---
  #######################
  # Project identifiers #
  #######################

  project:
    id: 3tr_ibd
    source: redcap
    ontology: ncit

  #################################
  # Beacon v2 Models: individuals #
  #################################

  # Term: diseases
  diseases:
    fields: [Inflammatory Bowel Disease]
    map:
      ageOfOnset: age_first_diagnosis
      familyHistory: family_history

  # Term: ethnicity
  ethnicity: ethnicity

  # Term: exposures
  exposures: 
    fields: [alcohol,smoking,cigarettes_days,cigarettes_years,packyears,smoking_quit]
    dict:
      alcohol: Alcohol
      smoking: Smoking
      cigarettes_days: Average Number Cigarettes Smoked a Day
      cigarettes_years: Total Years Have Smoked Cigarettes
      packyears: Pack Year
      smoking_quit: Smoking Cessation Year
    radio:
      #alcohol;anamnesis;;radio;Alcohol drinking habits";"0, Non-drinker | 1, Ex-drinker | 2, occasional drinking | 3, regular drinking | 4, unknown";;;;;;;y;;;;;
      #smoking;anamnesis;;radio;"Smoking habits";"0, Never smoked | 1, Ex-smoker | 2, Current smoker";;;;;;;y;;;;;
      #cigarettes_days;anamnesis;;text;"On average, how many cigarettes do/did you smoke per day?";;;integer;0;300;;"[smoking] = '2' or [smoking] = '1'";;;;;;
      #cigarettes_years;anamnesis;;text;"For how many years have you been smoking/did you smoke?";;;integer;0;100;;"[smoking] = '2' or [smoking] = '1'";;;;;;
      #packyears;anamnesis;;text;"Pack Years";;;integer;0;300;;"[smoking] = '2' or [smoking] = '1'";;;;;;
      #smoking_quit;anamnesis;;text;"When did you quit smoking?";;year;integer;1980;2030;;"[smoking] = '2'";;;;;;
      # radio
      smoking:
        Never smoked: Never Smoker
        Ex-smoker: Former Smoker
        Current smoker: Current Smoker
      alcohol:
        Non-drinker: Non-Drinker
        Ex-drinker: Current non-drinker with Past Alcohol Consumption
        occasional drinking: Alcohol Consumption Equal to or Less than 2 Drinks per Day for Men and 1 Drink or Less per Day for Women
        regular drinking: Alcohol Consumption More than 2 Drinks per Day for Men and More than 1 Drink per Day for Women
        unknown: Unknown

  # Term: geographicOrigin
  # geographicOrigin: null

  # Term: id
  id:
    fields: [study_id,redcap_event_name]

  # Term: info
  info:
   fields: [study_id,dob,diet,redcap_event_name,age,first_name,last_name,consent,consent_date,consent_noneu,consent_devices,consent_recontact,consent_week2_endo,education,zipcode,consents_and_demographics_complete]
   map:
     studyId: study_id

  # Term: interventionsOrProcedures
  interventionsOrProcedures: 
    fields: [surgery_details___1,surgery_details___2,surgery_details___3,surgery_details___4,surgery_details___5,surgery_details___6,surgery_details___7,surgery_details___8,surgery_details___99,endoscopy_performed,endoscopy_complete,endoscopy_date,intestinal_surgery,partial_mayo,complete_mayo,prev_endosc_dilatation]
    dict:
      surgery_details___1: Ileocolectomy
      surgery_details___2: Colostomy
      surgery_details___3: Ileostomy
      surgery_details___4: Fistula Repair
      surgery_details___5: Colectomy
      surgery_details___6: Hemicolectomy
      surgery_details___7: Colon Resection
      surgery_details___8: Strictureplasty
      surgery_details___99: Other
      endoscopy_peformed: Gastrointestinal Endoscopy
    map:
      dateOfProcedure: endoscopy_date

  # Term: karyotypicSex
  # karyotypicSex: null

  # Term: measures
  measures: 
    fields: [leucocytes,hemoglobin,hematokrit,mcv,mhc,thrombocytes,neutrophils,lymphocytes,eosinophils,creatinine,gfr,bilirubin,gpt,ggt,lipase,crp,iron,il6,calprotectin,nancy_index_acute,nancy_index_chronic,nancy_index_ulceration,endo_mayo]
    dict:
      # Unit
      xx.xx /10^-9 l: Cells per Microliter
      x.xx /10^-9 l: Cells per Microliter
      xxxx /10^-9 l: Cells per Microliter
      xx.x g/dl: Gram per Deciliter
      xx.x fl: Femtoliter
      xx.x: Picogram
      xx.x pg: Picogram
      xx.x µmol/l: Micromole per Liter
      xxx.x µmol/l: Micromole per Liter
      xxx µmol/l: Micromole per Liter 
      ml/min/1.73: Glomerular Filtration Rate Adjusted for BSA
      xxx ml/min/1.73: Glomerular Filtration Rate Adjusted for BSA
      xx.x U/l: International Unit per Liter
      pg/dl: Picogram per Deciliter
      mg/dl: Milligram per Deciliter
      xxx.x mg/l: Milligram per Liter per Milligram
      µg/dl: Microgram per Deciliter
      ng/dl: Nanogram per Deciliter
      xxxx.x ng/l: Nanogram per Liter
      mg/kg stool: Microgram per Kilogram
      'xx.x %': Percentage
      # Test
      hemoglobin: Hemoglobin Measurement
      leucocytes: Leukocyte Count
      hematokrit: Hematocrit Measurement
      mcv: Erythrocyte Mean Corpuscular Volume
      mhc: Erythrocyte Mean Corpuscular Hemoglobin
      thrombocytes: Platelet Count
      neutrophils: Neutrophil Count
      lymphocytes: Lymphocyte Count
      eosinophils: Eosinophil Count
      creatinine: Creatinine Measurement
      gfr: Glomerular Filtration Rate
      bilirubin: Total Bilirubin Measurement
      gpt: Serum Glutamic Pyruvic Transaminase, CTCAE
      ggt: Serum Gamma Glutamyl Transpeptidase Measurement
      lipase: Lipase Measurement
      crp: C-Reactive Protein Measurement
      iron: Iron Measurement
      il6: Interleukin-6
      calprotectin: Calprotectin Measurement
      # Index
      #nancy_index_ulceration: Nancy Index Ulceration
      #nancy_index_acute: 'Nancy histology index: Acute inflammatory cell infiltrate'
      #nancy_index_chronic: 'Nancy histology index: Chronic inflammatory infiltrates'

  # Term: pedigrees
  # pedigrees: null

  # Term: phenotypicFeatures
  phenotypicFeatures: 
    fields: [comorb_asthma,comorb_copd,comorb_ms,comorb_sle,comorb_ra,comorb_pso,comorb_ad,comorb_cancer,comorb_cancer_specified,comorb_hypertension,comorb_diabetes,comorb_lipids,comorb_stroke,comorb_other_ai,comorb_other_ai_specified,immunodeficiency,rectal_bleeding]
    ontology: ncit

  # Term: sex
  sex: sex

  # Term: treatments
  treatments:
    fields: [budesonide,prednisolone,asa,aza,mtx,mp]
    dict:
      aza: azathioprine
      asa: aspirin 
      mtx: methotrexate
      mp: mercaptopurine
    routesOfAdministration: [oral,rectal]
    ontology: ncit