Other formats

About other formats

Pheno-Ranker leverages the data harmonization provided by GA4GH standards. However, to promote broader adoption, we also support other formats like raw JSON/YAML and CSV.

YAML / JSONCSV

Pheno-Ranker a priori accepts as input "any" JSON or YAML array file. In order to do it, you'll need a configuration file. See a tutorial on how to use it here.

What do you mean by "any" JSON or YAML?

Pheno-Ranker can process deeply nested data structures. From v1.08 onward, arrays nested more than one level deep are canonicalized automatically from their meaningful content, so equivalent nested objects can match even if their order differs between records.

For first-level arrays in generic JSON, set format: JSON and declare indexed_terms. You can also add identity_paths to keep user-facing keys more interpretable, but from v1.08 onward generic JSON can infer default identities when those paths are absent. For deeper nested arrays, no extra identity path is required.

We developed an utility that converts CSV files to JSON and automatically creates the configuration file needed. See an example on how to use it here.