Appendix: source tables
Tables
Table: basedata.csv
| Field | Type | Most freq. value | Description | Concept | Mapped to table | |
|---|---|---|---|---|---|---|
| p_id | int | List truncated… | Already anonymised. Patient id unique in basedata. | Person | ||
| psa | real | 5.1 | Measuring prostate-specific antigen in ng/ml. | Total PSA level - 44793131, 8842 - nanogram per milliliter as unit_concept_id | Measurement | |
| prostatic_vol | real | 40 | Prostate volume measured in mL. | Size of prostate - 4096978, mL - 8587 as unit_concept_id. Do not map when value is empty. | Observation | |
| dre | varchar | T1c | Digital rectal examination. | Map variable and value separately. DRE - Digital rectal examination - 4254766 (variable) as target_concept_id, Tumor stage T1c - 4129916, Tumor stage T2a - 4129917, Tumor stage T2b - 4127611, Tumor stage T2c - 4129127, Tumor stage T3 - 4032012 (values) as target_concept_id as well. Split (*,*,*) before mapping. | Procedure occurrence, Condition occurrence | |
| num_cores | int | 12 | Number of core biopsies. | If value is ‘’, capture value as 0. Number of Cores Examined - 35917476 | Measurement | |
| num_cores_pc | int | 1 | Number of core biopsies that contained prostate cancer. | Number of Cores Positive - 35918000 | Measurement | |
| asa | int | 0 | Do not map this variable (empty and not in the current form). In follow up this contains the Charlson score (separate charlson variable in basedata). | |||
| log2psa | real | 2.26303 | Do not map. Derived variable from psa. | |||
| gleason1 | int | 3 | Gleason primary grade. | Observation | ||
| gleason2 | int | 3 | Gleason secondary grade. Take sum of Gleason1 and Gleason2, concatenate column names to Gleason1_Gleason2. | Total Gleason score - 4297949 (variable) as target_concept_id, following as value: ‘Gleason Grade Group 1’ - 1633550, ‘Grade Group 2: Gleason score 7 Gleason pattern 3+4’ - 1633826, ‘Grade Group 3: Gleason score 7 Gleason pattern 4+3’ - 1634459, ‘Grade Group 4: Gleason score 8’ - 1635079, ‘Grade Group 5: Gleason score 9 or 10’ - 1635009 | Observation | |
| gleason_sum | int | 6 | Do not map, info captured in more detail from gleason1 and 2. Gleason score (gleason1 + gleason2). Value 0 should not be possible (prostate cancer is inclusion criterum). | |||
| free_psa | real | 0 | Free-PSA test measures the percentage of unbound PSA. | Free prostate specific antigen level - 4194418, % - 8554 as unit_concept_id | Measurement | |
| pro_psa | int | Do not map. Barely filled in, same in follow-up. | ||||
| phi | int | Prostate Health Index. Derived variable from free-psa and pro-psa. Sometimes phi captured while free/pro not captured, so also save phi. | Map to concept ‘Prostate Health Index’ - 1620024. Do not map when value is empty. | Measurement | ||
| charlson | int | 0 | Charlson Comorbidity Index (CCI) predicts the ten-year mortality for a patient who may have a range of comorbid conditions. | Charlson Comorbidity Index - 42538860 | Measurement | |
| tnm | int | 1992 | Do not map. Not relevant, always the same. TNM version from 1992 (not 1998 or 2002). | |||
| method_detection | varchar | Screen-detected | Do not map. This type of low-grade prostate cancer would not give complaints? Clinically = by doctor during hospital visit due to complaints, screen-detected = by routine check without complaints. | |||
| length | int | 0 | Length of patient (in cm). | Body height measured - 3023540, cm - 8582 as unit_concept_id. Do not capture when value < 50 | Measurement | |
| weight | int | 0 | Weight of patient (in kg). | Body weight measured - 3013762, kg - 9529 as unit_concept_id. Do not capture when value is 0 | Measurement | |
| num_cores2 | int | 0 | Number of core biopsies. | If value is ‘’, capture value as 0. Number of Cores Examined - 35917476 | Measurement | |
| num_cores_pc2 | int | 0 | Number of core biopsies that contained prostate cancer. | Number of Cores Positive - 35918000 | Measurement | |
| gleason1_2 | int | 0 | Gleason primary grade. | Observation | ||
| gleason2_2 | int | 0 | leason secondary grade. Take sum of Gleason1_2 and Gleason2_2, concatenate column names to Gleason1_2_Gleason2_2. | Total Gleason score - 4297949 (variable) as target_concept_id, following as value: ‘Gleason Grade Group 1’ - 1633550, ‘Grade Group 2: Gleason score 7 Gleason pattern 3+4’ - 1633826, ‘Grade Group 3: Gleason score 7 Gleason pattern 4+3’ - 1634459, ‘Grade Group 4: Gleason score 8’ - 1635079, ‘Grade Group 5: Gleason score 9 or 10’ - 1635009 | Observation | |
| no_co_morbidity | int | 1 | Do not map. Other comorbidities. Should always be true (no comorbitidy), if other, it is an error as patient should then not be included. | |||
| active_visit | int | 1 | Do not map. Always active at basedata (=1). | |||
| biopt_prob_type | int | 0 | Antibioticum given (profylaxe). 0 - data not provided (empty), 1 - no antibioticum used (capture, to distinguish from missing), 2 - yes, fluoroquinolones, 3 - yes, tmp smx, 4 - yes, other. | Do not capture when value is 0. Antibiotics - 40792781 (variable - non-standard concept) as target_concept_id, following as value: None - 45878582, Fluoroquinolone - 1176676 (non-standard concept), Trimethoprim+Sulfamethoxazole - 40792503 (non-standard concept), Other Antibiotic - 40779119 (non-standard concept) | Measurement | |
| biopt_infection | int | 0 | Infection occurred after biopsy. 0 - not provided (does not mean no complications occurred), 1 - yes 2 - no | Do not capture when value is 0. Map to custom concept ‘Infection occurred after biopsy’ - 2000000023 as target_concept_id, following as value: Yes - 45877994, No - 45878245 | Observation | |
| biopt_inf_urine_culture | int | 0 | Urine culture measured. 0 - not provided or not measured (empty) 1 - positive (bacterium is cultured, is an infection), 2 - negative (no bacterium cultered, not an infection) | Do not capture when value is 0. Urine culture - 4024509 (variable) as target_concept_id, following as value: Positive - 9191, Negative - 9189 | Measurement | |
| biopt_inf_urine_bacterium | int | Type of urine bacterium measured. 0 - not filled in, 1 - E.coli, 2 - pseudomonas, 3 - Enterococci, 4 - proteus, 5 - Staphylococci, 6 - Klebsiella, 7 - other enterobacteria, 8 - other | Do not capture when value is 0. Bacteria [Presence] in Urine - 36304419, Escherichia coli - 4011683, Pseudomonas - 4211547, Genus Enterococcus - 4101235, Proteus - 4196666, Staphylococcus - 4278981, Klebsiella - 4327473, Enterobacter - 4242438, Other - 9177. Do not map when value is empty. | Measurement | ||
| biopt_inf_unrine_resistant | varchar | Do not map. To which antibiotic is the urine bacteria resistant. 0 - not filled in, 1 - Fluoroquinolones, 2 - Trimethoprim-sulfonamide (TMP-SMX) combination, 3 - Cephalosporin (group 1 or 2), 4 - Cephalosporin (group >=3), 5 - Carbapenems, 6 - Penicillins (without B-lactam), 7 - Aminoglycosides, 8 - Nitrofuran, 9 - other. | Measurement | |||
| biopt_inf_antibiotic_therapy | int | 0 | Do not map. If antibiotic therapy is given. 0 - not filled in, 1 - yes, 2 - no. | Procedure occurrence | ||
| biopt_inf_antibiotic_type | int | Do not map. What kind of antibiotic is given. 0 - not filled in, 1 - Fluoroquinolones, 2 - trimethoprim-sulfamethoxazole (TMP-SMX) combination, 3 - Cephalosporin (group 1 or 2), 4 - Cephalosporin (group >=3), 5 - Carbapenems, 6 - Penicillins (without B-lactam), 7 - Penicillins (with B-lactam), 8 - Aminoglycosides, 9 - Nitrofuran, 10 - other. | Measurement | |||
| biopt_inf_hospitalisation | int | 0 | Hospitalisation due to bioptic infection. 0 - not filled in, 1 - yes, 2 - no. | Map biopt_inf_hospitalisation_days if biopt_inf_hospitalisation is 1 (“yes”). Do not map this variable separately. | Observation | |
| biopt_inf_hospitalisation_days | int | 0 | Days in hospital. | Only map if biopt_inf_hospitalisation is 1 (“yes). Map to Hospitalized or emergency room [ESRD] - 42869434 as target_concept_id. Store value as value_as_number and day - 8512 as unit_concept_id. | Observation | |
| biopt_inf_outcome | int | 0 | Cured or death. 0 = not given (empty) 1 = cured 2 = death (not in baseline). | Do not capture when value is 0. Patient cured - 4159637, Patient died - 4216643 | Condition occurrence | |
| biopt_hematuria | int | 0 | Hematuria for more than 3 days. 0 - not filled in, 1 - yes 2 - no. | Only map if value is 1 (“yes”), map as variable_value. Blood in urine - 437038 | Condition occurrence | |
| biopt_hemospermia | int | 0 | Hemospermia. 0 - not filled in, 1 - yes 2 - no. | Only map if value is 1 (“yes”), map as variable_value. Hemospermia - 439871 | Condition occurrence | |
| biopt_pain | int | 0 | Pain after biopsy. 0 - not filled in, 1 - yes 2 - no. | Only map if value is 1 (“yes”), map as variable_value. Custom concept 2000000026 - Pain after biopsy | Condition occurrence | |
| biopt_route | int | 0 | 0 - not given, 1 - transrectal 2 - transperineal. | Do not capture when value is 0. Transrectal biopsy of prostate - 4339403, Transperineal needle biopsy of prostate - 4142388 | Procedure occurrence | |
| biopt_max_cancer_score_lenght | int | 0 | Size of prostate cancer (in millimeters) in a prostate cancer biopsy (size of largest cancer part). | Map to custom concept ‘Size of prostate cancer in biopt’ - 2000000027 as target_concept_id, millimeter - 8588 as unit_concept_id | Measurement | |
| mri_included | int | 0 | Do not map. Whether patient has been selected for MRI side study. | |||
| bonescan | varchar | Do not map. Old variable. | ||||
| mri_taken.0 | int | 0 | MRI made at baseline. Result MRI does not always have to be given, so save separately. 0 - ‘’, 1 - Yes, 2 - No. | Only map if value is 1 (“yes”), map as variable_value. MRI of prostate - 4192638 | Procedure occurrence | |
| mri_lesions.0 | int | 0 | Abnormalities detected on MRI. 0 - ‘’, 1 - Yes, 2 - No. | Only map if mri_taken.0 value is 1 (“yes”). Only map if value is 1 (“yes”), map as variable_value. MRI scan abnormal - 4059669 | Condition occurrence | |
| mri_suspected_number.0 | int | 0 | Number of suspected abnormalities/lesions on MRI. 0 - 0, 1 - 1, 2 - 2, 3 - 3, 4 - >3 | Only map if mri_taken.0 value is 1 (“yes”). Number of lesions - 4085855. When value is 4, value_as_number is 3 and operator_concept_id is > - 4172704 | Observation | |
| mri_pirads_1.0 | int | 0 | The PIRADS score is given for each suspected lesion (maximum of 3). 0 - ‘’, 1 - 3 cancer is equivocal, 2 - 4 cancer is likely, 3 - 5 cancer is very likely | Only map if mri_taken.0 value is 1 (“yes”). Do not map when value is 0. Map to custom concept ‘PI-RADS score’ - 2000000028 as target_concept_id. Only map score as value_as_number. | Measurement | |
| mri_largest_dia_1.0 | int | 0 | The largest diameter in mm of lesion 1. | Only map if mri_taken.0 value is 1 (“yes”). Lesion size - 4084390, millimeter - 8588 | Observation | |
| mri_location_1.0 | int | 0 | Location of lesion 1 in the prostate. 0 - ‘’, 1 - anterior half, 2 - posterior half, 3 - both | Only map if mri_taken.0 value is 1 (“yes”). Do not map if value is 0. Site of tumor - 4135405 (variable) as target_concept_id, following as value: Anterior - 4115458, Posterior - 4116868, Both - 45883500 | Observation | |
| mri_location_free_1.0 | varchar | Text field for extra information for mri_location_1.0 | Only map if mri_taken.0 value is 1 (“yes”). Site of tumor - 4135405 (variable) as target_concept_id, following as value: Right - 45881626, Left - 45883143. Do not map when value is empty. | Observation | ||
| mri_pirads_2.0 | int | 0 | The PIRADS score is given for each suspected lesion (maximum of 3). 0 - ‘’, 1 - 3 cancer is equivocal, 2 - 4 cancer is likely, 3 - 5 cancer is very likely | Only map if mri_taken.0 value is 1 (“yes”). Do not map when value is 0. Map to custom concept ‘PI-RADS score’ - 2000000028 as target_concept_id. Only map score as value_as_number. | Measurement | |
| mri_largest_dia_2.0 | int | 0 | The largest diameter in mm of lesion 2. | Only map if mri_taken.0 value is 1 (“yes”). Lesion size - 4084390, millimeter - 8588 | Observation | |
| mri_location_2.0 | int | 0 | Location of lesion 2 in the prostate. 0 - ‘’, 1 - anterior half, 2 - posterior half, 3 - both | Only map if mri_taken.0 value is 1 (“yes”). Do not map when value is 0. Site of tumor - 4135405 (variable) as target_concept_id, following as value: Anterior - 4115458, Posterior - 4116868, Both - 45883500 | Observation | |
| mri_location_free_2.0 | varchar | Text field for extra information for mri_location_2.0 | Only map if mri_taken.0 value is 1 (“yes”). Site of tumor - 4135405 (variable) as target_concept_id, following as value: Right - 45881626, Left - 45883143. Do not map when value is empty. | Observation | ||
| mri_pirads_3.0 | int | 0 | The PIRADS score is given for each suspected lesion (maximum of 3). 0 - ‘’, 1 - 3 cancer is equivocal, 2 - 4 cancer is likely, 3 - 5 cancer is very likely | Only map if mri_taken.0 value is 1 (“yes”). Do not map when value is 0. Map to custom concept ‘PI-RADS score’ - 2000000028 as target_concept_id. Only map score as value_as_number. | Measurement | |
| mri_largest_dia_3.0 | int | 0 | The largest diameter in mm of lesion 3. | Only map if mri_taken.0 value is 1 (“yes”). Lesion size - 4084390, millimeter - 8588 | Observation | |
| mri_location_3.0 | int | 0 | Location of lesion 3 in the prostate. 0 - ‘’, 1 - anterior half, 2 - posterior half, 3 - both | Only map if mri_taken.0 value is 1 (“yes”). Do not map when value is 0. Site of tumor - 4135405 (variable) as target_concept_id, following as value: Anterior - 4115458, Posterior - 4116868, Both - 45883500 | Observation | |
| mri_location_free_3.0 | varchar | Text field for extra information for mri_location_3.0 | Only map if mri_taken.0 value is 1 (“yes”). Site of tumor - 4135405 (variable) as target_concept_id, following as value: Right - 45881626, Left - 45883143. Do not map when value is empty. | Observation | ||
| mri_progrssion_lesions.0 | int | Whether there is change compared to the previous MRI, about lesion 1. 0 - empty (not given), use PRECISE recommendations (make stages for each score). | Only map if mri_taken.0 value is 1 (“yes”). Do not capture when value is 0 or when value is empty. Progression - 4077864 (variable) as target_concept_id, value as value_as_number | Observation | ||
| mri_targeted_biopsy.0 | int | 0 | Targeted biopsies taken at MRI. 0 - empty, 1 - yes, 2 - no | Only map if mri_taken.0 value is 1 (“yes”). Only map if value is 1 (“yes”), map as variable_value. Map to MRI targeted biopsy of prostate - 37109819 | Procedure occurrence | |
| mri_targeted_cores.0 | int | 0 | Number of cores with prostate cancer from targeted biopsies taken. Only use when targeted biopsies - yes (0 can mean both not given and no pc cores found). | Only map if mri_taken.0 value is 1 (“yes”). Only map if mri_targeted_biopsy.0 is 1 (“yes). Number of Cores Positive - 35918000 | Measurement | |
| mri_targeted_taken.0 | int | 0 | Number of cores taken from the abnormalities seen on MRI (targeted). | Only map if mri_taken.0 value is 1 (“yes”). Number of Cores Examined - 35917476 | Measurement | |
| mri_targeted_gleason1.0 | int | 0 | Gleason primary grade at MRI | |||
| mri_targeted_gleason2.0 | int | 0 | Gleason secondary grade at MRI. Take sum of Mri_Targeted_Gleason1.0 and Mri_Targeted_Gleason2.0, concatenate column names to Mri_Targeted_Gleason1.0_Mri_Targeted_Gleason2.0 | Only map if mri_taken.0 value is 1 (“yes”). Total Gleason score - 4297949 (variable) as target_concept_id, following as value: ‘Gleason Grade Group 1’ - 1633550, ‘Grade Group 2: Gleason score 7 Gleason pattern 3+4’ - 1633826, ‘Grade Group 3: Gleason score 7 Gleason pattern 4+3’ - 1634459, ‘Grade Group 4: Gleason score 8’ - 1635079, ‘Grade Group 5: Gleason score 9 or 10’ - 1635009 | Observation | |
| mri_lesion_positive.0 | int | Number of lesions that are confirmed by biopt as prostate cancer. 0 can mean both not recorded and no positive found. | Only map if mri_taken.0 value is 1 (“yes”). Number of Cores Positive - 35918000. Do not map when value is empty. | Measurement | ||
| mri_method_used.0 | int | 0 | Combine with mri_targeted_biopsy.0, if done also include this method. 0 - ‘’, 1 - Visual, 2 - Software, 3 - Inbore | Only map if mri_taken.0 and mri_targeted_biopsy.0 value is 1 (“yes”). Map as variable_value. ‘Visual targeting of MRI lesions’ - 2000000042, ‘Software targeting of MRI lesions’ - 2000000043, ‘In-bore targeting of MERI lesions’ - 2000000044 | Procedure occurrence | |
| mri_prostate_volume.0 | int | Not measured by MRI, but manually entered based on MRI in ml. | Only map if mri_taken.0 value is 1 (“yes”). Map as value of the variable mri_prostate_volume_method.0. Unit mL - 8587 | Measurement | ||
| mri_prostate_volume_method.0 | int | Combine with mri_prostate_volume.0. 0 - ‘’, 1- Ellipsoid (W*H*L*0.52), 2- Segmentation, 3 - Other, specify in comment | Only map if mri_taken.0 value is 1 (“yes”). Do not map if value is 0 or empty. Map to custom concept as variable_value: ‘Prostate MRI ellipsiod’ - 2000000045, ‘Prostate MRI segmentation’ - 2000000046, ‘Prostate MRI volume’ - 2000000047 | Measurement | ||
| age_diagnosis | real | 66.92 | Age at diagnosis (observation). Include to be complete. | Age - 4265453 | Observation | |
| year_diagnosis | int | 2015 | Year of diagnosis | Observation period, Visit occurrence | ||
| year_birth | int | 1946 | Year of birth | |||
| first_500 | int | 0 | Indicates whether a patient is one of the first 500. | Observation |
Table: fulong.csv
| Field | Type | Most freq. value | Description | Concept | Mapped to table | |
|---|---|---|---|---|---|---|
| p_id | int | 3064 | Patient id | Person | ||
| time | int | 1 | Visit number | Visit occurrence | ||
| psa_fu | real | 5.8 | Measuring prostate-specific antigen in ng/ml | Total PSA level - 44793131, nanogram per milliliter - 8842 as unit_concept_id | Measurement | |
| dre_fu | varchar | Digital rectal examination If empty, this visit only measured psa (do not capture). | Map variable and value separately. Do not capture when value is empty. DRE - Digital rectal examination - 4254766 (variable) as target_concept_id, Tumor stage T1c - 4129916, Tumor stage T2a - 4129917, Tumor stage T2b - 4127611, Tumor stage T2c - 4129127, Tumor stage T3 - 4032012 (values) as target_concept_id as well. Split (*,*,*) before mapping. | Procedure occurrence, Condition occurrence | ||
| dre_fu_recode | int | Do not map. Administrative. Use actual dre_fu. | ||||
| num_cores_biop_fu | int | 0 | Number of core biopsies. | If value is ‘’, capture value as 0. Number of Cores Examined - 35917476 | Measurement | |
| num_cores_pc_fu | int | 0 | Number of core biopsies that contained prostate cancer. | Number of Cores Positive - 35918000 | Measurement | |
| asa_fu | int | 0 | Charlson score (see charlson variable in basedata). | Charlson Comorbidity Index - 42538860 | Measurement | |
| log2psa_fu | real | 2.58496 | Do not map. Log2 of the PSA value. | Do not map. Log2 of the PSA value. | ||
| psadt | real | -0.8 | PSA doubling time | Map to custom concept concept ‘PSA doubling time’ - 2000000041, year - 9448 as unit_concept_id | Measurement | |
| gleason1_fu | int | 0 | Gleason primary grade | Observation | ||
| gleason2_fu | int | 0 | Gleason secondary grade. Take sum of Gleason1_FU and Gleason2_FU | Total Gleason score - 4297949 (variable) as target_concept_id, following as value: ‘Gleason Grade Group 1’ - 1633550, ‘Grade Group 2: Gleason score 7 Gleason pattern 3+4’ - 1633826, ‘Grade Group 3: Gleason score 7 Gleason pattern 4+3’ - 1634459, ‘Grade Group 4: Gleason score 8’ - 1635079, ‘Grade Group 5: Gleason score 9 or 10’ - 1635009 | Observation | |
| gleason_sum_fu | int | 0 | Do not map, info captured in more detail from Gleason1_FU and Gleason2_FU. Gleason score (gleason1 + gleason2). | |||
| slope | real | 0 | Do not map, captured by psadt. Used to calculate psadt (doubling time) | |||
| free_psa_fu | real | 0 | Free-PSA test measures the percentage of unbound PSA. | Free prostate specific antigen level - 4194418, % - 8554 | Measurement | |
| pro_psa_fu | int | Do not map, given for just one person. | ||||
| phi_fu | int | Prostate Health Index. Derived variable from free-psa and pro-psa. | Map to concept ‘Prostate Health Index’ - 1620024. Do not map when value is empty. | Measurement | ||
| visit_action | varchar | LAB | Do not map. Does not always match. The actual measurements done decided by clincians. Administrative field. | |||
| active_visit | int | 1 | Do not map. 1 - yes, 0 - No. | |||
| biopt_prob_type_fu | int | 0 | Antibioticum given (profylaxe). 0 - data not provided (empty), 1 - no antibioticum used (capture, to distinguish from missing), 2 - yes, fluorquinolones, 3 - yes, tmp smx, 4 - yes, other. | Do not capture when value is 0. Antibiotics - 40792781 (variable, non-standard concept) as target_concept_id, following as value: None - 45878582, Fluoroquinolone - 1176676 (non-standard concept), Trimethoprim+Sulfamethoxazole - 40792503 (non-standard concept), Other Antibiotic - 40779119 (non-standard concept) | Measurement | |
| biopt_infection_fu | int | 0 | Infection occurred after biopsy. 0 - not provided (does not mean no complications occurred), 1 - yes 2 - no | Do not capture when value is 0. Map to custom concept ‘Infection occurred after biopsy’ - 2000000023 as target_concept_id, following as value: Yes - 45877994, No - 45878245 | Observation | |
| biopt_inf_urine_culture_fu | int | 0 | Urine culture measured. 0 - not provided or not measured (empty) 1 - positive (bacterium is cultured, is an infection), 2 - negative (no bacterium cultered, not an infection) | Do not capture when value is 0. Urine culture - 4024509 (variable) as target_concept_id, following as value: Positive - 9191, Negative - 9189 | Measurement | |
| biopt_inf_urine_bacterium_fu | int | Type of urine bacterium measured. Type of urine bacterium measured. 0 - not filled in, 1 - E.coli, 2 - pseudomonas, 3 - Enterococci, 4 - proteus, 5 - Staphylococci, 6 - Klebsiella, 7 - other enterobacteria, 8 - other. Do not map when value is empty. | Do not capture when value is 0. Bacteria [Presence] in Urine - 36304419, Escherichia coli - 4011683, Pseudomonas - 4211547, Genus Enterococcus - 4101235, Proteus - 4196666, Staphylococcus - 4278981, Klebsiella - 4327473, Enterobacter - 4242438, Other - 9177 | Measurement | ||
| biopt_inf_unrine_resistant_fu | varchar | Do not map. To which antibioticum is the urine bacteria resistant. 0 - not filled in, 1 - Fluoroquinolones, 2 - Trimethoprim-sulfonamide (TMP-SMX) combination, 3 - Cephalosporin (group 1 or 2), 4 - Cephalosporin (group >=3), 5 - Carbapenems, 6 - Penicillins (without B-lactam), 7 - Aminoglycosides, 8 - Nitrofuran, 9 - other. | Measurement | |||
| biopt_inf_antibiotic_therapy_fu | int | 0 | Do not map. If antibiotic therapy is given. If antibiotic therapy is given. 0 - not filled in, 1 - yes, 2 - no. | Procedure occurrence | ||
| biopt_inf_antibiotic_type_fu | varchar | Do not map. What kind of antibiotic is given. 0 - not filled in, 1 - Fluoroquinolones, 2 - Trimethoprim-sulfonamide (TMP-SMX) combination, 3 - Cephalosporin (group 1 or 2), 4 - Cephalosporin (group >=3), 5 - Carbapenems, 6 - Penicillins (without B-lactam), 7 - Penicillins (with B-lactam), 8 - Aminoglycosides, 9 - Nitrofuran, 10 - other. | Measurement | |||
| biopt_inf_hospitalisation_fu | int | 0 | Hospitalisation due to bioptic infection. 0 - not filled in, 1 - yes, 2 - no. | Map biopt_inf_hospitalisation_days_fu if biopt_inf_hospitalisation_fu is 1 (“yes”). Do not map this variable separately. | Observation | |
| biopt_inf_hospitalisation_days_fu | int | 0 | Days in hospital. | Only map if biopt_inf_hospitalisation_fu is 1 (“yes). Map to Hospitalized or emergency room [ESRD] - 42869434 as target_concept_id. Store value as value_as_number and day - 8512 as unit_concept_id. | Observation | |
| biopt_inf_outcome_fu | int | 0 | Cured or death. 0 - not given (empty) 1 - cured 2 - death. | Do not capture when value is 0. Patient cured - 4159637, Patient died - 4216643 | Condition occurrence | |
| biopt_hematuria_fu | int | 0 | Hematuria for more than 3 days. 0 - not filled in, 1 - yes, 2 - no. | Only map if value is 1 (“yes”), map as variable_value. Blood in urine - 437038 | Condition occurrence | |
| biopt_hemospermia_fu | int | 0 | Hemospermia. 0 - not filled in, 1 - yes, 2 - no. | Only map if value is 1 (“yes”), map as variable_value. Hemospermia - 439871 | Condition occurrence | |
| biopt_pain_fu | int | 0 | Pain after biopsy. 0 - not filled in , 1 - yes, 2 - no. | Only map if value is 1 (“yes”), map as variable_value. Custom concept 2000000026 - Pain after biopsy | Condition occurrence | |
| biopt_route_fu | int | 0 | 0 - not given, 1 - transrectal 2 - transperineal. | Do not capture when value is 0. Transrectal biopsy of prostate - 4339403, Transperineal needle biopsy of prostate - 4142388 | Procedure occurrence | |
| biopt_max_cancer_score_lenght_fu | int | 0 | Size of prostate cancer (in millimeters) in a prostate cancer biopsy (size of largest cancer part). | Map to custom concept ‘Size of prostate cancer in biopt’ - 2000000027 as target_concept_id, unit concept is millimeter - 8588 | Measurement | |
| mri_taken | int | 0 | MRI made at baseline. Result MRI does not always have to be given, so save separately. 0 - ‘’, 1 - Yes, 2 - No. | Only map if value is 1 (“yes”), map as variable_value. MRI of prostate - 4192638 | Procedure occurrence | |
| mri_lesions | int | 0 | Abnormalities detected on MRI. 0 - ‘’, 1 - Yes, 2 - No. | Only map if mri_taken value is 1 (“yes”). Only map if value is 1 (“yes”), map as variable_value. MRI scan abnormal - 4059669 | Condition occurrence | |
| mri_suspected_number | int | 0 | Number of suspected abnormalities/lesions on MRI. 0 - 0, 1 - 1, 2 - 2, 3 - 3, 4 - >3 | Only map if mri_taken value is 1 (“yes”). Number of lesions - 4085855. Do not map when value is empty. | Observation | |
| mri_pirads_1 | int | 0 | The PIRADS score is given for each suspected lesion (maximum of 3). 0 - ‘’, 1 - 3 cancer is equivocal, 2 - 4 cancer is likely, 3 - 5 cancer is very likely | Only map if mri_taken value is 1 (“yes”). Do not map when value is 0 or empty. Map to custom concept ‘PI-RADS score’ - 2000000028 as target_concept_id. Only map score as value_as_number. | Measurement | |
| mri_largest_dia_1 | int | 0 | The largest diameter in mm of lesion 1. | Only map if mri_taken value is 1 (“yes”). Lesion size - 4084390, millimeter - 8588. Do not map when value is empty. | Observation | |
| mri_location_1 | int | 0 | Location of lesion 1 in the prostate. 0 - ‘’, 1 - anterior half, 2 - posterior half, 3 - both | Only map if mri_taken value is 1 (“yes”). Site of tumor - 4135405 (variable) as target_concept_id, following as value: Anterior - 4115458, Posterior - 4116868, Both - 45883500. Do not map when value is empty. | Observation | |
| mri_location_free_1 | varchar | Text field for extra information for mri_location_1. | Only map if mri_taken value is 1 (“yes”). Site of tumor - 4135405 (variable) as target_concept_id, following as value: Right - 45881626, Left - 45883143, Mid - 42531097, Apex - 21498546, Base - 21499230.Do not map when value is empty. | Observation | ||
| mri_pirads_2 | int | 0 | The PIRADS score is given for each suspected lesion (maximum of 3). 0 - ‘’, 1 - 3 cancer is equivocal, 2 - 4 cancer is likely, 3 - 5 cancer is very likely | Only map if mri_taken value is 1 (“yes”). Do not map when value is 0 or empty. Map to custom concept ‘PI-RADS score’ - 2000000028 as target_concept_id. Only map score as value_as_number. | Measurement | |
| mri_largest_dia_2 | int | 0 | The largest diameter in mm of lesion 2. | Only map if mri_taken value is 1 (“yes”). Lesion size - 4084390, millimeter - 8588. Do not map when value is empty. | Observation | |
| mri_location_2 | int | 0 | Location of lesion 2 in the prostate. 0 - ‘’, 1 - anterior half, 2 - posterior half, 3 - both | Only map if mri_taken value is 1 (“yes”). Site of tumor - 4135405 (variable) as target_concept_id, following as value: Anterior - 4115458, Posterior - 4116868, Both - 45883500. Do not map when value is empty. | Observation | |
| mri_location_free_2 | varchar | Text field for extra information for mri_location_2. | Only map if mri_taken value is 1 (“yes”). Site of tumor - 4135405 (variable) as target_concept_id, following as value: Right - 45881626, Left - 45883143, Mid - 42531097, Apex - 21498546, Base - 21499230. Do not map when value is empty. | Observation | ||
| mri_pirads_3 | int | 0 | The PIRADS score is given for each suspected lesion (maximum of 3). 0 - ‘’, 1 - 3 cancer is equivocal, 2 - 4 cancer is likely, 3 - 5 cancer is very likely | Only map if mri_taken value is 1 (“yes”). Do not map when value is 0 or empty. Map to custom concept ‘PI-RADS score’ - 2000000028 as target_concept_id. Only map score as value_as_number. | Measurement | |
| mri_largest_dia_3 | int | 0 | The largest diameter in mm of lesion 3. | Only map if mri_taken value is 1 (“yes”). Lesion size - 4084390, millimeter - 8588. Do not map when value is empty. | Observation | |
| mri_location_3 | int | 0 | Location of lesion 3 in the prostate. 0 - ‘’, 1 - anterior half, 2 - posterior half, 3 - both | Only map if mri_taken value is 1 (“yes”). Site of tumor - 4135405 (variable) as target_concept_id, following as value: Anterior - 4115458, Posterior - 4116868, Both - 45883500. Do not map when value is empty. | Observation | |
| mri_location_free_3 | varchar | Text field for extra information for mri_location_3. | Only map if mri_taken value is 1 (“yes”). Site of tumor - 4135405 (variable) as target_concept_id, following as value: Right - 45881626, Left - 45883143, Mid - 42531097, Apex - 21498546, Base - 21499230. Do not map when value is empty. | Observation | ||
| mri_progrssion_lesions | real | Progressions of lesions on MRI compared to previous MRI. | Only map if mri_taken value is 1 (“yes”). Do not capture when value is 0 or when value is empty. Progression - 4077864 (variable) as target_concept_id, capture values as value_as_number | Observation | ||
| mri_targeted_biopsy | int | 0 | Targeted biopsies. 0 - empty, 1 - yes, 2 - no | Only map if mri_taken value is 1 (“yes”). Only map if value is 1 (“yes”), map as variable_value. Map to MRI guided biopsy of prostate - 37109819 | Procedure occurrence | |
| mri_targeted_cores | int | 0 | Number of cores with prostate cancer from targeted biopsies taken. Only use when targeted biopsiess - yes (0 can mean both not given and no pc cores found). | Only map if mri_taken value is 1 (“yes”). Only map if mri_targeted_biopsy.0 is 1 (“yes). Number of Cores Positive - 35918000. Do not map when value is empty. | Measurement | |
| mri_targeted_taken | int | 0 | Number of cores taken from the abnormalities seen on MRI (targeted). | Only map if mri_taken value is 1 (“yes”). Number of Cores Examined - 35917476. Do not map when value is empty. | Measurement | |
| mri_targeted_gleason1 | int | 0 | Gleason primary grade at MRI | |||
| mri_targeted_gleason2 | int | 0 | Gleason secondary grade at MRI. Take sum of Mri_Targeted_Gleason1 and Mri_Targeted_Gleason2, concatenate column names to Mri_Targeted_Gleason1_Mri_Targeted_Gleason2 | Only map if mri_taken.0 value is 1 (“yes”). Total Gleason score - 4297949 (variable) as target_concept_id, following as value: ‘Gleason Grade Group 1’ - 1633550, ‘Grade Group 2: Gleason score 7 Gleason pattern 3+4’ - 1633826, ‘Grade Group 3: Gleason score 7 Gleason pattern 4+3’ - 1634459, ‘Grade Group 4: Gleason score 8’ - 1635079, ‘Grade Group 5: Gleason score 9 or 10’ - 1635009. Do not map when mri_targeted_gleason1 or mri_targeted_gleason2 value is empty. | Observation | |
| mri_lesion_positive | real | 0 | Number of lesions that are confirmed by biopt as prostate cancer. 0 can mean both not recorded and no positive found. | Only map if mri_taken value is 1 (“yes”). Number of Cores Positive - 35918000. Do not map when value is empty. | Measurement | |
| mri_method_used | int | 0 | Combine with mri_targeted_biopsy, if done also include this method. 0 - ‘’, 1 - Visual, 2 - Software, 3 - Inbore | Only map if mri_taken value and mri_targeted_biopsy is 1 (“yes”). Map as variable_value. ‘Visual targeting of MRI lesions’ - 2000000042, ‘Software targeting of MRI lesions’ - 2000000043, ‘In-bore targeting of MRI lesions’ - 2000000044. Do not map when value is empty. | Procedure occurrence | |
| mri_prostate_volume | int | Not measured by MRI, but manually entered based on MRI in ml. | Only map if mri_taken value is 1 (“yes”). Map as value of the variable mri_prostate_volume_method. Unit mL - 8587 | Measurement | ||
| mri_prostate_volume_method | int | Combine with mri_prostate_volume. 0 - ‘’, 1- Ellipsoid (W*H*L*0.52), 2- Segmentation, 3 - Other, specify in comment | Only map if mri_taken value is 1 (“yes”). Map to custom concept as variable_value: ‘Prostate MRI ellipsiod’ - 2000000045, ‘Prostate MRI segmentation’ - 2000000046, ‘Prostate MRI volume’ - 2000000047. Do not map when value is empty. | Measurement | ||
| year_visit | int | 2017 | Do not map, use days_psa_diag | |||
| days_psa_diag | int | Days since prostate cancer diagnosis (from the basedata table). If negative, report and do not include (to be fixed on source side). | Visit occurrence |
Table: enddata.csv
| Field | Type | Most freq. value | Description | Concept | Mapped to table |
|---|---|---|---|---|---|
| p_id | int | List truncated… | Patient id | Person | |
| nr_fuvisits | int | 4 | Number of follow up visits. Do not map, administrative (max from time in fudata) | ||
| discontinued | varchar | Robot radical prostatectomy | Given therapy Except; death, lost to follow-up and on request | If “Died”, map to PERSON.death_datetime, Withdrawn from research study - 44810920 (variable) as target_concept_id, following as value_concept_id: Robot assisted laparoscopic radical prostatectomy - 46270921, Teleradiotherapy procedure - 4141448 (synonym is External beam radiotherapy), No anti-cancer treatment - watchful waiting - 4190466, Radical prostatectomy - 4096783, Laparoscopic radical prostatectomy - 44809585, Other - 9177, Low dose rate brachytherapie - 4040610, Lost to follow-up - 4163894, Death - 4306655, Brachytherapy - 40317890, High dose rate brachytherapy - 4038003, Gonadotropin releasing hormone receptor antagonist - 4217107, Request status - 4202313, Androgen receptor antagonist - 35621899, High intensity focused ultrasound of prostate - 44791407 | Person, Observation |
| days_discontinued_diagnosis | int | 385 | Days from diagnosis to discontinuation? | Visit occurrence | |
| reason_treatment | varchar | Based on protocol advice | General reason for discontinuation in Active Surveillance (additional information may be still collected, not in extract) | Reason for discontinuation of care plan - 44807628 (variable) as target_concept id, following as value_concept_id: Following protocol - 44790553, Other - 9177, Not applicable - 4294169, Anxiety - 441542, Lost to follow-up - 4163894, Request status - 4202313. Do not map if value is empty. | Observation |
| days_surgery_diagnosis | int | Days from diagnosis to surgery. This is often later than discontinued Do not map, Often not given, use days_discontinued | |||
| pt | varchar | Surgery T stadium by pathologist Same mapping as dre | TNM Prostate tumor staging - 4110284 (variable) as target_concept_id, following as value: T0 category - 4243213, Tumor stage T1a - 4130414, Tumor stage T1b - 4129126, Tumor stage T1c - 4129916, Tumor stage T2a - 4129917, Tumor stage T2b - 4127611, Tumor stage T2c - 4129127, T3 category - 4032012, Tumor stage T3a - 4129918, Tumor stage T3b - 4130416, Tumor stage T3c - 4129919, Tumor stage T4a - 4127612, Tumor stage T4a - 4129920, Tumor stage T4c - 4129921, Tumor stage T4d - 4129129, TX category - 4282467. Split (*,*,*) before mapping. Do not map when value is empty. | Measurement | |
| pn | int | N stadium. 9 - pnx, unknown (no prostatectomy) 0 - pn0 1 - pn1 | TNM Prostate tumor staging - 4110284 (variable) as target_concept_id, following as value: NX category - 4195718, N0 category - 4266674, N1 category - 4203608. Do not map when value is empty. | Measurement | |
| pm | int | M stadium. 9 - pmx (no prostatectomy) 0 - pm0 1 - pm1 | TNM Prostate tumor staging - 4110284 (variable) as target_concept_id, following as value: MX category - 4098852, M0 category - 4149726, M1 category - 4205430. Do not map when value is empty. | Measurement | |
| gleason1_rad_prost | int | Radical (geheel verwijderd) prostatectomy - take sum of gleason1_rad_prost and gleason2_rad_prost | Measurement | ||
| gleason2_rad_prost | int | Radical (geheel verwijderd) prostatectomy - take sum of gleason1_rad_prost and gleason2_rad_prost | Gleason’s Score on Prostatectomy/Autopsy - 35918021 (variable) as target_concept_id, following as value: ‘Gleason Grade Group 1’ - 1633550, ‘Grade Group 2: Gleason score 7 Gleason pattern 3+4’ - 1633826, ‘Grade Group 3: Gleason score 7 Gleason pattern 4+3’ - 1634459, ‘Grade Group 4: Gleason score 8’ - 1635079, ‘Grade Group 5: Gleason score 9 or 10’ - 1635009. Do not map when gleason1_rad_prost or gleason2_rad_prost value is empty. | Measurement | |
| prostatevolume | varchar | Volume in ml as by pathologist | Prostate size - 4096978 as variable, remove “ml” when present in value, milliliter - 8587 as unit_concept_id | Observation | |
| tumorvolume | real | Volume in ml of only the tumor | Tumor volume - 4121185. Do not map when value is empty. | Observation | |
| ece | int | Extra capsulaire extension (yes/no/unknown) 0 - no 1 - yes 9 - unknown (do not map) | Only map if value is 1 (“yes”). T3a: Prostate tumor with extracapsular extension - 4241310. Do not map when value is empty. | Condition occurrence | |
| svi | int | Seminal vesical invasion (yes/no/unknown) 0 - no 1 - yes 9 - unknown (do not map, might not be different from empty) To be checked | Only map if value is 1 (“yes”). T3b: Prostate tumor invades the semical vesicle(s) - 4240691. Do not map when value is empty. | Condition occurrence | |
| pos_surgical_margins | int | Positive surgical margins Is the tumor completely (cleanly) removed? 0 - no 1 - yes 9 - unknown (do not map) | Do not map if value is 9 (“unknown”) or empty. Surgical margins cancer involvement - 3000370 (variable) as target_concept_id, following as value: 45882793 - Margins Involved, NOS, 45881006 - All margins negative | Measurement | |
| postoperative_psa | varchar | PSA level after surgery. Typical 6 weeks-3months after surgery | Split operator from value (e.g. “<” when present), map to operator_concept_id ‘<’ - 4171756. Map to custom concept ‘Total PSA level - postoperative’ - 2000000021. Do not map when value is empty. | Measurement | |
| pathology_reported | int | Do not map, administrative whether pathology done. | |||
| adjuvant_radiotherapy | int | Radiotherapy after surgery 1 - yes 0 - no 9 - unknown Only map 1 | Only map if value is 1 (“yes”). Adjuvant radiotherapy - 2000000019 as target_concept_id. | Measurement | |
| year_discontinued | int | 2015 | Year of discontinuation Do not use, instead use days discontinued and year_diag as proxy |