Development of the Reference Plant Trait Ontology: A Unified Resource for Plant Phenomics

TitleDevelopment of the Reference Plant Trait Ontology: A Unified Resource for Plant Phenomics
Publication TypeConference Presentation
AuthorsCooper L
Secondary AuthorsMoore L, Arnaud E, Nelson RT, Menda N, Shrestha R, Grant D, Matteis L, Mungall CJ, Bastow R, McLaren G, Jaiswal P
Conference Name

Plant and Animal Genome XXI Conference

Conference Date2013
Date PresentedJan. 11-16, 2013

One of the central principles of biology is the concept that an organism’s genotype interacts with the environment to produce the observable characteristics, or phenotype. Understanding this interaction is a core goal of modern biology, and enables development of organisms with commercially useful characteristics through modern breeding programs. A number of crop- or clade-specific plant trait ontologies have been developed to describe plant traits important for agriculture in order to address major scientific challenges such as food security. Traditionally, phenotype information has been captured in a free text manner, which cannot be easily indexed and presents an obstacle to data sharing. Recent advances in next generation sequencing and phenotyping technologies have allowed researchers to access a growing mountain of data, resulting in an emerging gap between the genomics information and the quantitative information describing phenotypes and traits. One approach to overcome this obstacle is through the annotation of data using a common controlled vocabulary or “ontology". We present our vision of a species-neutral Reference Plant Trait Ontology (Ref-TO) which would be the basis for linking the disparate knowledge domains and that will support data integration and data mining across species. The Ref-TO is one of the modules for the Common Reference Ontology for Plant Science (cROP) which is being developed.

Type of WorkPoster presentation
Conference Location

San Diego, CA