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create_source_tables.sql
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load_stage.sql
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readme.md
readme.md
 
 

readme.md

Update of CIEL

CIEL vocabulary source files can be requested from Andrew Kanter (IMO). These source files come already with mapping that is translated to OMOP relationships in the process of "load stage".

The files had to be post-processed for a couple of small formatting issues (e.g. extra TAB characters) The processed csv files can be found here: https://drive.google.com/drive/folders/15omdYTgmftnUm0TA3D498yE8aSWw-SG3?usp=sharing

Prerequisites:

  • Schema DevV5 with copies of tables concept, concept_relationship and concept_synonym from ProdV5, fully indexed.
  • RxNorm, ICD10 (WHO), NDFRT, UCUM, LOINC and SNOMED must be loaded first.
  • Working directory CIEL.
  1. Run create_source_tables.sql
  2. Import source files into source tables (in DevV5 (with fresh vocabulary date and version): SELECT sources.load_input_tables('CIEL',TO_DATE('20210312','YYYYMMDD'),'OpenMRS 2.11.0 20210312');
  3. Run load_stage.sql
  4. Run generic_update: devv5.GenericUpdate();