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Tools for working with HPO

TODO somewhat more detailed description of software for working with HPO

Java

  • phenol is a Java library for working with JSON phenotype ontologies including especially the HPO and the Mammalian Phenotype Ontology and associated phenotype annotation files.

Python

  • hpo-toolkit is a toolkit for working with HPO and HPO disease annotations in Python.
  • OAK, the Ontology Access Kit, is a Python lib for common ontology operations over a variety of backends.

R

  • HPOExplorer contains useful functions for working with the HPO. It allows you to create interactive phenotype network plots, as well as many other useful functions.