Phenopackets: An Ontology-Based Expressive Exchange Format for Phenotype and Trait Data

Standardized genomic data exchange formats and models make it easier for researchers and informaticians to combine different programs and datasets in large analyses. However, we currently lack a single exchange format capable of a wide range of phenotypic data. This is in part, due to the fact that phenotypic data encompassed a wide variety of scales and observation types. Ontologies produced by the Planteome project such as the Trait Ontology (TO) allow for the description of phenotypic data in a computable way, but are not in themselves sufficient for the exchange of data.

We have created an extensible exchange format for exchange of data relating to phenotypes called Phenopackets. This allows for phenotypic associations about plant entities such as germplasm or genes, qualified by environmental modifiers. The format uses JSON which is easily consumed in most programming environments, and semantics are provided by the use of JSON-LD.