pumpkin-py 0.0.1a3

PumpkinPy - Semantic similarity implemented in python

About

PumpkinPy uses IC ordered bitmaps for fast ranking of genes and diseases. This is useful for larger ontologies such as Upheno and large datasets such as ranking all mouse genes given a set of input HPO terms. This approach was first used in OWLTools and OwlSim-v3.

The goal of this project was to build an implementation of the PhenoDigm algorithm in python. There are also implementations for common measures for distance and similarity (euclidean, cosine, Jin-Conrath, Resnik, jaccard)

Disclaimer: This is a side project and has little documetation and only a modest amount of testing

Getting Started

Requires python 3.8+ and python3-dev to install pyroaring

python3.8 -m venv venv
source venv/bin/activate
pip install -r requirements.txt
export PYTHONPATH=.:$PYTHONPATH

Fetching annotations and closures

Uses robot and sparql to generate closures and class labels

Annotation data is fetched from the latest Monarch release

• Requires >Java 8

cd data/monarch/ && make

PhenoDigm Reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3649640/
Exomiser: https://github.com/exomiser/Exomiser
OWLTools: https://github.com/owlcollab/owltools
OWLSim-v3: https://github.com/monarch-initiative/owlsim-v3