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Open Data: Ontologies & Genomes

Booth 46

Open Data Access, Standards, Ontologies, Tools, and Applications for Genomics, Breeding, Food, Nutrition and Health

New and improved technologies combined with high-throughput output and analytics are evolving to revolutionize the application of BIG-data driven studies on improving crops for yield, post-harvest traits, genetics, genomics, plant breeding, microbiome, and quality. These applications are currently prioritized to meet the sustainable access to healthy food, nutrition, and diet required for avoiding hunger and sustain healthy human population, healthy planet, and healthy environment, all of which are challenged by the biotic (disease and pests) and abiotic (drought, salinity, temperature) stresses on food and feedstock crops confounded by climate change.


Various open data portals are doing their best on building good data repositories and quality annotation to help find trends, patterns and perform better analytics supporting the research programs and management practices. However, often times we observe deficiencies in integrating standards for semantic data format, exchange, and annotations, thus making it difficult to review, reuse and research the existing and new incoming BIG-data. Therefore, this group of collaborators is working on developing plant data commons, standards and ontologies for defining traits, best management practices, food, nutrition, environment, treatments, stresses, diseases, genomics, genetics, systems biology and education and training.

The group includes, the NSF-funded projects namely the, Planteome (project developing common reference ontologies for plant biology) and Gramene (a plant comparative genomics and genetics database with resources for about 40 plant genomes and pathways); the CGIAR’s Crop Ontology project and the Agricultural Nutrition and Technology ontology (ANT) and Agronomy Ontology (AgrO); the IC3-FOODS, International Conference/Consortium/Center for Food Ontology Operability Data and Semantics at University of California, Davis.

Contact: jaiswalp@oregonstate.edu

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