#######################
# Project identifiers #
#######################
project:
id: 3tr_ibd
source: redcap
ontology: ncit
version: 3TR-dev-0.1
description: Mapping file for a REDCap project exported as raw data
baselineFieldsToPropagate: [ids_complete,consent,consent_date,consent_noneu,consent_devices,consent_recontact,consent_week2_endo,diagnosis,diagnosis_year,used_drug,sex,gender,age,age_first_diagnosis,ethnicity,education,height,consents_and_demographics_complete,comorb_asthma,comorb_copd,comorb_ms,comorb_sle,comorb_ra,comorb_pso,comorb_ad,comorb_cancer,comorb_hypertension,comorb_diabetes,comorb_lipids,comorb_stroke,comorb_other_ai,diet,food_intolerance___1,food_intolerance___2,food_intolerance___3,food_intolerance___4,food_intolerance___5,food_intolerance___6,smoking,alcohol,recreational_drugs,family_history,familymember___1,familymember___2,familymember___3,familymember___4,familymember___5,familymember___6,familymember___7,familymember___8,familymember___9,immunodeficiency,past_surgery,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,extraintestinal_details___1,extraintestinal_details___2,extraintestinal_details___3,extraintestinal_details___4,extraintestinal_details___5,extraintestinal_details___6,prior_biologics___1,prior_biologics___2,prior_biologics___3,prior_biologics___4,prior_biologics___5,prior_biologics___6,prior_biologics___7,prior_biologics___8,prior_biologics___9,prednisolone_status,prednisolone_dose,prednisolone_duration,prednisolone_start,budesonide_oral_status,budesonide_rectal_status,asa_oral_status,asa_rectal_status,mtx_status,aza_status,mp_status,anamnesis_complete,covid19_complete,response,low_activity,remission,cdeis]
#################################
# Beacon v2 Models: individuals #
#################################
# Term: diseases
diseases:
fields: [diagnosis]
dictionary:
'Ulcerative Colitis (UC)': Ulcerative Colitis
"Crohn's Disease (CD)": Crohn Disease
ageOfOnset:
diagnosis: age_first_diagnosis
familyHistory:
diagnosis: family_history
# Term: ethnicity
ethnicity:
fields: ethnicity
dictionary:
Caucasian: White
# Term: exposures
exposures:
fields: [alcohol,smoking,cigarettes_days,cigarettes_years,packyears,smoking_quit]
dictionary:
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
selector:
#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'";;;;;;
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]
mapping:
primary_key: study_id
# 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]
mapping:
age: age
# 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,intestinal_surgery,partial_mayo,complete_mayo,prev_endosc_dilatation]
assignTermIdFromHeader: [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]
dictionary:
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_performed: Gastrointestinal Endoscopy
dateOfProcedure:
endoscopy_performed: endoscopy_date
bodySite:
surgery_details___1: Intestine
surgery_details___2: Intestine
surgery_details___3: Intestine
surgery_details___4: Intestine
surgery_details___5: Intestine
surgery_details___6: Intestine
surgery_details___7: Intestine
surgery_details___8: Intestine
surgery_details___99: Intestine
# 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]
dictionary:
# 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:
#comorbities here as they are 0/1 (excluded/included)
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
dictionary:
comorb_asthma: Asthma
comorb_copd: Chronic Obstructive Pulmonary Disease
comorb_ms: Multiple Sclerosis
comorb_sle: Systemic Lupus Erythematosus
comorb_ra: Rheumatoid Arthritis
comorb_pso: Psoriasis
comorb_ad: Atopy
comorb_cancer: Cancer Diagnosis
comorb_cancer_specified: Cancer Diagnosis
comorb_hypertension: Hypertension
comorb_diabetes: Diabetes Mellitus
comorb_lipids: Dyslipidemia
comorb_stroke: Stroke
comorb_other_ai: Other
comorb_other_ai_specified: Other
atopic dermatitis: eczema
cancer: Cancer Patient
COPD: Chronic Obstructive Pulmonary Disease
'demyelating disease/multiple sclerosis': Multiple Sclerosis
'Hyper-/dyslipidemia': Dyslipidemia
'Primary immunodeficiency known?': Primary Immunodeficiency Syndrome
# Term: sex
sex:
fields: sex
# Term: treatments
treatments:
fields: [asa_oral_status,aza_oral_status,mtx_oral_status,mp_oral_status,prednisolone_status]
assignTermIdFromHeader: [asa_oral_status,aza_oral_status,mtx_oral_status,mp_oral_status,prednisolone_status]
dictionary:
asa_oral_status: aspirin
asa_oral_status: azathioprine
mtx_oral_status: methotrexate
mp_oral_status: mercaptopurine
prednisolone_status: prednisolone
drugDose:
asa_oral_status: asa_oral_dose
aza_oral_status: aza_oral_dose
mtx_oral_status: mtx_oral_dose
mp_oral_status: mp_oral_dose
prednisolone_status: prednisolone_dose
drugUnit:
asa_oral_status: Milligram
aza_oral_status: Milligram
mtx_oral_status: Milligram
mp_oral_status: Milligram
prednisolone_status: Milligram
duration:
asa_oral_status: asa_oral_duration
aza_oral_status: aza_oral_duration
mtx_oral_status: mtx_oral_duration
mp_oral_status: mp_oral_duration
prednisolone_status: prednisolone_duration
durationUnit:
asa_oral_status: Week
aza_oral_status: Week
mtx_oral_status: Week
mp_oral_status: Week
prednisolone_status: Week
routeOfAdministration:
asa_oral_status: oral
aza_oral_status: oral
mtx_oral_status: oral
mtx_oral_status: oral
prednisolone_status: oral