Crop Plant Trait Ontology Workshop, Oregon State University

Categories: guest blogger, Workshops
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Published on: October 9, 2012

For the last few months, Ruth has been involved in organising a Crop Plant Trait Ontology Workshop which happened at Oregon State University on 13-15 September. Laura Cooper and the Crop Ontology Workshop Planning Committee put together a news piece about the event.

Plant breeders, biologists and bioinformatics specialists from ten countries and two plant agribusinesses gathered in Corvallis, Oregon for the Crop Plant Trait Ontology Workshop. The workshop was hosted by the Plant Ontology and the Trait Ontology consortiums, and co-organised 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, in order to widen their awareness about ontologies and showcase the latest developments in ontologies for plants. In addition to hearing presentations, participants learned to use the ontology editor OBO-Edit and worked in small groups to classify plant trait terms which had been submitted in advance.

The main conclusion of the workshop was that there is a need for a broad, co-ordinated 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.

The hope is that in creating a Common Reference Trait Ontology for Plants, we will facilitate plant genetic and phenotypic data discovery and exchange.

For further information including a list of participants and sponsors, and links to presentations, visit the workshop wiki page at http://tinyurl.com/Trait-Ontology.

Other links:

Plant Ontology http://www.plantontology.org

Trait Ontology: http://www.gramene.org/plant_ontology/ontology_browse.html#to

TransPlant: http://transplantdb.eu/

European Bioinformatics Institute: http://www.ebi.ac.uk

GARNet: http://www.garnetcommunity.org.uk

Generation Challenge Program: http://www.generationcp.org

Sol Genomics Network: http://solgenomics.net/

SoyBase: http://soybase.org/

OBO-Edit; http://oboedit.org/

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