mappingVersion: 2
source:
profile: redcap
target:
model: beacon
schemaVersion: '2.0.0'
project:
id: 3tr_ibd
version: 3TR-dev-0.1
description: Mapping file for a REDCap project exported as raw data
defaults:
ontology: ncit
records:
visitId:
sourceField: redcap_event_name
baseline:
strategy: firstNonNull
sourceFields: [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:
individuals:
id:
sourceFields: [study_id, redcap_event_name]
primaryKey: study_id
separator: ':'
missingValue: NA
sex:
sourceField: sex
query: { from: value }
ethnicity:
sourceField: ethnicity
query:
from: value
aliases:
Caucasian: White
diseases:
rules:
- sourceField: diagnosis
when: { nonEmpty: true }
diseaseCode:
query:
from: value
aliases:
'Ulcerative Colitis (UC)': Ulcerative Colitis
"Crohn's Disease (CD)": Crohn Disease
ageOfOnset:
sourceField: age_first_diagnosis
familyHistory:
sourceField: family_history
exposures:
defaults:
unit: { query: { from: value } }
rules:
- sourceField: alcohol
when: { notValues: ['No', 'False'] }
exposureCode: { query: Alcohol }
unit:
query:
from: value
aliases:
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
- sourceField: smoking
when: { notValues: ['No', 'False'] }
exposureCode: { query: Smoking }
unit:
query:
from: value
aliases:
Never smoked: Never Smoker
Ex-smoker: Former Smoker
Current smoker: Current Smoker
- sourceField: cigarettes_days
exposureCode: { query: Average Number Cigarettes Smoked a Day }
- sourceField: cigarettes_years
exposureCode: { query: Total Years Have Smoked Cigarettes }
- sourceField: packyears
exposureCode: { query: Pack Year }
- sourceField: smoking_quit
exposureCode: { query: Smoking Cessation Year }
info:
sourceFields: [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]
ageRange: { sourceField: age }
interventionsOrProcedures:
rules:
- sourceField: surgery_details___1
procedureCode: { query: Ileocolectomy }
bodySite: { query: Intestine }
- sourceField: surgery_details___2
procedureCode: { query: Colostomy }
bodySite: { query: Intestine }
- sourceField: surgery_details___3
procedureCode: { query: Ileostomy }
bodySite: { query: Intestine }
- sourceField: surgery_details___4
procedureCode: { query: Fistula Repair }
bodySite: { query: Intestine }
- sourceField: surgery_details___5
procedureCode: { query: Colectomy }
bodySite: { query: Intestine }
- sourceField: surgery_details___6
procedureCode: { query: Hemicolectomy }
bodySite: { query: Intestine }
- sourceField: surgery_details___7
procedureCode: { query: Colon Resection }
bodySite: { query: Intestine }
- sourceField: surgery_details___8
procedureCode: { query: Strictureplasty }
bodySite: { query: Intestine }
- sourceField: surgery_details___99
procedureCode: { query: Other }
bodySite: { query: Intestine }
- sourceField: endoscopy_performed
procedureCode: { query: Gastrointestinal Endoscopy }
dateOfProcedure: { sourceField: endoscopy_date }
- sourceField: endoscopy_complete
procedureCode: { query: { from: value } }
- sourceField: intestinal_surgery
procedureCode: { query: { from: value } }
- sourceField: partial_mayo
procedureCode: { query: { from: value } }
- sourceField: complete_mayo
procedureCode: { query: { from: value } }
- sourceField: prev_endosc_dilatation
procedureCode: { query: { from: value } }
measures:
defaults:
measurementValue:
quantity:
unit:
query:
from: fieldNote
aliases:
'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
referenceRange: { from: redcapDictionary }
procedure:
procedureCode: { query: Blood Test Result }
rules:
- { sourceField: leucocytes, assayCode: { query: Leukocyte Count } }
- { sourceField: hemoglobin, assayCode: { query: Hemoglobin Measurement } }
- { sourceField: hematokrit, assayCode: { query: Hematocrit Measurement } }
- { sourceField: mcv, assayCode: { query: Erythrocyte Mean Corpuscular Volume } }
- { sourceField: mhc, assayCode: { query: Erythrocyte Mean Corpuscular Hemoglobin } }
- { sourceField: thrombocytes, assayCode: { query: Platelet Count } }
- { sourceField: neutrophils, assayCode: { query: Neutrophil Count } }
- { sourceField: lymphocytes, assayCode: { query: Lymphocyte Count } }
- { sourceField: eosinophils, assayCode: { query: Eosinophil Count } }
- { sourceField: creatinine, assayCode: { query: Creatinine Measurement } }
- { sourceField: gfr, assayCode: { query: Glomerular Filtration Rate } }
- { sourceField: bilirubin, assayCode: { query: Total Bilirubin Measurement } }
- { sourceField: gpt, assayCode: { query: 'Serum Glutamic Pyruvic Transaminase, CTCAE' } }
- { sourceField: ggt, assayCode: { query: Serum Gamma Glutamyl Transpeptidase Measurement } }
- { sourceField: lipase, assayCode: { query: Lipase Measurement } }
- { sourceField: crp, assayCode: { query: C-Reactive Protein Measurement } }
- { sourceField: iron, assayCode: { query: Iron Measurement } }
- { sourceField: il6, assayCode: { query: Interleukin-6 } }
- sourceField: calprotectin
assayCode: { query: Calprotectin Measurement }
procedure: { procedureCode: { query: Feces } }
- sourceField: nancy_index_acute
assayCode: { query: nancy_index_acute }
procedure: { procedureCode: { query: Histologic } }
- sourceField: nancy_index_chronic
assayCode: { query: nancy_index_chronic }
procedure: { procedureCode: { query: Histologic } }
- sourceField: nancy_index_ulceration
assayCode: { query: nancy_index_ulceration }
procedure: { procedureCode: { query: Histologic } }
- { sourceField: endo_mayo, assayCode: { query: endo_mayo } }
phenotypicFeatures:
rules:
- { sourceField: comorb_asthma, featureType: { query: Asthma } }
- { sourceField: comorb_copd, featureType: { query: Chronic Obstructive Pulmonary Disease } }
- { sourceField: comorb_ms, featureType: { query: Multiple Sclerosis } }
- { sourceField: comorb_sle, featureType: { query: Systemic Lupus Erythematosus } }
- { sourceField: comorb_ra, featureType: { query: Rheumatoid Arthritis } }
- { sourceField: comorb_pso, featureType: { query: Psoriasis } }
- { sourceField: comorb_ad, featureType: { query: Atopy } }
- { sourceField: comorb_cancer, featureType: { query: Cancer Diagnosis } }
- sourceField: comorb_cancer_specified
when: { nonEmpty: true }
featureType:
query:
from: value
aliases: { cancer: Cancer Patient }
- { sourceField: comorb_hypertension, featureType: { query: Hypertension } }
- { sourceField: comorb_diabetes, featureType: { query: Diabetes Mellitus } }
- { sourceField: comorb_lipids, featureType: { query: Dyslipidemia } }
- { sourceField: comorb_stroke, featureType: { query: Stroke } }
- { sourceField: comorb_other_ai, featureType: { query: Other } }
- sourceField: comorb_other_ai_specified
when: { nonEmpty: true }
featureType:
query:
from: value
aliases:
atopic dermatitis: eczema
COPD: Chronic Obstructive Pulmonary Disease
'demyelating disease/multiple sclerosis': Multiple Sclerosis
'Hyper-/dyslipidemia': Dyslipidemia
- { sourceField: immunodeficiency, featureType: { query: Primary Immunodeficiency Syndrome } }
- { sourceField: rectal_bleeding, featureType: { query: Rectal Hemorrhage } }
treatments:
defaults:
routeOfAdministration: { query: Oral Route of Administration }
cumulativeDose:
unit: { query: Week }
doseIntervals:
quantity:
unit: { query: Milligram }
rules:
- sourceField: asa_oral_status
when: { values: [former treatment, current treatment] }
treatmentCode: { query: aspirin }
cumulativeDose:
value: { sourceField: asa_oral_duration }
doseIntervals:
quantity:
value: { sourceField: asa_oral_dose }
- sourceField: aza_status
when: { values: [former treatment, current treatment] }
treatmentCode: { query: azathioprine }
cumulativeDose: { value: { sourceField: aza_duration } }
doseIntervals: { quantity: { value: { sourceField: aza_dose } } }
- sourceField: mtx_status
when: { values: [former treatment, current treatment] }
treatmentCode: { query: methotrexate }
cumulativeDose: { value: { sourceField: mtx_duration } }
doseIntervals: { quantity: { value: { sourceField: mtx_dose } } }
- sourceField: mp_status
when: { values: [former treatment, current treatment] }
treatmentCode: { query: mercaptopurine }
cumulativeDose: { value: { sourceField: mp_duration } }
doseIntervals: { quantity: { value: { sourceField: mp_dose } } }
- sourceField: prednisolone_status
when: { values: [former treatment, current treatment] }
treatmentCode: { query: prednisolone }
cumulativeDose: { value: { sourceField: prednisolone_duration } }
doseIntervals: { quantity: { value: { sourceField: prednisolone_dose } } }
biosamples:
defaults:
id: { from: sourceValue }
individualId: { from: individualId }
biosampleStatus:
term: { id: 'NCIT:C126101', label: Not Available }
sampleOriginType: { query: Whole Blood }
collectionDate: { sourceField: study_blood_date }
rules:
- sourceField: id_pbmc
sampleOriginType: { query: Peripheral Blood Mononuclear Cell }
info: { sourceFields: [number_pbmc, study_blood_remarks] }
- sourceField: id_heparin
optional: true
info: { sourceFields: [number_heparin, study_blood_remarks] }
- sourceField: id_smart
optional: true
info: { sourceFields: [number_smart, study_blood_remarks] }
- sourceField: id_serum
sampleOriginType: { query: Serum }
info: { sourceFields: [number_serum, study_blood_remarks] }
- sourceField: id_cispt
info: { sourceFields: [number_cispt, study_blood_remarks] }
- sourceField: id_plasma
sampleOriginType: { query: Plasma }
info: { sourceFields: [number_plasma, study_blood_remarks] }
- sourceField: id_pax
info: { sourceFields: [number_pax, study_blood_remarks] }
- sourceField: id_least_bio_native
sampleOriginType: { query: Tissue }
collectionDate: { sourceField: endoscopy_date }
info: { sourceFields: [number_least_bio_native, biopsy_remarks] }
- sourceField: id_least_bio_native_2
sampleOriginType: { query: Tissue }
collectionDate: { sourceField: endoscopy_date }
info: { sourceFields: [number_least_bio_native_2, biopsy_remarks] }
- sourceField: id_least_bio_freezing
sampleOriginType: { query: Tissue }
collectionDate: { sourceField: endoscopy_date }
info: { sourceFields: [number_least_bio_freezing, biopsy_remarks] }
- sourceField: id_least_bio_freezing_2
sampleOriginType: { query: Tissue }
collectionDate: { sourceField: endoscopy_date }
info: { sourceFields: [number_least_bio_freezing_2, biopsy_remarks] }
- sourceField: id_most_bio_native
sampleOriginType: { query: Tissue }
collectionDate: { sourceField: endoscopy_date }
info: { sourceFields: [number_most_bio_native, biopsy_remarks] }
- sourceField: id_most_bio_native_2
sampleOriginType: { query: Tissue }
collectionDate: { sourceField: endoscopy_date }
info: { sourceFields: [number_most_bio_native_2, biopsy_remarks] }
- sourceField: id_most_bio_freezing
sampleOriginType: { query: Tissue }
collectionDate: { sourceField: endoscopy_date }
info: { sourceFields: [number_most_bio_freezing, biopsy_remarks] }
- sourceField: id_most_bio_freezing_2
sampleOriginType: { query: Tissue }
collectionDate: { sourceField: endoscopy_date }
info: { sourceFields: [number_most_bio_freezing_2, biopsy_remarks] }