Blogs

NSF Funds Development of Common Reference Ontologies and Applications for Plant Biology

The Plant Genome Research Program (National Science Foundation) recently awarded funding for three years to The Planteome Project (http://www.planteome.org), an international collaboration to support the development of “Common Reference Ontologies and Applications for Plant Biology”.

The goals of the Planteome Project are to provide researchers and agricultural breeding programs a common semantic framework ,and a focused set of comparative analysis tools to leverage the scientific value of the ever-expanding array of sequenced plant genomes and phenotype data. The Planteome Project will develop a set of common data standards and universal reference vocabularies to describe plant biology and plant stresses, and standardized plant gene and phenotype annotation workflows.
As part of the project’s outreach effort the project team will reach out to K-12 and undergraduate students and the plant research community. The project will conduct annual hands-on STEM summer camps to teach high school students about plant genomics and computational biology and will organize exhibits at the New York Botanical Garden, as well as hosting workshops and webinars, and producing publications for plant scientists.
The Planteome Project database and data resources are freely accessible online under the Creative Commons License, and are available from the project website http://www.planteome.org.

The Planteome Project:
Link to NSF award abstract: http://www.nsf.gov/awardsearch/showAward?AWD_ID=1340112

Principle Investigator:
Pankaj Jaiswal, Associate Professor, Department of Botany and Plant Pathology, Oregon State University (OSU: http://www.oregonstate.edu)
CO-Investigators:
Dennis Stevenson, New York Botanical Garden (http://www.nybg.org)
Chris Mungall Lawrence Berkeley National Laboratory (http://www.lbl.gov)
Elizabeth Arnaud, Bioversity International, France (a CGIAR Institute) http://www.bioversityinternational.org/
Sinisa Todorovic, School of Electrical Engineering and Computer Science (EECS), OSU
Eugene Zhang, EECS, OSU
Senior Collaborators:
Georgios Gkoutos, Aberystwyth University, UK, http://www.aber.ac.uk/en/
John Doonan, Director National Plant Phenomics Centre, Aberystwyth University, UK,
Consultant: Barry Smith, National Center for Ontological Research, and University of Buffalo, NY, Founding member of the OBO Foundry Initiative (http://www.obofoundry.org/)

Postdoctoral Scholar Position Available: Biocuration and Ontology Development for Plant Genomics and Phenomics

The Jaiswal Lab (Department of Botany and Plant Pathology, Oregon State University) has available an immediate full-time job opening at the level of Postdoctoral Scholar for a Biocurator-Ontology Developer for the Planteome Project (http://planteome.org/). The ideal candidate will be a recent PhD (within 0-5 years) with strong publication record, and experience in one or more of the following areas: plant biology, bioinformatics, genomics, phenomics, quantitative genetics, molecular biology, and next generation sequencing-based large data analytics.

Experience with, and knowledge of genes, genomes, genetic diversity, mutations, phenotypes, gene expression analyses, biological databases and biological ontologies is highly desirable. If successful, you will work with a team of curators, software engineers, bioinformatics scientists, and database developers of the Planteome Project. It is a newly-funded initiative with a mandate to develop and enrich reference ontologies for plants, and develop a suite of analysis tools with a wide array of visual, statistical, and biological utility to provide new insights into plant phenotypes, genetic diversity, genomes, gene homology and molecular functions of genes.

The successful candidate will have a demonstrated ability for independent, critical thinking, attention to detail, excellent communication, and teamwork skills. Familiarity with spreadsheets, literature databases, basic UNIX commands, and commonly-used biological research tools such as BLAST is desired. A working knowledge of Perl and/or SQL will be considered an asset but is not required. Excellent English, written and oral, and interpersonal communication skills are essential. Must be willing to travel and present at national and international meetings, and able to function as a communicative, pragmatic, and diplomatic member of a research team with diverse expertise and perspectives.

Interested candidates should submit (1) a cover letter citing your experience and interest in the position, (2) curriculum vitae, (3) your current and future research interests and (4) names and full contact information of three references to: jaiswalp@oregonstate.edu. One of your references should be your current major supervisor.

If shortlisted, the candidate must be available for an online interview, and/or willing to travel for an onsite interview on short notice.

Syndicate content