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Data dictionary v1

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└── brca-psj-path
    ├── csv
    │   ├── metastatic-dx.csv
    │   ├── outcomes.csv
    │   └── slide-biopsy-map.csv
    └── ndpi
        ├── 2017
        │   ├── 0f12826b-e163-41a7-ae9d-f77a483132b9.ndpi
        │   └── ...    
        ├── 2018
        │   ├── 0001669a-9515-42f2-926b-48f153fd9643.ndpi
        │   └── ...    
        ├── 2019
        │   ├── 00039118-e679-40af-8101-7da02995c392.ndpi
        │   └── ...    
        └── 2020
            ├── 00d89c92-d0b7-4fc7-a9b9-97661b3145a4.ndpi
            └── ...    

Slide biopsy mapping

slide-biopsy-map.csv contains the mapping to connect each biopsy slide file with the biopsy case. The number of slides for each biopsy varies.

Column Name Description Sample
slide_id Unique identifier for each digital pathology image file .ndpi ef996991-e4ec-442e-a26c-07ad30cb330c
biopsy_id Unique identifier for each biopsy case 8dc5bacb-5904-45c4-9136-8aa8e16c3711

Outcomes table

outcomes.csv contains the outcomes for each biopsy case. There are patient that have multiple biopsies. The times in this table are relative to the biopsy.

Column Name Description Sample
biopsy_id Unique identifier for each biopsy case 8dc5bacb-5904-45c4-9136-8aa8e16c3711
patient_ngsci_id Unique patient identifier 850087af-b4ff-4894-b13d-633c29073d93
case_year Year of biopsy 2018
mortality If there is a record of patient death
0: no death record
1: death
1
time_to_death Time after biopsy until death (days) 71
stage First cancer stage determined after biopsy for patient within a year IA
stage_max Highest cancer stage determined after biopsy for patient within a year IIA
metastatic_dx Whether patient has a metastasis diagnosis
0: no
1: yes
0
time_to_metastasis Time to first metastatic disease diagnosis (days). 60

Metastatic diagnosis

metastatic-dx.csv contains metastatic ICD-9 diagnosis codes with the whole number 174, 175, 196, 197, 198.

Column Name Description Sample
biopsy_id Unique identifier for each biopsy case 8dc5bacb-5904-45c4-9136-8aa8e16c3711
time_to_dx Time to diagnosis (days). 72
icd9 ICD-9 diagnosis codes for the patient with the whole number 174, 175, 196, 197, 198 175.1

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