Building a reference plant ontology

2nd Oct 2012

Plant breeders, biologists and bioinformatics specialists from ten countries, seven US states and two plant agribusinesses gathered in Corvallis, Oregon, September 13th-15th, 2012 for a Crop Plant Trait Ontology Workshop. The workshop was hosted by the Plant Ontology and the Trait Ontology, and co-organized by TransPlant, European Bioinformatics Institute, GARNet, Generation Challenge Program, Sol Genomics Network, and SoyBase. The goal of the workshop was to engage researchers associated with major cultivated crops worldwide, widen their awareness and showcase the latest developments in ontologies for plants. We concluded that there is a need for a broad, coordinated effort to create a semantic framework for meaningful cross-species queries using a Common Reference Ontology for Plants. This Reference Ontology will encompass all green plants and will facilitate queries for related gene expression and phenotype data from plant genomics, genetics experiments from the various species- and clade-specific databases and describe accessions in the various international crop germplasm collections. In addition to the presentations, participants engaged in hands-on activities, learning to use the ontology editor OBO-Edit and working in small groups to classify plant trait terms which had been submitted in advance. By creating a Common Reference Trait Ontology for Plants, we can achieve the goal of facilitating plant genetic and phenotypic data discovery and exchange. For further information, list of participants and sponsors, links to presentations and more details, please visit the workshop wiki page at

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