @@ -318,7 +317,7 @@ union --4 -- S, NR, H
where sex.c_fullname like '\PCORI\DEMOGRAPHIC\SEX%'
and sex.c_visualattributes like 'L%'
union --5 -- NS, NR, H
select 'insert into PMNDEMOGRAPHIC(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HISPANIC, RACE) '+
select 'insert into person(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HISPANIC, RACE) '+
' select ''5'',patient_num, '+
' birth_date, '+
' substring(convert(varchar,birth_date,20),12,5), '+
Expand All @@ -330,7 +329,7 @@ union --5 -- NS, NR, H
' and lower(isnull(p.race_cd,''xx'')) not in (select lower(code) from omop_codelist where codetype=''RACE'') '+
' and lower(isnull(p.race_cd,''xx'')) in (select lower(code) from omop_codelist where codetype=''HISPANIC'')'
union --6 -- NS, NR, nH
select 'insert into PMNDEMOGRAPHIC(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HISPANIC, RACE) '+
select 'insert into person(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HISPANIC, RACE) '+
' select ''6'',patient_num, '+
' birth_date, '+
' substring(convert(varchar,birth_date,20),12,5), '+
Expand Down Expand Up @@ -380,11 +379,11 @@ go
-- TODO: This version does not translate codes in the visit_dimension columns, except inout_cd (enc_type)
-- Bugfix: Multiple DRGs in one encounter no longer causes error
----------------------------------------------------------------------------------------------------------------------------------------
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'PCORNetEncounter') AND type in (N'P', N'PC'))
DROP PROCEDURE PCORNetEncounter
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'OMOPencounter') AND type in (N'P', N'PC'))
DROP PROCEDURE OMOPencounter
GO

create procedure PCORNetEncounter as
create procedure OMOPencounter as

DECLARE @sqltext NVARCHAR(4000);
begin
Expand Down Expand Up @@ -427,10 +426,10 @@ go
-- now ignores facts with a condition modifier
-- 6.1. optimized for temp tables
----------------------------------------------------------------------------------------------------------------------------------------
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'PCORNetDiagnosis') AND type in (N'P', N'PC')) DROP PROCEDURE PCORNetDiagnosis
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'OMOPdiagnosis') AND type in (N'P', N'PC')) DROP PROCEDURE OMOPdiagnosis
go

create procedure PCORNetDiagnosis as
create procedure OMOPdiagnosis as
declare @sqltext nvarchar(4000)
begin

Expand Down Expand Up @@ -486,10 +485,10 @@ go
-- Notes: in the current version condition_status is imputed from resolve_date (which is derived from end_date)
-- and onset_date is not supported
----------------------------------------------------------------------------------------------------------------------------------------
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'PCORNetCondition') AND type in (N'P', N'PC')) DROP PROCEDURE PCORNetCondition
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'OMOPcondition') AND type in (N'P', N'PC')) DROP PROCEDURE OMOPcondition
go

create procedure PCORNetCondition as
create procedure OMOPcondition as
declare @sqltext nvarchar(4000)
begin

Expand Down Expand Up @@ -529,10 +528,10 @@ go
-- 0.6.4 - NI in px_source, fixed encounter start vs. fact start
-- 0.6.5 - Somehow was referencing the wrong column name from encounter table for admit date
----------------------------------------------------------------------------------------------------------------------------------------
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'PCORNetProcedure') AND type in (N'P', N'PC')) DROP PROCEDURE PCORNetProcedure
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'OMOPprocedure') AND type in (N'P', N'PC')) DROP PROCEDURE OMOPprocedure
go

create procedure PCORNetProcedure as
create procedure OMOPprocedure as

begin
insert into pmnprocedure(
Expand All @@ -559,11 +558,11 @@ go
-- v0.6.4 now correctly merges modifiers
-- TODO: This does not do unit conversions.

IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'PCORNetVital') AND type in (N'P', N'PC'))
DROP PROCEDURE PCORNetVital
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'OMOPvital') AND type in (N'P', N'PC'))
DROP PROCEDURE OMOPvital
GO

create procedure PCORNetVital as
create procedure OMOPvital as
begin
-- jgk: I took out admit_date - it doesn't appear in the scheme. Now in SQLServer format - date, substring, name on inner select, no nested with. Added modifiers and now use only pathnames, not codes.
insert into pmnVITAL(patid, encounterid, measure_date, measure_time,vital_source,ht, wt, diastolic, systolic, original_bmi, bp_position,smoking,tobacco,tobacco_type)
Expand Down Expand Up @@ -660,11 +659,11 @@ go
-- Written by Jeff Klann, PhD
-- v6 Updated 9/30/15 - now supports loyalty cohort (be sure view at the top of the script is updated)
-- Bugfix 1/11/16 - BASIS should be called ENR_BASIS
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'PCORNetEnroll') AND type in (N'P', N'PC'))
DROP PROCEDURE PCORNetEnroll
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'OMOPenroll') AND type in (N'P', N'PC'))
DROP PROCEDURE OMOPenroll
GO

create procedure PCORNetEnroll as
create procedure OMOPenroll as
begin

INSERT INTO [pmnENROLLMENT]([PATID], [ENR_START_DATE], [ENR_END_DATE], [CHART], [ENR_BASIS])
Expand All @@ -687,9 +686,9 @@ go
-- 12/9/15 - Optimized to use temp tables
-- Written by Jeff Klann, PhD and Arturo Torres

IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'PCORNetLabResultCM') AND type in (N'P', N'PC')) DROP PROCEDURE PCORNetLabResultCM;
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'OMOPlabResultCM') AND type in (N'P', N'PC')) DROP PROCEDURE OMOPlabResultCM;
GO
create procedure PCORNetLabResultCM as
create procedure OMOPlabResultCM as
begin

-- Optimized to use temp tables; also, removed "distinct" - much faster and seems unnecessary - 12/9/15
Expand Down Expand Up @@ -812,9 +811,9 @@ GO
----------------------------------------------------------------------------------------------------------------------------------------
-- BUGFIX 04/22/16: Needed leading zeros on numbers

IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'PCORNetHarvest') AND type in (N'P', N'PC')) DROP PROCEDURE PCORNetHarvest;
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'OMOPharvest') AND type in (N'P', N'PC')) DROP PROCEDURE OMOPharvest;
GO
create procedure PCORNetHarvest as
create procedure OMOPharvest as
begin

INSERT INTO [dbo].[pmnharvest]([NETWORKID], [NETWORK_NAME], [DATAMARTID], [DATAMART_NAME], [DATAMART_PLATFORM], [CDM_VERSION], [DATAMART_CLAIMS], [DATAMART_EHR], [BIRTH_DATE_MGMT], [ENR_START_DATE_MGMT], [ENR_END_DATE_MGMT], [ADMIT_DATE_MGMT], [DISCHARGE_DATE_MGMT], [PX_DATE_MGMT], [RX_ORDER_DATE_MGMT], [RX_START_DATE_MGMT], [RX_END_DATE_MGMT], [DISPENSE_DATE_MGMT], [LAB_ORDER_DATE_MGMT], [SPECIMEN_DATE_MGMT], [RESULT_DATE_MGMT], [MEASURE_DATE_MGMT], [ONSET_DATE_MGMT], [REPORT_DATE_MGMT], [RESOLVE_DATE_MGMT], [PRO_DATE_MGMT], [REFRESH_DEMOGRAPHIC_DATE], [REFRESH_ENROLLMENT_DATE], [REFRESH_ENCOUNTER_DATE], [REFRESH_DIAGNOSIS_DATE], [REFRESH_PROCEDURES_DATE], [REFRESH_VITAL_DATE], [REFRESH_DISPENSING_DATE], [REFRESH_LAB_RESULT_CM_DATE], [REFRESH_CONDITION_DATE], [REFRESH_PRO_CM_DATE], [REFRESH_PRESCRIBING_DATE], [REFRESH_PCORNET_TRIAL_DATE], [REFRESH_DEATH_DATE], [REFRESH_DEATH_CAUSE_DATE])
Expand All @@ -830,9 +829,9 @@ GO
-- You must have run the meds_schemachange proc to create the PCORI_NDC and PCORI_CUI columns
-- TODO: The first encounter inner join seems to slow things down

IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'PCORNetPrescribing') AND type in (N'P', N'PC')) DROP PROCEDURE PCORNetPrescribing;
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'OMOPprescribing') AND type in (N'P', N'PC')) DROP PROCEDURE OMOPprescribing;
GO
create procedure PCORNetPrescribing as
create procedure OMOPprescribing as
begin

-- Griffin's optimization: use temp tables rather than left joining directly - 12/9/15
Expand Down Expand Up @@ -946,9 +945,9 @@ GO
----------------------------------------------------------------------------------------------------------------------------------------
-- You must have run the meds_schemachange proc to create the PCORI_NDC and PCORI_CUI columns

IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'PCORNetDispensing') AND type in (N'P', N'PC')) DROP PROCEDURE PCORNetDispensing;
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'OMOPdispensing') AND type in (N'P', N'PC')) DROP PROCEDURE OMOPdispensing;
GO
create procedure PCORNetDispensing as
create procedure OMOPdispensing as
begin

-- Griffin's optimizations - 12/9/15
Expand Down Expand Up @@ -1010,11 +1009,11 @@ GO
-- 10. Death - v1 by Jeff Klann, PhD
-- Simple transform only pulls death date from patient dimension, does not rely on an ontology
----------------------------------------------------------------------------------------------------------------------------------------
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'PCORNetDeath') AND type in (N'P', N'PC')) DROP PROCEDURE PCORNetDeath
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'OMOPdeath') AND type in (N'P', N'PC')) DROP PROCEDURE OMOPdeath
go


create procedure PCORNetDeath as
create procedure OMOPdeath as

begin
insert into pmndeath(
Expand All @@ -1036,10 +1035,10 @@ go
----------------------------------------------------------------------------------------------------------------------------------------
-- 10. clear Program - includes all tables
----------------------------------------------------------------------------------------------------------------------------------------
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'pcornetclear') AND type in (N'P', N'PC')) DROP PROCEDURE pcornetclear
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'OMOPclear') AND type in (N'P', N'PC')) DROP PROCEDURE OMOPclear
go

create procedure pcornetclear
create procedure OMOPclear
as
begin

Expand All @@ -1062,27 +1061,27 @@ go
----------------------------------------------------------------------------------------------------------------------------------------
-- 11. Load Program
----------------------------------------------------------------------------------------------------------------------------------------
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'pcornetloader') AND type in (N'P', N'PC')) DROP PROCEDURE pcornetloader
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'OMOPloader') AND type in (N'P', N'PC')) DROP PROCEDURE OMOPloader
go

create procedure pcornetloader
create procedure OMOPloader
as
begin

exec pcornetclear
exec PCORNetHarvest
exec PCORNetDemographics
exec PCORNetEncounter
exec PCORNetDiagnosis
exec PCORNetCondition
exec PCORNetProcedure
exec PCORNetVital
exec PCORNetEnroll
exec PCORNetLabResultCM
exec PCORNetPrescribing
exec PCORNetDispensing
exec PCORNetDeath
exec pcornetreport
exec OMOPclear
exec OMOPharvest
exec OMOPdemographics
exec OMOPencounter
exec OMOPdiagnosis
exec OMOPcondition
exec OMOPprocedure
exec OMOPvital
exec OMOPenroll
exec OMOPlabResultCM
exec OMOPprescribing
exec OMOPdispensing
exec OMOPdeath
exec OMOPreport

end
go
Expand All @@ -1091,10 +1090,10 @@ go
-- 12. Report Results - Version 5.1 by Aaron Abend and Jeff Klann
-- This version is useful to check against i2b2, but consider running the more detailed annotated data dictionary tool also.
----------------------------------------------------------------------------------------------------------------------------------------
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'pcornetReport') AND type in (N'P', N'PC')) DROP PROCEDURE pcornetReport
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'OMOPreport') AND type in (N'P', N'PC')) DROP PROCEDURE OMOPreport
go

CREATE PROCEDURE [dbo].[pcornetReport]
CREATE PROCEDURE [dbo].[OMOPreport]
as
declare @i2b2vitald numeric
declare @i2b2dxd numeric
Expand Down

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