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


More documentation at the Phenex wiki

View the Project on GitHub phenoscape/Phenex

Running Phenex

To download and install Phenex, follow the instructions on the Phenoscape wiki. To launch Phenex, click (or double click, depending in your OS) the application.

When you see a message that Phenex is checking for ontology updates, the application has launched successfully. It may take a few minutes, particularly on the first run, to download ontology content.

Getting ontologies


Phenex requires Java 7 or higher. Follow this link to install the latest version of Java.