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NSF Funds iPlant-Supported Initiative, The Planteome Project

By Shelley Littin, iPlant Collaborative

The iPlant Collaborative-supported Planteome Project, an international collaboration to develop ‘Common Reference Ontologies and Applications for Plant Biology’ has been awarded three years’ funding by the National Science Foundation’s Plant Genome Research Program.

The Planteome Project will leverage cyberinfrastructure provided by the iPlant Collaborative, a NSF-funded initiative to provide computational infrastructure and software for life science research.

The goal of the Planteome Project is to develop data standards and reference vocabularies that can be used universally to describe plant gene and phenotype annotation. This will aid scientists to develop improved plant genotypes leading to agricultural crops capable of delivering higher yields and withstanding climate pressures.

The basic nutritional needs of the human population are provided by a few agricultural crops, which are struggling in the face of climate change. The continued production of adequate crops to serve human nutritional needs, especially as the climate changes and human population continues to grow, will require crops capable of producing higher yields while tolerating environmental stressors such as temperature, drought, and disease.

Source: Planteome Project

To advance research aimed at improving crops through bioinformatics and data-driven methods, plant scientists will require access to the results of a wide range of genomic and genetic studies. Current studies struggle with ontological inconsistencies, as researchers collecting and analyzing data rarely use the same annotations and terminologies to document their findings.

The Planteome Project aims to remedy this inconsistency by providing plant science with standardized reference vocabularies – including images to describe plant biology and stresses – and plant gene and phenotype annotation workflows.

“There are also significant benefits to general research,” said Pankaj Jaiswal, associate professor in the Department of Botany and Plant Pathology at Oregon State University, and leader of the Planteome Project. “By providing a non-redundant framework to analyze annotated plant genomic data, the Planteome expects to improve analysis capabilities. It will also save considerable resources as individual plant research groups will be encouraged to coalesce around common ontologies and avoid duplication of effort.”

“The project will work with iPlant in many ways,” Jaiswal continued. “The Planteome platform will leverage the iPlant Collaborative cyberinfrastructure for server, data, and service hosting, reducing the need for redundant infrastructure and increasing service integration opportunities with other iPlant-hosted and external projects.”

"As datasets become larger and more complex, we will increasingly need ontologies to be able to link data from different sources and make sense of the data," said Ramona Walls, an iPlant scientific analyst who has worked closely with the Planteome Project leaders on developing ontologies. "Projects like Planteome play a key part in iPlant's development of data management, search, and discovery tools."

A standardized gene and phenotype annotation workflow for plants will give plant researchers the ability to quickly and efficiently share discoveries, streamlining the advancement of plant genetic knowledge.

The international Planteome team also will develop a centralized web portal and data warehouse to host the vocabularies, images, and annotation information resulting from the project’s efforts, giving researchers in all areas of plant sciences a set of common reference points for comparative analysis of genomics and genetics data.

“The live database and the website will be hosted from the iPlant virtual machines, where it will benefit the tools and resources hosted by iPlant with unrestricted access to this data and resource,” said Jaiswal. “When mature, standardized workflow for gene function and phenotype annotations will be served from the iPlant’s Discovery Environment for anyone to use.”

“The goal,” he went on, “is that any new plant genome or transcriptome can pass through this workflow to get the same quality of annotation. The common reference ontologies would help in the annotation of common features and meta-data, thus allowing inter- and intra-specific comparison and analyses of datasets hosted by the iPlant tools.”

The Planteome Project database and resources are publicly available online under the Creative Commons License.

The Planteome Project includes co-investigators Dennis Stevenson of New York Botanical Garden, Chris Mungall of Lawrence Berkeley National Laboratory, Sinisa Todorovic and Eugene Zhang of the School of Electrical Engineering and Computer Science at Oregon State University, Elizabeth Arnaud of Bioversity International, France (A CGIAR Institute) and Georgios Gkoutos and John Doonan of Aberystwyth University, UK. In a consultative role for the project is Barry Smith of the National Center for Ontological Research and University of Buffalo, NY and founding member of the OBO Foundry initiative.

The iPlant Collaborative is a federation of the University of Arizona, Texas Advanced Computing Center, Cold Spring Harbor Laboratory, and the University of North Carolina Wilmington. iPlant is funded by National Science Foundation award numbers DBI-0735191 and DBI-1265383.