Phenote is both a complete piece of software and a software toolkit designed to facilitate the annotation of biological phenotypes using ontologies. It provides an interface and infrastructure to record genotype-phenotype pairs, together with the provenance for the annotation. Typical users of Phenote include literature curators, laboratory researchers, and clinicians looking for a method to record data in a user-friendly and computable way.

Data annotated with Phenote is based on the EQ model for representing phenotypes, combining entities from any ontology with qualities (such as those in PATO).

Features include:

• Friendly spreadsheet-like interface
• Type-ahead-suggest (autocompletion) for terms within ontologies
• Use of any OBO-format ontology (or OWL->OBO converted)
• Ontology navigation and all-in-one term information display
• Bulk copy/edit/delete/sort of phenotype-genotype character entries
• Excel-compatible output format (tab-delimited)
• Additional export formats: phenosyntax, xml
• Configurable input fields to allow custom data entry and user-specified ontologies
• Preconfigurations available for different communities
• Easy to customize your own configuration