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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, where entity, quality, and possibly related entities are drawn from requisite ontologies. In addition, taxa (the rows of a character matrix) can be annotated with identifiers from a taxonomy ontology. Phenex saves ontology annotations alongside the original free-text character matrix data using the new NeXML format standard for evolutionary data.

Download & Installation

Phenex releases may include installers for certain platforms. To install Phenex on platforms for which the desired release does not contain an installer, the software needs to be built from source. Details can be found in the README.

Release Notes

See the Phenex release history for the list of issues addressed in each version.

Using Phenex

Please see the documentation and troubleshooting pages.

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. http://dx.doi.org/10.1371/journal.pone.0010500.

• 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. http://dx.doi.org/10.1186/2041-1480-5-45

Reporting bugs and feature requests

Report any bugs and make feature requests using the Phenex issue tracker.