CIM10 upload/update

Prerequisites

• Basic knowledge of the OMOP representation of the ICD10 vocabulary
• Schema DevV5 with copies of tables concept, concept_relationship and concept_synonym from ProdV5, fully indexed.
• SNOMED and ICD10 must be loaded first
• Working directory dev_icd10gm
• Manual tables must be filled (e.g. for translations)

Sequence of actions

1. Download the latest CIM10 version
2. Run create_source_tables.sql
3. Run in devv5 (with fresh vocabulary date and version):

SELECT sources.load_input_tables('ICD10GM',TO_DATE('20200101','YYYYMMDD'),'2020 Release');

4. Run FULL FastRecreate:

SELECT devv5.FastRecreateSchema(main_schema_name=>'devv5', include_concept_ancestor=>false, include_deprecated_rels=>true, include_synonyms=>true);

5. Run load_stage for the first time to define problems in mapping
6. Perform manual work described in manual_work folder
7. Run load_stage
8. Run generic_update:

SELECT devv5.GenericUpdate();

10. Run manual_checks_after_generic.sql
11. If no problems, enjoy!