HPO survey analysis

A library for analyzing surveys utilizing the HPO

What's Included?

• phenom: a python library with modules for querying monarch remote services, working with ontologies, and performing semantic similarity and distance computations
• Jupyter notebooks demoing various tasks
• Scripts for generating synthetic patient data, clustering, and evaluation

Getting Started

virtualenv

virtualenv venv -p /usr/bin/python3.7
source venv/bin/activate
pip install -r requirements.txt
export PYTHONPATH=.:$PYTHONPATH

Running notebooks with docker

docker build . --tag hpo-subset:latest
docker run --rm -it -p 8888:8888 --hostname localhost -v $PWD/notebooks/:/hpo-subset/notebooks/ hpo-subset jupyter notebook notebooks --ip=0.0.0.0 --allow-root --no-browser
Copy the URL and replace "(localhost or 127.0.0.1)" with either "localhost" or "127.0.0.1" (without quotes)

Features

• Implementations of common semantic similarity algorithms
• Disease and/or phenotype class enrichment (fisher exact)
• Clustering phenotype profiles
• Utilities for generating derived profiles from hpo rare disease annotations
• Simulate patient data

Example Surveys of Interest

• Phenotypr: http://body.phenotypr.com/phenotypr/
• GenomeConnect: https://www.genomeconnect.org/