Phenol: Ontology Library for Phenomics and Genomics

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

In Brief

• Language/Platform: Java >=8

• License: BSD 3-Clause Clear

• Version: 1.2.5-SNAPSHOT

• Authors:

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

• Availability:

  • Maven module phenol-core for dealing with (biological) ontologies (Javadoc via javadoc.io).
  • Maven module phenol-io for reading ontologies from OBO files (Javadoc via javadoc.io).
  • Maven module phenol-cli for performing empirical score distribution computation as a stand-alone program.
  • Maven module phenol-analysis -- still experimental module for enrichment analysis).

Usage

We are working on the first public distribution of phenol, which we will make available on maven central. For now, to use phenol in application code, it must be installed locally by cloning this GitHub repository and entering the following command.

$ mvn install

This will install the phenol library code into your local maven repository (.m2 directory) and thereby make it available to application code, which can use phenol by adding the following stanza to the pom.xml file.

<dependency>
    <groupId>org.monarchinitiative.phenol</groupId>
    <artifactId>phenol-io</artifactId>
    <version>${phenol.version}</version>
    <exclusions>
        <exclusion>
            <groupId>org.slf4j</groupId>
            <artifactId>slf4j-api</artifactId>
        </exclusion>
    </exclusions>
</dependency>

The above stanza shows the code that is needed for the phenol-io component, and also shows how to exclude the slf4j version from the application code (which can help to avoid maven enforcer errors). Add analogous stanzas for other phenol modules.

Input files

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.