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updated transform to conform to OMOP v5.1 spcifications
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@matthewjoss
matthewjoss committed Feb 16, 2017
1 parent 7abef91 commit 17ccd5c
Showing 1 changed file with 18 additions and 18 deletions.
36 changes: 18 additions & 18 deletions MSSQL/OMOPLoader.sql
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
----------------------------------------------------------------------------------------------------------------------------------------
----------------------------------------------------------------------------------------------------------------------------------------
-- OMOPLoader Script
-- OMOPLoader Script for OMOP v5.1
-- Contributors: Jeff Klann, PhD; Matthew Joss; Aaron Abend; Arturo Torres
-- Version now managed by changelog. Last update 12/7/16@6pm
-- NOT NEARLY FINISHED! FOR DEVELOPERS ONLY!
Expand Down Expand Up @@ -63,7 +63,7 @@ create synonym pcornet_demo for PMI..pcornet_demo
GO
create synonym pcornet_proc for PMI..pcornet_proc
GO
create synonym pcornet_vital for PMI..pcornet_vital
create synonym pcornet_vital for PMI..pcornet_vital_30
GO
create synonym pcornet_enc for PMI..pcornet_enc_15
GO
Expand Down Expand Up @@ -297,7 +297,7 @@ DECLARE @sqltext NVARCHAR(4000);
DECLARE @batchid numeric
declare getsql cursor local for
--1 -- S,R,NH
select 'insert into person(gender_source_value,race_source_value,ethnicity_source_value,person_id,year_of_birth,month_of_birth,day_of_birth,time_of_birth,gender_concept_id,ethnicity_concept_id,race_concept_id) '+ --person(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HISPANIC, RACE)
select 'insert into person(gender_source_value,race_source_value,ethnicity_source_value,person_id,year_of_birth,month_of_birth,day_of_birth,birth_datetime,gender_concept_id,ethnicity_concept_id,race_concept_id) '+ --person(raw_sex,PATID, BIRTH_DATE, BIRTH_TIME,SEX, HISPANIC, RACE)
' select p.sex_cd+'':'+sex.c_name+''',p.race_cd+'':'+race.c_name+''',p.race_cd+'':Unknown'',patient_num, '+
' year(birth_date), '+
' month(birth_date), '+
Expand All @@ -316,7 +316,7 @@ 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 person(gender_source_value,race_source_value,ethnicity_source_value,person_id,year_of_birth,month_of_birth,day_of_birth,time_of_birth,gender_concept_id,ethnicity_concept_id,race_concept_id) '+
select 'insert into person(gender_source_value,race_source_value,ethnicity_source_value,person_id,year_of_birth,month_of_birth,day_of_birth,birth_datetime,gender_concept_id,ethnicity_concept_id,race_concept_id) '+
' select p.sex_cd+'':'+sex.c_name+''',p.race_cd+'':'+race.c_name+''',p.race_cd+'':'+hisp.c_name+''',patient_num, '+ --' select p.sex_cd+'':''+sex.c_name,p.race_cd+'':''+race.c_name,p.race_cd+'':''+hisp.c_name,patient_num, '+
' year(birth_date), '+
' month(birth_date), '+
Expand All @@ -338,7 +338,7 @@ select 'insert into person(gender_source_value,race_source_value,ethnicity_sourc
and sex.c_fullname like '\PCORI\DEMOGRAPHIC\SEX%'
and sex.c_visualattributes like 'L%'
union --2 S, nR, nH
select 'insert into person(gender_source_value,race_source_value,ethnicity_source_value,person_id,year_of_birth,month_of_birth,day_of_birth,time_of_birth,gender_concept_id,ethnicity_concept_id,race_concept_id) '+
select 'insert into person(gender_source_value,race_source_value,ethnicity_source_value,person_id,year_of_birth,month_of_birth,day_of_birth,birth_datetime,gender_concept_id,ethnicity_concept_id,race_concept_id) '+
' select p.sex_cd+'':'+sex.c_name+''',p.race_cd+'':Unknown'',p.race_cd+'':Unknown'',patient_num, '+ --' select p.sex_cd,p.race_cd,p.race_cd,patient_num, '+
' year(birth_date), '+
' month(birth_date), '+
Expand All @@ -355,7 +355,7 @@ 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 person(gender_source_value,race_source_value,ethnicity_source_value,person_id,year_of_birth,month_of_birth,day_of_birth,time_of_birth,gender_concept_id,ethnicity_concept_id,race_concept_id) '+
select 'insert into person(gender_source_value,race_source_value,ethnicity_source_value,person_id,year_of_birth,month_of_birth,day_of_birth,birth_datetime,gender_concept_id,ethnicity_concept_id,race_concept_id) '+
' select p.sex_cd,p.race_cd+'':'+race.c_name+''',p.race_cd+'':Unknown'',patient_num, '+
' year(birth_date), '+
' month(birth_date), '+
Expand All @@ -372,7 +372,7 @@ 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 person(gender_source_value,race_source_value,ethnicity_source_value,person_id,year_of_birth,month_of_birth,day_of_birth,time_of_birth,gender_concept_id,ethnicity_concept_id,race_concept_id) '+
select 'insert into person(gender_source_value,race_source_value,ethnicity_source_value,person_id,year_of_birth,month_of_birth,day_of_birth,birth_datetime,gender_concept_id,ethnicity_concept_id,race_concept_id) '+
' select p.sex_cd,p.race_cd+'':'+race.c_name+''',p.race_cd+'':'+hisp.c_name+''',patient_num, '+
' year(birth_date), '+
' month(birth_date), '+
Expand All @@ -392,7 +392,7 @@ 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 person(gender_source_value,race_source_value,ethnicity_source_value,person_id,year_of_birth,month_of_birth,day_of_birth,time_of_birth,gender_concept_id,ethnicity_concept_id,race_concept_id) '+
select 'insert into person(gender_source_value,race_source_value,ethnicity_source_value,person_id,year_of_birth,month_of_birth,day_of_birth,birth_datetime,gender_concept_id,ethnicity_concept_id,race_concept_id) '+
' select p.sex_cd+'':'+sex.c_name+''',p.race_cd+'':Unknown'',p.race_cd+'':Hispanic'',patient_num, '+
' year(birth_date), '+
' month(birth_date), '+
Expand All @@ -409,7 +409,7 @@ 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 person(gender_source_value,race_source_value,ethnicity_source_value,person_id,year_of_birth,month_of_birth,day_of_birth,time_of_birth,gender_concept_id,ethnicity_concept_id,race_concept_id) '+
select 'insert into person(gender_source_value,race_source_value,ethnicity_source_value,person_id,year_of_birth,month_of_birth,day_of_birth,birth_datetime,gender_concept_id,ethnicity_concept_id,race_concept_id) '+
' select p.sex_cd,p.race_cd+'':Unknown'',p.race_cd+'':Hispanic'',patient_num, '+
' year(birth_date), '+
' month(birth_date), '+
Expand All @@ -423,7 +423,7 @@ 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 person(gender_source_value,race_source_value,ethnicity_source_value,person_id,year_of_birth,month_of_birth,day_of_birth,time_of_birth,gender_concept_id,ethnicity_concept_id,race_concept_id) '+
select 'insert into person(gender_source_value,race_source_value,ethnicity_source_value,person_id,year_of_birth,month_of_birth,day_of_birth,birth_datetime,gender_concept_id,ethnicity_concept_id,race_concept_id) '+
' select p.sex_cd,p.race_cd+'':Unknown'',p.race_cd+'':Unknown'',patient_num, '+
' year(birth_date), '+
' month(birth_date), '+
Expand Down Expand Up @@ -474,8 +474,8 @@ create procedure OMOPencounter as
DECLARE @sqltext NVARCHAR(4000);
begin

insert into visit_occurrence(person_id,visit_occurrence_id,visit_start_date,visit_start_time,
visit_end_date,visit_end_time,provider_id,
insert into visit_occurrence(person_id,visit_occurrence_id,visit_start_date,visit_start_datetime,
visit_end_date,visit_end_datetime,provider_id,
visit_concept_id ,care_site_id,visit_type_concept_id,visit_source_value)
select distinct v.patient_num, v.encounter_num,
start_Date,
Expand Down Expand Up @@ -523,13 +523,13 @@ inner join visit_occurrence enc on enc.person_id = factline.patient_num and enc.
inner join pcornet_diag dxsource on factline.modifier_cd =dxsource.c_basecode
and dxsource.c_fullname like '\PCORI_MOD\PDX\%'

insert into condition_occurrence (person_id, visit_occurrence_id, condition_start_date, provider_id, condition_concept_id, condition_type_concept_id, condition_end_date, condition_source_value, condition_source_concept_id) --pmndiagnosis (patid,encounterid, X enc_type, admit_date, providerid, dx, dx_type, dx_source, pdx)
insert into condition_occurrence (person_id, visit_occurrence_id, condition_start_date, provider_id, condition_concept_id, condition_type_concept_id, condition_end_date, condition_source_value, condition_source_concept_id, condition_start_datetime) --pmndiagnosis (patid,encounterid, X enc_type, admit_date, providerid, dx, dx_type, dx_source, pdx)
select distinct factline.patient_num, factline.encounter_num encounterid, enc.visit_start_date, enc.provider_id, --bug fix MJ 10/7/16
isnull(omap.concept_id, '0'),
CASE WHEN (sf.c_fullname like '\PCORI_MOD\CONDITION_OR_DX\DX_SOURCE\%' or sf.c_fullname is null) THEN
CASE WHEN pf.pdxsource = 'P' THEN 44786627 WHEN pf.pdxsource= 'S' THEN 44786629 ELSE '0' END
ELSE 38000245 END,
end_date, pcori_basecode, diag.omop_sourcecode
end_date, pcori_basecode, diag.omop_sourcecode, factline.start_date
from i2b2fact factline
inner join visit_occurrence enc on enc.person_id = factline.patient_num and enc.visit_occurrence_id = factline.encounter_Num
left outer join #sourcefact sf
Expand Down Expand Up @@ -585,7 +585,7 @@ where pxsource.c_fullname like '\PCORI\PROCEDURE\%'
---------------------- Old PCORI Columns----------------------------------------------------------
-- patid, encounterid, enc_type, admit_date, providerid, px, px_type, px_source,px_date)
---------------------------------------------------------------------------------------------------
insert into procedure_occurrence( person_id, procedure_concept_id, procedure_date, procedure_type_concept_id, modifier_concept_id, quantity, provider_id, visit_occurrence_id, procedure_source_value, procedure_source_concept_id, qualifier_source_value)
insert into procedure_occurrence( person_id, procedure_concept_id, procedure_date, procedure_type_concept_id, modifier_concept_id, quantity, provider_id, visit_occurrence_id, procedure_source_value, procedure_source_concept_id, qualifier_source_value, procedure_datetime)
---------------------- Old PCORI values ----------------------------------------------------------------
--enc.encounterid, fact.patient_num, enc.enc_type, enc.admit_date,
-- enc.providerid, substring(pr.pcori_basecode,charindex(':',pr.pcori_basecode)+1,11) px, substring(pr.c_fullname,18,2) pxtype, 'NI' px_source,fact.start_date
Expand All @@ -602,7 +602,7 @@ insert into procedure_occurrence( person_id, procedure_concept_id, procedure_da
-- procedure_source_value ----------> PCORI base code from ontology -------------------------------> Done
-- procuedure_source_concept_id ----> OMOP source code from ontology ------------------------------> Done
-- qualifier_source_value ----------> The source code for the qualifier as it appears in the source data. What is this?????????????
select distinct fact.patient_num, isnull(omap.concept_id, '0'), enc.visit_start_date, 0, 0, null, 0, fact.encounter_num, pproc.PCORI_BASECODE, pproc.OMOP_SOURCECODE, null
select distinct fact.patient_num, isnull(omap.concept_id, '0'), enc.visit_start_date, 0, 0, null, 0, fact.encounter_num, pproc.PCORI_BASECODE, pproc.OMOP_SOURCECODE, null, fact.start_date
from i2b2fact fact
---------------------------------------------------------
-- For every procedure there must be a corresponding visit
Expand Down Expand Up @@ -646,7 +646,7 @@ INSERT INTO dbo.[measurement]
,[visit_occurrence_id]--[ENCOUNTERID]
,[measurement_source_value]--[LAB_LOINC]
,[measurement_date]--[RESULT_DATE]
,[measurement_time]--[RESULT_TIME]
,[measurement_datetime]--[RESULT_TIME]
,[value_as_concept_id]--[RESULT_QUAL]
,[value_as_number]--[RESULT_NUM]
,[unit_source_value]--[RESULT_UNIT]
Expand Down Expand Up @@ -737,7 +737,7 @@ INSERT INTO dbo.[measurement]
--,[]--[LAB_PX]
--,[]--[LAB_PX_TYPE]
,[measurement_date]--[RESULT_DATE]
,[measurement_time]--[RESULT_TIME]
,[measurement_datetime]--[RESULT_TIME]
,[value_as_concept_id]--[RESULT_QUAL]
,[value_as_number]--[RESULT_NUM]
--,[]--[RESULT_MODIFIER]
Expand Down

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