README.md

metadata

title: PhenoGenius
emoji: genie
sdk: streamlit
sdk_version: 1.25.0
app_file: phenogenius_app.py
python_version: 3.8
pinned: true

PhenoGenius

Symptom interaction modeling for precision medicine

Overview

Symptom interaction model provide a method to standardize clinical descriptions and fully exploit phenotypic data in precision medicine.

This repository contains scripts and files to use PhenoGenius, the phenotype matching system for genetic disease based on this model. Please try PhenoGenius in the cloud at https://huggingface.co/spaces/kyauy/PhenoGenius.

If you use PhenoGenius, please cite:

Yauy et al., Learning phenotypic patterns in genetic disease by symptom interaction modeling. medrXiv (2023). https://doi.org/10.1101/2022.07.29.22278181

Install

• Requirements

python == 3.8 #(pyenv install 3.8)
poetry #(https://python-poetry.org/docs/#installation)

• Install dependencies

poetry install

Use streamlit webapp in your desktop

Run

poetry shell
streamlit run phenogenius_app.py

Use command-line client

Run

poetry shell
python phenogenius_cli.py --hpo_list HP:0000107,HP:0000108,HP:0001407,HP:0005562 --result_file PKD1.tsv

Usage: phenogenius_cli.py [OPTIONS]

Options:
  --result_file TEXT  Output file name, default = match.tsv
  --hpo_list TEXT     (Mandatory) List of HPO terms to match, separated with
                      commas
  --gene_list TEXT    (Optional) List of genes in NCBI ID format to match,
                      separated with commas

Explore interactive graphs of symptoms interactions

Human Phenotype Ontology

Click on the image!

Groups of interacting symptoms

Click on the image!

Enjoy !

License

PhenoGenius is licensed under the Apache License, Version 2.0. See LICENSE for the full license text.

Misc

PhenoGenius is a collaboration of :