Phenol: Ontology Library for Phenomics and Genomics

A Java library for working with JSON phenotype ontologies including especially the Human Phenotype Ontology and the Mammalian Phenotype Ontology and associate phenotype annotation files.

In Brief

• Language/Platform: Java >=11

• License: BSD 3-Clause Clear

• Version: 2.0.0-RC5

• Authors:

  • Sebastian Bauer
  • Peter N. Robinson
  • Sebastian Koehler
  • Max Schubach
  • Manuel Holtgrewe
  • HyeongSik Kim
  • Michael Gargano
  • Daniel Danis
  • Jules Jacobsen

• Availability:

  • phenol-core for dealing with (biological) ontologies.
  • phenol-io for reading ontologies from JSON files.
  • phenol-annotations for reading computational disease models of the HPO project
  • phenol-analysis several demo apps showing how to use phenol.
  • phenol-cli for performing empirical score distribution computation as a stand-alone program.

Usage

We recommend indicating the phenol version in the properties section of the pom file of the application.

<properties>
  (...)
  <phenol.version>2.0.0-RC5</phenol.version>
</properties>

Then import the phenol modules that are needed for your application.

<dependency>
    <groupId>org.monarchinitiative.phenol</groupId>
    <artifactId>phenol-core</artifactId>
    <version>${phenol.version}</version>
</dependency>
<!-- ... and other modules -->

History

Phenol was initially forked from ontolib in February 2018, but was extensively refactored and extended. The API of phenol and ontolib are not compatible with each other.