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.

Annotations recorded by Phenote are based on the EQ model for representing phenotypes, combining entities from any ontology with qualities (such as 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