Phenex is an application for annotating character matrix files with ontology terms using the Entity-Quality syntax for describing phenotypes.
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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 builds on Phenote and OBO-Edit from the OBO project. Phenex has been initially developed as part of the Phenoscape project. If you use Phenex in your research, please cite the following publication: 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. [doi:10.1371/journal.pone.0010500](http://dx.doi.org/10.1371/journal.pone.0010500).