merged result_qual valueSets

National-Clinical-Cohort-Collaborative · Oct 14, 2020 · 56a0e17 · 56a0e17
1 parent 94cb4ff
commit 56a0e17
Showing 1 changed file with 38 additions and 19 deletions.
diff --git a/ETLProcess/scripts/p2o_term_xwalk.sql b/ETLProcess/scripts/p2o_term_xwalk.sql
@@ -1,19 +1,17 @@
-------------------------------------------------------------------------------------
--- PROJECT : N3C
--- CDM data source: PCORnet
--- Description: P2O_TERM_XWALK to omop concept ids
--- Reviewers : Clair Blacketer, Kristin Kostka, SMEs, Samvit, DI&H team
--- Author: Stephanie Hong
--- Edit Date: JUNE 7, 2020
--- DDL and valueSet mapping for Table P2O_TERM_XWALK
--- Edit History:
--- Date:     Initials:  Edit History:
--- 6/6/2020  SHONG      Initial version
--- 6/26/2020 shong      Added Procedure and Diagnosis terms using updated valueSet mapping document dated 6/23/20 update
--- 8/30/2020 shong      update for v1
--- 9/28/2020 shong 		updated dx_origin billing target_concept_id to 32821. 
--------------------------------------------------------------------------------------
-
+--------------------------------------------------------
+project : N3C DI&H
+Author : Stephanie Hong
+project : N3C DI&H
+Initial valueSet map from Samvit : 5/16/2020
+Reviewers: Kristin Kostka, Davera Gabriel, Emily Pfaff, Clair Blacketer
+Authors: 
+Stephanie Hong, Sandeep Naredla, Richard Zhu, Tanner Zhang
+File: P2O_TERM_XWALK - Merged list from oracle PROD version ported to Palantir
+Edit History: 
+Date: 	Intials: 	Description:
+09/20/2020  SHONG 	    Merged valueSet values for PCORnet CDM pull from Oracle to port to Palantir pipleline.
+10/14/2020  SHONG merge result_qual valueSets and its target_concept_ids. 
+----------------------------------------------------------------------------------------------
 
   CREATE TABLE "JHU_SHONG"."P2O_TERM_XWALK" 
    (	"CDM_SOURCE" VARCHAR2(20 BYTE), 
@@ -28,9 +26,8 @@
 	"TARGET_CONCEPT_CLASS_ID" VARCHAR2(20 BYTE), 
 	"TARGET_STANDARD_CONCEPT" VARCHAR2(1 BYTE), 
 	"TARGET_CONCEPT_CODE" VARCHAR2(50 BYTE)
-   );
-
-
+   ) ;
+
 Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','PRESCRIBING','RX_DOSE_ORDERED_UNIT','ng/(8.h)','nanogram per 8 hour',44777624,'(unit) nanogram per 24 hours (concept_id = 44777624)','Unit','UCUM','Unit','S','ng/(24.h)');
 Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','PRESCRIBING','RX_DOSE_ORDERED_UNIT','ng/h','nanogram per hour',44777594,'(unit) gram per hour (concept_id = 44777594)','Unit','UCUM','Unit','S','g/h');
 Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','PRESCRIBING','RX_DOSE_ORDERED_UNIT','ng/kg/(8.h)','nanogram per kilogram per 8 hour',9602,'(unit) nanogram per kilogram (concept_id = 9602)','Unit','UCUM','Unit','S','ng/kg');
@@ -1477,6 +1474,28 @@ Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC
 Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','ENCOUNTER','ADMITTING_SOURCE','UN','Unknown',0,'(other_ni_unk) Unknown (concept_id = 45877986)','Meas Value','LOINC','Answer','S','LA4489-6');
 Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','ENCOUNTER','ADMITTING_SOURCE','AF','Adult  Foster  Home',8882,'(visit) Adult Living Care Facility (concept_id = 8882)','Visit','CMS Place of Service','Visit','S','35');
 Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','ENCOUNTER','ADMITTING_SOURCE','IH','Intra-hospital',0,'IH=Intra-hospital','gap','-','-','-','-');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','POSITIVE','Positive',45884084,'Positive Measurement Value','Meas Value','LOINC','Answer','S','LA6576-8');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','NEGATIVE','Negative',45878583,'Negative Measurement Value','Meas Value','LOINC','Answer','S','LA6577-6');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','BORDERLINE','Borderline',45880922,'Borderline Measurement Value','Meas Value','LOINC','Answer','S','LA4259-3');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','ELEVATED','Elevated',4328749,'Elevated Measurement Value','Meas Value','LOINC','Answer','S','LA4677-6');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','ABNORMAL','Abnormal',45878745,'Abnormal Measurement Value','Meas Value','LOINC','Answer','S','LA12748-2');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','HIGH','High',45876384,'High Measurement Value','Meas Value','LOINC','Answer','S','LA9193-9');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','LOW','Low',45881666,'Low','Meas Value','LOINC','Answer','S','LA9194-7');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','NORMAL','Normal',45884153,'Normal','Meas Value','LOINC','Answer','S','LA6626-1');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','UNDETECTABLE','Undetectable',45878583,'Undetectable','Meas Value','LOINC','Answer','S','LA10607-2');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','UNDETERMINED','Undetermined',45880649,'Undetermined','Meas Value','LOINC','Answer','S','LA14100-4');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','POS','Pos',45884084,'Positive Measurement Value','Meas Value','LOINC','Answer','S','LA6576-8');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','NEG','Neg',45878583,'Negative Measurement Value','Meas Value','LOINC','Answer','S','LA6577-6');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','PRESUMPTIVE POSITIVE','Presumptive Positive',45884084,'Positive Measurement Value','Meas Value','LOINC','Answer','S','LA6576-8');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','PRESUMPTIVE NEGATIVE','Presumptive Negative',45878583,'Negative Measurement Value','Meas Value','LOINC','Answer','S','LA6577-6');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','DETECTED','Detected',45884084,'Positve Measurement Value','Meas Value','LOINC','Answer','S','LA6576-8');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','NOT DETECTED','Not Detected',45878583,'Not Detected Measurement Value','Meas Value','LOINC','Answer','S','LA6577-6');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','INCONCLUSIVE','Inconclusive',45877990,'Inconclusive','Meas Value','LOINC','Answer','S','LA9663-1');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','REACTIVE','Reactive',45884084,'Reactive','Meas Value','LOINC','Answer','S','LA15255-5');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','PENDING','Pending',1177297,'Pending','Meas Value','LOINC','Answer','S','LA29487-8');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','NI','NI',0,'NI OT UN','Meas Value','LOINC','Answer','S','0');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','OT','OT',0,'NI OT UN','Meas Value','LOINC','Answer','S','0');
+Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','LAB_RESULT_CM','RESULT_QUAL','UN','UN',0,'NI OT UN','Meas Value','LOINC','Answer','S','0');
 Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','DEMOGRAPHIC','PAT_PREF_LANGUAGE_SPOKEN','EKA','Ekajuk',0,'Gap','-','-','-','-','-');
 Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','DEMOGRAPHIC','PAT_PREF_LANGUAGE_SPOKEN','EUS','Basque',44784498,'(obs_spoken_language_4152283) Main spoken language Basque (concept_id = 44784498)','Observation','SNOMED','Clinical Finding','S','698654008');
 Insert into JHU_SHONG.P2O_TERM_XWALK (CDM_SOURCE,CDM_TBL,CDM_TBL_COLUMN_NAME,SRC_CODE,SRC_CD_DESCRIPTION,TARGET_CONCEPT_ID,TARGET_CONCEPT_NAME,TARGET_DOMAIN_ID,TARGET_VOCABULARY_ID,TARGET_CONCEPT_CLASS_ID,TARGET_STANDARD_CONCEPT,TARGET_CONCEPT_CODE) values ('PCORnet','DEMOGRAPHIC','PAT_PREF_LANGUAGE_SPOKEN','EWE','Ewe',46285406,'(obs_spoken_language_4152283) Main spoken language Ewe (concept_id = 46285406)','Observation','SNOMED','Clinical Finding','S','9.71E+14');