- 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 must be loaded first
- Working directory dev_icd10
- Download the latest ICD-10 version (e.g. ICD-10 2016 version) on the WHO Website
- Unzip the file icdClaMLYYYYens.xml and rename to icdClaML.xml
- Run in devv5 (with the fresh vocabulary date and version):
SELECT sources.load_input_tables('ICD10',TO_DATE('20161201','YYYYMMDD'),'2016 Release');
- Run FULL FastRecreate:
SELECT devv5.FastRecreateSchema(main_schema_name=>'devv5', include_concept_ancestor=>false, include_deprecated_rels=>true, include_synonyms=>true);
- As described in the "manual_work" folder, upload concept_manual.csv and concept_relationship_manual.csv into eponymous tables, which exist by default in the dev schema after the FastRecreate. If you already have manual staging tables, obligatory create backups of them (e.g. concept_relationship_manual_backup_ddmmyy, concept_manual_backup_ddmmyy)
- Run load_stage.sql for the first time to define problems in mapping
- Perform manual work described in manual_work folder
- Run load_stage.sql for the second time to refresh ICD10
- Run generic_update:
SELECT devv5.GenericUpdate();
- Run manual_checks_after_generic.sql
- If no problems, enjoy!