🧬 BFF

BFF stands for Beacon Friendly Format. The BFF is a data exchange format composed of 7 JSON files. These files correspond to the 7 entities of the Beacon v2 Models.

Entities in Beacon v2 Models

About Beacon v2 Models' entities

Of the seven entities (a.k.a., entry types) in the Beacon v2 Models, individuals is typically the only one that contains phenotypic data (represented at record-level granularity).

As an input, Pheno-Ranker accepts data from the individuals entity, serialized in BFF format (individuals.json).

Browsing BFF JSON data

You can browse a public BFF v2 file with the following JSON viewers:

• JSON Hero
• Datasette

BFF (individuals) as input

When using the pheno-ranker command-line interface, simply ensure the correct syntax is provided.

Cohort modePatient mode

Basic run:

pheno-ranker -r individuals.json

The default output is named matrix.txt and it's a N x N bidimensional matrix with a pairwise comparison of all individuals.

For more information visit the cohort mode page.

Basic run:

pheno-ranker -r individuals.json -t patient.json

The output will be printed to STDOUT and to a file named rank.txt. The matching individuals will be sorted according to their Hamming distance to the reference patient. See aditional details in the Patient Mode page.

For more information visit the patient mode page.