Introducing Phenex

After a summer of intensive development, at our recent Data Roundup we introduced curators to our new phenotype annotation software, Phenex. 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 replaces Phenote as our data curation tool.  Phenote was developed by the Berkeley Bioinformatics and Ontologies Project to facilitate the annotation of biological phenotypes using ontologies.  By creating a custom configuration of Phenote to support our data requirements, we were able to immediately begin annotating phenotypes.  Because Phenote provides a flat table of annotations, it works well for curation of the prominent phenotypes of a few genotypes at a time, such as in model organism mutants.  However, evolutionary data is usually collected in the form of a character by taxon matrix, recording a value for each character for every taxon.  Over time we added several custom interface features to Phenote to better support annotation of evolutionary data.  However curation of data from real publications at our first Data Jamboree, in April 2008, revealed that our initial workflow was cumbersome and error prone.

Like Phenote, Phenex facilitates the construction of annotations using ontology terms.  In Phenex, however, the data model and interface are organized in a format that will be familiar to any evolutionary biologist who has used a character matrix.  The new design addresses several requirements highlighted by user testing at the April Data Jamboree:


  • Manage independent lists of Taxa, Characters, and States, tied together via a data matrix.
  • Facilitate entry of basic free text matrix data by undergraduate assistants.
  • Allow morphology experts to focus on translating character state descriptions into ontology annotations without simultaneously managing unwieldy lists of taxa.
  • Easily import data from published NEXUS matrix files.
  • Include ontology annotations within a standard evolutionary data matrix file format.


We addressed this last requirement by adopting the new NeXML file format.  Being an XML schema, NeXML allows us to embed ontological annotations directly within standard evolutionary data.  Thus the standard data in Phenex documents should be usable in any evolutionary analysis software which supports NeXML.

Although Phenex began as an offshoot of Phenote, it is now a completely separate application hosted at the OBO project site.  Like Phenote, Phenex builds upon OBO-Edit as an application framework for working with ontologies.  While Phenex has been developed with the needs of Phenoscape in mind, it should be useful to anyone working with ontologies and evolutionary data.  We hope it can become a general tool for evolutionary biologists incorporating ontologies into their work.  More information about Phenex can be found on its homepage, including instructions for downloading the application and obtaining its source code.

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