config3.yaml

concept_sets:
  version: "v1.0.4"
  omop:
    vocabulary_id: "ACMC_Example"
    vocabulary_name: "ACMC example phenotype"
    vocabulary_reference: "https://www.it-innovation.soton.ac.uk/projects/meldb/concept-processing/example"
  concept_set:
    - concept_set_name: "CVD_EVENTS"
      metadata: {}
    - concept_set_name: "DID_NOT_ATTEND"
      metadata: {}
    - concept_set_name: "HYPERTENSION"
      metadata: {}     
    - concept_set_name: "DEPRESSION"
      metadata: {}        

codes:
  - folder: "clinical-codes-org"
    description: "Downloaded 16/11/23"
    files:
      - file: "Cardiovascular events (ICD10)/res52-cardiovascular-events-icd10.csv"
        columns:
          icd10: "code"
          metadata: []
        concept_set:
          - name: "CVD_EVENTS"
      - file: "Non-attendance codes/res201-did-not-attend-appointment.csv"
        columns:
          read2: "code"
          metadata: []
        concept_set:
          - name: "DID_NOT_ATTEND"
  - folder: hanlon
    description: Hanlon Paper Code Lists
    files:
      - file: Read_codes_for_diagnoses.csv
        columns:
          read2: Read Code      
        actions:
          divide_col: MMCode
        concept_set:
          - name: HYPERTENSION
            category: "2"
          - name: DEPRESSION
            category: "3"