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Phenol: Ontology Library for Phenomics and Genomics

A Java library for working with JSON phenotype ontologies including especially the Human Phenotype Ontology (HPO), Gene Ontology (GO), and the Mammalian Phenotype Ontology (MP) and associated phenotype annotation files.

History

Phenol was forked from Ontolib <https://github.com/Phenomics/ontolib> in April 2018, and since has been extensively refactored and extended to provide additional functionality for working with phenotype annotations. Several classes from the Ontologizer <http://ontologizer.de/>, which we initially programmed in Java 1.5, have been refactored to support Gene Ontology overrepresentation analysis (see Bauer et al., 2008.

Authors

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

Feedback

The best place to leave feedback, ask questions, and report bugs is the Phenol Issue Tracker.