Software libraries for Working with the HPO

Below is a collection of software libraries that make it easy to work with the Human Phenotype Ontology across different programming languages.

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Python

Python Libraries

hpo-toolkit
GitHub

A Python toolkit for working with HPO and HPO disease annotations.
Lightweight, fast, and easy to integrate into analysis workflows.

Ontology Access Kit (OAK)
GitHub

A powerful library for accessing and manipulating ontologies using multiple backends (SQLite, pronto, OBOGraph, APIs, etc.). Supports querying, transformation, and validation.

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Rust

Rust libraries

ontolius crates.io

A fast and safe crate for working with biomedical ontologies including HPO.

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Java

Java Libraries

phenol
GitHub

A high-performance Java library for working with JSON-based phenotype ontologies including the HPO and Mammalian Phenotype Ontology (MP). Includes tools for parsing, annotation handling, and ontology traversal.

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R

R Libraries

HPOExplorer
GitHub

A feature-rich R toolkit for visualizing and analyzing the HPO. Includes interactive phenotype networks, semantic similarity, and annotation utilities.