Bio-Ontologies for the Plant Sciences
International Botanical Congress 2011 Symposium Proposal
Symposium Title: Bio-ontologies for plant science
Organizers: Ramona Walls (NYBG) and Pankaj Jaiswal (OSU)
The age of “omics” is the age of mass information. Complete genomes for at least 40 plant species have been generated or are in progress (Joint Genome Institute: http://www.jgi.doe.gov/genome-projects), and new EST, QTL, and other genomic data sets are being generated continuously. All this information creates exciting new possibilities for comparative developmental, genetic, and genomic studies but comes with the challenge of integrating data from disparate sources. Biological ontologies (bio-ontologies) have become an indispensable tool for organizing and accessing the massive amounts of genomic/genetic data being created and for insuring the consistent use of vocabulary across taxa and disciplines. An ontology is a structured vocabulary, containing terms, attributes of terms, and relationships among terms. Bio-ontologies are used for the systematic annotation (or ‘tagging’) of data, documenting associations between genes, gene products, and sequences and the structures, processes, and functions to which they contribute. This symposium provides an overview of the bio-ontologies available to plant scientists as well as the current and potential uses of these ontologies. In conjunction with the symposium, the organizers would like to conduct outreach activities to engage research groups that are working in genomic/genetic data generation and analysis. These include an annotation workshop and hands-on demonstrations of the Plant Ontology. Although many groups working on the genomics of well-studied model organisms are already actively involved in ontology use, those working on non-model species may not be taking advantage of the resources offered by bio-ontologies. We aim to engage a broader user base through this symposium, anticipating that advances in comparative genomics will require concerted annotation efforts and collaboration throughout the plant science community.
The symposium will begin with an introduction to bio-ontologies and ontologies in general. This talk will describe what ontologies are, how they work, and the existing bio-ontologies that are relevant to plant sciences. It will include information on the ongoing efforts to increase interoperability among ontologies within the framework of the OBO (Open Biomedical Ontologies) Foundry. The next two talks will describe the bio-ontologies most widely used by plant scientists to study gene expression: the Gene Ontology (GO) and the Plant Ontology (PO). The GO consists of 3 sub-ontologies – cellular components, biological processes, and molecular functions – that are applicable to all living organism and are in broad use by the genomics community. The PO contains ontologies for plant structures as well as plant growth and developmental stages, with terms that are applicable to all plants, from algae to angiosperms. Each of these talks will provide sufficient information to allow audience members to access and begin using the ontologies. The three remaining talks will focus on applications of bio-ontologies, including studies that have used ontologies in their analyses and reports from organizations that are developing organism-specific ontologies to advance their agendas. We have several prospective speakers for this part of the symposium, but welcome participation from other presenters who are working in ontology development or applications.
