Skip to content


Repository files navigation

Phenex - Ontological Annotation of Phenotypic Diversity

Phenex is an application for annotating character matrix files with ontology terms. Character states can be annotated using the Entity-Quality syntax for ontologically describing phenotypes. In addition, taxon entries can be annotated with identifiers from a taxonomy ontology. Phenex saves ontology annotations alongside traditional character matrix data using the new NeXML format standard for evolutionary data.

More information, including documentation of system requirements, installation, and usage, can be found at the Phenex website.


Phenex releases include installers for certain platforms.

To install on platforms for which an installer is not provided, Phenex needs to be built from source. To do so, you must have sbt (the Scala Build Tool) installed. (On MacOSX, a convenient way to do so is using Homebrew: brew install sbt.) Then run the following command:

$ sbt jdkPackager:packageBin

The build process will automatically download all dependencies, and hence may take some time when you run it for the first time.


Phenex has been developed as part of the Phenoscape project. It was influenced by and builds on Phenote and OBO-Edit from the OBO project.


Phenex source code can be used, modified, and distributed under the terms of the MIT License. Please see the file LICENSE for details.

How to cite

If you use Phenex in your research, please cite the following publications:

  • Balhoff, James P., Wasila M. Dahdul, Cartik R. Kothari, Hilmar Lapp, John G. Lundberg, Paula Mabee, Peter E. Midford, Monte Westerfield, and Todd J. Vision. 2010. Phenex: Ontological Annotation of Phenotypic Diversity. PLoS ONE 5:e10500.

  • Balhoff, James, Wasila Dahdul, T. Alexander Dececchi, Hilmar Lapp, Paula Mabee, and Todd Vision. 2014. “Annotation of Phenotypic Diversity: Decoupling Data Curation and Ontology Curation Using Phenex.” Journal of Biomedical Semantics 5 (1): 45.


Phenex is an application for annotating character matrix files with ontology terms using the Entity-Quality syntax for describing phenotypes.








No packages published