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Planteome 1.0 Release, September 2016

The Planteome project (www.planteome.org), an international collaborative effort, is pleased to announce their first full release of the database and ontology browser. This is a centralized portal where common reference ontologies (structured, controlled vocabularies) for plants are used to annotate gene expression, traits, phenotypes, genomes, and genetic diversity, across a wide range of plant taxa. Reference ontologies for plants, developed by the Planteome, include the Plant Ontology (PO), Plant Trait Ontology (TO), and the Plant Environment Ontology (EO), and the Planteome portal also provides reference ontologies developed by collaborating groups: the Gene Ontology (GO), the Phenotypic Qualities Ontology (PATO), the Chemical Entities of Biological Interest (ChEBI), and the NCBI taxonomy. In addition, Release 1.0 includes for the first time, four species-specific trait ontologies for wheat, rice, lentil and cassava, developed by the Crop Ontology (http://www.cropontology.org/), a project of the CGIAR. These species-specific ontologies have been mapped to the relevant reference Trait Ontology terms for data integration.  

In the current Release 1.0, the Planteome database includes 67,272 ontology terms with links to approximately 1.9 million (M) bioentities (data objects) including proteins, genes, RNA transcripts and gene models, germplasm, and QTLs. Bioentities were often annotated to more than one ontology term, resulting in approximately 17.2M annotations. Annotated data was sourced from 24 unique database resources and covers 86 different plant taxa. Functional GO annotations are available for 62 species, which, for many of these species, the Planteome is a unique annotation resource.

You can view or download a brochure about Planteome Project here: http://planteome.org/documents

The Planteome browser can also be accessed by visiting our mirror site at CyVerse: http://draco.cyverse.org/amigo

The Planteome Project (http://planteome.org/) is funded by the National Science Foundation (NSF Award #1340112), and is accessible for use from the Planteome project website.

Open Data: Ontologies & Genomes to be presented at the GODAN Summit 2016

The Planteome Project is partnering with Gramene and other ontology developers at the CGIAR, and Univ. of California, Davis, to present Open data, Tools and Standards at the #GODANSummit2016.

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. Food and feedstock crops are often challenged by biotic (disease and pests) and abiotic (e.g. drought, salinity, temperature) stresses, which can be confounded by climate change.  Emerging technologies are prioritized to ensure sustainable access to healthy food, nutrition and diet, to prevent hunger, and to sustain a healthy human population,  environment and planet.

Open data portals are building robust data repositories, with quality data annotation, to help find trends, patterns and perform better analytics in support of research programs and management practices.  However, deficiencies still exist 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.

This group of collaborators is developing plant data standards, commons and ontologies for defining plant traits, best management practices for food, nutrition, environment, treatments, stresses, diseases, genomics, genetics, systems biology, and education and training.

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

Information adapted from:  http://goo.gl/gz1VzG

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