Phenofhy

Data model ​

Phenofhy uses a simple naming convention for fields:

  • Raw fields are entity.field (for example, participant.birth_year).
  • Derived fields live under derived.* (for example, derived.age_at_registration).

Metadata dictionaries ​

Phenofhy uses three dictionary files exported from DNAnexus:

  • *.codings.csv for code-to-label mappings
  • *.data_dictionary.csv for descriptions
  • *.entity_dictionary.csv for entity metadata

These files are loaded into ./metadata by pipeline.metadata().

Coding names ​

Coding names are matched using the field suffix, for example:

  • questionnaire.smoke_status_2_1 maps to coding name SMOKE_STATUS_2_1.