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pushing Kevin Embree's update to the transform
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@matthewjoss
matthewjoss committed Feb 10, 2017
1 parent 1b0e512 commit 629067a
Showing 1 changed file with 59 additions and 33 deletions.
92 changes: 59 additions & 33 deletions MSSQL/OMOPLoader.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -181,6 +181,13 @@ Alter Table measurement
Add measurement_id Int Identity(1, 1)
Go

Alter Table drug_exposure Drop Column drug_exposure_id
Go

Alter Table drug_exposure
Add drug_exposure_id Int Identity(1, 1)
Go


----------------------------------------------------------------------------------------------------------------------------------------
-- Prep-to-transform code
Expand Down Expand Up @@ -835,75 +842,94 @@ 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'OMOPprescribing') AND type in (N'P', N'PC')) DROP PROCEDURE OMOPprescribing;
IF EXISTS (SELECT * FROM sys.objects WHERE object_id = OBJECT_ID(N'OMOPdrug_exposure') AND type in (N'P', N'PC')) DROP PROCEDURE OMOPdrug_exposure;
GO
create procedure OMOPprescribing as
create procedure OMOPdrug_exposure as
begin
select patient_num, encounter_num, factline.provider_id, concept_cd, start_date, pxsource.pcori_basecode dxsource, pxsource.c_fullname
into #procedurefact
from i2b2fact factline
inner join visit_occurrence enc on enc.person_id = factline.patient_num and enc.visit_occurrence_id = factline.encounter_Num
inner join PCORNET_PROC pxsource on factline.concept_cd =pxsource.c_basecode
where pxsource.c_fullname like '\PCORI\PROCEDURE\%'


-- Griffin's optimization: use temp tables rather than left joining directly - 12/9/15
select pcori_basecode,c_fullname,instance_num,start_date,provider_id,concept_cd,encounter_num,modifier_cd
select pcori_basecode,c_fullname,instance_num,start_date,basis.provider_id,concept_cd,encounter_num,modifier_cd
into #basis
from i2b2fact basis
inner join pmnENCOUNTER enc on enc.patid = basis.patient_num and enc.encounterid = basis.encounter_Num
inner join visit_occurrence enc on enc.person_id = basis.patient_num and enc.visit_occurrence_id = basis.encounter_Num
join pcornet_med basiscode
on basis.modifier_cd = basiscode.c_basecode
and basiscode.c_fullname like '\PCORI_MOD\RX_BASIS\%'

select pcori_basecode,instance_num,start_date,provider_id,concept_cd,encounter_num,modifier_cd
select pcori_basecode,instance_num,start_date,freq.provider_id,concept_cd,encounter_num,modifier_cd
into #freq
from i2b2fact freq
inner join pmnENCOUNTER enc on enc.patid = freq.patient_num and enc.encounterid = freq.encounter_Num
inner join visit_occurrence enc on enc.person_id = freq.patient_num and enc.visit_occurrence_id = freq.encounter_Num
join pcornet_med freqcode
on freq.modifier_cd = freqcode.c_basecode
and freqcode.c_fullname like '\PCORI_MOD\RX_FREQUENCY\%'

select nval_num,instance_num,start_date,provider_id,concept_cd,encounter_num,modifier_cd
select nval_num,instance_num,start_date,quantity.provider_id,concept_cd,encounter_num,modifier_cd
into #quantity
from i2b2fact quantity
inner join pmnENCOUNTER enc on enc.patid = quantity.patient_num and enc.encounterid = quantity.encounter_Num
inner join visit_occurrence enc on enc.person_id = quantity.patient_num and enc.visit_occurrence_id = quantity.encounter_Num
join pcornet_med quantitycode
on quantity.modifier_cd = quantitycode.c_basecode
and quantitycode.c_fullname like '\PCORI_MOD\RX_QUANTITY\'

select nval_num,instance_num,start_date,provider_id,concept_cd,encounter_num,modifier_cd
select nval_num,instance_num,start_date,refills.provider_id,concept_cd,encounter_num,modifier_cd
into #refills
from i2b2fact refills
inner join pmnENCOUNTER enc on enc.patid = refills.patient_num and enc.encounterid = refills.encounter_Num
inner join visit_occurrence enc on enc.person_id = refills.patient_num and enc.visit_occurrence_id = refills.encounter_Num
join pcornet_med refillscode
on refills.modifier_cd = refillscode.c_basecode
and refillscode.c_fullname like '\PCORI_MOD\RX_REFILLS\'

select nval_num,instance_num,start_date,provider_id,concept_cd,encounter_num,modifier_cd
select nval_num,instance_num,start_date,supply.provider_id,concept_cd,encounter_num,modifier_cd
into #supply
from i2b2fact supply
inner join pmnENCOUNTER enc on enc.patid = supply.patient_num and enc.encounterid = supply.encounter_Num
inner join visit_occurrence enc on enc.person_id = supply.patient_num and enc.visit_occurrence_id = supply.encounter_Num
join pcornet_med supplycode
on supply.modifier_cd = supplycode.c_basecode
and supplycode.c_fullname like '\PCORI_MOD\RX_DAYS_SUPPLY\'

-- insert data with outer joins to ensure all records are included even if some data elements are missing
insert into pmnprescribing (
PATID
,encounterid
,RX_PROVIDERID
,RX_ORDER_DATE -- using start_date from i2b2
,RX_ORDER_TIME -- using time start_date from i2b2
,RX_START_DATE
,RX_END_DATE
,RXNORM_CUI --using pcornet_med pcori_cui - new column!
,RX_QUANTITY ---- modifier nval_num
,RX_REFILLS -- modifier nval_num
,RX_DAYS_SUPPLY -- modifier nval_num
,RX_FREQUENCY --modifier with basecode lookup
,RX_BASIS --modifier with basecode lookup
-- ,RAW_RX_MED_NAME, --not filling these right now
-- ,RAW_RX_FREQUENCY,
-- ,RAW_RXNORM_CUI
insert into drug_exposure(
-- drug_exposure_id -------- --------> set to identity column (not shown here)----------------------> Done
person_id -----------------------> patient_num unique identifier for the patient in i2b2--------> Done
, drug_concept_id -------------> i2o_mapping concept_id---------------------------------------> Done
, drug_exposure_start_date --------> i2b2fact visit_start_date ----------------------------------> Done
, drug_exposure_start_datetime -----> i2b2fact visit_start_date ---------------------------------> Done
, drug_exposure_end_date -----------> i2b2fact end_end ------------------------------------> Done
, drug_exposure_end_datetime -----------> i2b2fact end_end --------------------------------> Done
, drug_type_concept_id -------> physician admistered, prescription, Inpatient... how do we know the difference?----This is a modifier called event \PCORI_MOD\RX_BASIS\DI and RX_BASIS\PR----> NOT DONE
, stop_reason ------------------> Reason the drug was stoppped varchar(20) ... Do we have this?---> NO
, refills --------------------------> from ontology \PCORI_MOD\RX_REFILLS\ ----------------> Done
, quantity --------------------------> from ontology \PCORI_MOD\RX_QUANTITY ----------------> Done
, days_supply --------------------------> from ontology \PCORI_MOD\RX_DAYS_SUPPLY ----------> Done
, sig----------------------------> The directions "signetur" on the Drug prescription as recorded in the original prescription or dispensing record -- Passing the frequency---> Done
, route_concept_id ---------------> routes of administrating medication oral, intravenous, etc... Need a mapping ---------------------------> NOT DONE
, effective_drug_dose ------------> Numerical Value of Drug dose for this Drug_Exposure... Do we have this? --> No
, dose_unit_concept_id -----------> UCUM Codes concpet c where c.vocabulary_id = 'UCUM and c.standard_concept='S' and c.domain_id='Unit'----> NOT DONE
, lot_number ----------------------> varchar... do we have this value?------------------------> No
, provider_id ---------------------> (Set to 0 for Data Sprint 2)-----------------------------> Done
, visit_occurrence_id -----------------> observation_fact.encounter_num i2b2 id for the encounter (visit)-> Done
, drug_source_value ----------> PCORI base code from ontology preffered vocabularies RxNorm, NDC, CVX, or the name, do we have this? ---> Use the base_code which NDC or RXNorm ---> Done
, drug_source_concept_id ----> OMOP source code from ontology do we have this mapping?-------> NOT DONE
, route_source_value ----------> Varchar ....Do we have this?-------yes-----------------------> NOT DONE
, dose_unit_source_value ----------> Varchar .....Do we have this?--yes-----------------------> NOT DONE
)
select distinct m.patient_num, m.Encounter_Num,m.provider_id, m.start_date order_date, substring(convert(varchar,m.start_date,8),1,5), m.start_date start_date, m.end_date, mo.pcori_cui
,quantity.nval_num quantity, refills.nval_num refills, supply.nval_num supply, substring(freq.pcori_basecode,charindex(':',freq.pcori_basecode)+1,2) frequency, substring(basis.pcori_basecode,charindex(':',basis.pcori_basecode)+1,2) basis
from i2b2fact m inner join pcornet_med mo on m.concept_cd = mo.c_basecode
inner join pmnENCOUNTER enc on enc.encounterid = m.encounter_Num
select distinct m.patient_num, omap.concept_id, m.start_date, cast(m.start_Date as time), m.end_date, cast(m.end_date as time), 1, null
, refills.nval_num refills, quantity.nval_num quantity, supply.nval_num supply, substring(freq.pcori_basecode,charindex(':',freq.pcori_basecode)+1,2) frequency
, null, null, null, null
, 0, m.Encounter_num, mo.C_BASECODE, null, null, null
from i2b2fact m
inner join pcornet_med mo on m.concept_cd = mo.c_basecode
inner join visit_occurrence enc on enc.person_id = m.patient_num and enc.visit_occurrence_id = m.encounter_Num
inner join i2o_mapping omap on mo.omop_sourcecode=omap.omop_sourcecode and omap.domain_id='Drug'

-- TODO: This join adds several minutes to the load - must be debugged

left join #basis basis
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