From the Phenex home page:
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. Phenex is hosted by the OBO project and builds on Phenote and OBO-Edit. Jim Balhoff is the lead developer of Phenex.