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

• 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 importing the phenol modules that are needed for your application.

For instance:

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

where ${phenol.version} corresponds to the desired version, such as 2.1.0.

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.