Data dictionary v1

File tree

.
└── 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