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ICD10PCS

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manual work
manual work
 
 
snomed_hierarchy
snomed_hierarchy
 
 
create_source_tables.sql
create_source_tables.sql
 
 
load_stage.sql
load_stage.sql
 
 
readme.md
readme.md
 
 

readme.md

Update of ICD10PCS

Prerequisites:

  • Schema DevV5 with copies of tables concept, concept_relationship and concept_synonym from ProdV5, fully indexed.
  • Working directory ICD10PCS.

  1. Run create_source_tables.sql

  2. Download the latest file from https://www.cms.gov/medicare/coding-billing/icd-10-codes, file name YYYY-ICD-10-PCS-Order-File.zip (e.g. 2019-ICD-10-PCS-Order-File.zip) listed as "ICD-10-PCS Order File (Long and Abbreviated Titles)"

  3. Exctract icd10pcs_order_YYYY.txt and rename to icd10pcs.txt

  4. Run in devv5 (with fresh vocabulary date and version): SELECT sources.load_input_tables('ICD10PCS',TO_DATE('20180101','YYYYMMDD'),'ICD10PCS 20180101'); (pVocabularyDate=YYYY-1)

  5. Run FastRecreateSchema:

   SELECT devv5.FastRecreateSchema(main_schema_name=>'devv5', include_concept_ancestor=> true, include_deprecated_rels=> true, include_synonyms=> true);
  1. Run load_stage.sql.
  2. Run generic_update:
 DO $_$
 BEGIN
     PERFORM devv5.GenericUpdate();
 END $_$;
  1. Run basic tables check (should retrieve NULL):
   SELECT * FROM qa_tests.get_checks();
  1. Perform manual work described in the readme.md file in the 'manual_work' folder.

Repeat steps 5-10.

  1. Run scripts to get summary, and interpret the results: 
    SELECT DISTINCT * FROM qa_tests.get_summary('concept','devv5');
SELECT DISTINCT * FROM qa_tests.get_summary('concept_relationship','devv5');
  2. Run scripts to collect statistics, and interpret the results: 
    SELECT DISTINCT * FROM qa_tests.get_domain_changes('devv5');
SELECT DISTINCT * FROM qa_tests.get_newly_concepts('devv5');
SELECT DISTINCT * FROM qa_tests.get_standard_concept_changes('devv5');
SELECT DISTINCT * FROM qa_tests.get_newly_concepts_standard_concept_status('devv5');
SELECT DISTINCT * FROM qa_tests.get_changes_concept_mapping('devv5');
  3. Run manual_checks_after_generic.sql, and interpret the results.
  4. Run project_specific_manual_checks_after_generic.sql, and interpret the results.
  5. If no problems, enjoy!

Directory snomed_hierarchy contains unrefined version of tools to build automated relationship to SNOMED concepts currently stored in concept_relationship_manual. These scripts are early version and require a thorough refactoring before being reused.

Attribute mappings for SNOMED are available under: https://drive.google.com/drive/u/2/folders/17PPiksUxXYNQ6batNduHpGxO-CDC1ZqV