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ICD10 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 must be loaded first
  • Working directory dev_icd10

Sequence of actions

  1. Download the latest ICD-10 version (e.g. ICD-10 2016 version) on the WHO Website
  2. Unzip the file icdClaMLYYYYens.xml and rename to icdClaML.xml
  3. Run in devv5 (with the fresh vocabulary date and version):
SELECT sources.load_input_tables('ICD10',TO_DATE('20161201','YYYYMMDD'),'2016 Release');
  1. Run FULL FastRecreate:
SELECT devv5.FastRecreateSchema(main_schema_name=>'devv5', include_concept_ancestor=>false, include_deprecated_rels=>true, include_synonyms=>true);
  1. 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)
  2. Run load_stage.sql for the first time to define problems in mapping
  3. Perform manual work described in manual_work folder
  4. Run load_stage.sql for the second time to refresh ICD10
  5. Run generic_update:
SELECT devv5.GenericUpdate();
  1. Run manual_checks_after_generic.sql
  2. If no problems, enjoy!