Phenofhy

Environment and setup ​

Phenofhy is designed to run in the Our Future Health (OFH) trusted research environment (TRE) with DNAnexus tooling inside a JupyterLab notebook.

Prerequisites ​

  • Working knowledge of Python is requried and an understanding of how to launch and run analyses in the Our Future Health DNAnexus TRE using JupyterLab.
  • For reference, an overview of resources for getting up to speed with DNAnexus TRE, the dx toolkit, and working on phenotypic data with JupyterLab is provided here.

Requirements ​

  • All you need is an active OFH TRE project on the DNAnexus platform and working knowledge of how to use JupyterLab (see Introduction to Jupyterlab)
  • DX_PROJECT_CONTEXT_ID set (already configured automatically in the TRE).
  • It is recommened you configure a config.json file in /mnt/project/helpers with file IDs and base paths (see Installation).

Metadata files ​

Phenofhy can automatically create the metadata files (codings, data_dictionary, entity_dictionary) that come with OFH and which can also be created with dx (see documentation provided by UK Biobank).

The helper load.metadata() downloads them into ./metadata if missing.

python
from phenofhy import load

meta = load.metadata()
# meta["codings"], meta["data_dictionary"], meta["entity_dictionary"]

TRE-only usage ​

Phenofhy can in theory be used on similuated data outside the OFH TRE for local testing but it is intended to be run inside the TRE.