PI: Pankaj Jaiswal (Oregon State University) CoPIs: Maria Gandolfo-Nixon (Cornell University), Dennis Stevenson (New York Botanical Garden)

Plant Ontology (PO) is a uniquely effective tool to bridge the knowledge developed by genetics, molecular biology, cell biology, taxonomy, botany, and the genomics research communities. During the course of this project, a common set of controlled vocabulary terms describing anatomical structures and developmental stages of the flowering and non-flowering plants will be developed. This will produce resolution to the divergences between the numerous terminologies used by different genomics projects and the nomenclatures used for various plant parts as described classically by plant taxonomists and anatomists as well as across other botanical subdisciplines. The standardization of definitions and naming of the vocabulary terms in the PO that describe either a plant structure or developmental stage provides a framework for fostering consistency in describing gene expression profiles and observed phenotypic traits. The consistent use of PO in descriptions, allows plant biologists and breeders to make meaningful cross-database and cross-species queries to discover patterns of similarities and dissimilarities, and discover the nature of evolutionary innovations. Also, it will allow the examination of the functions of genes and the genetic interactions associated with plant developmental processes and their contribution to agronomic and commercially significant phenotypic traits, such as improved disease resistance and biomass yield.

The project website is www.plantontology.org. All the contents and results of the project will be released to the public from this website resource. The project outreach program will organize teachers' training workshops and exhibits for students and general public. The focus of these workshops/exhibits will be Plant Biology awareness.

Project Report

(PO) project over the period of the award were (1) to develop a standardized, controlled vocabulary (ontology) to describe plant anatomy and growth and developmental stages of green plants, and (2) to use terms in these vocabularies to tag or annotatea diverse set of plant genetics and genomics experiments, covering a wide array of crops and plant species. There are numerous online databases and resources that host plant genomics and genetics data, many of which initially used non-standardized vocabularies in their data curation process. The PO fostered collaboration among these resources by bridging gaps and similarities between these non-standardized vocabularies, thus becoming a reference standard for plant anatomy and growth stage nomenclature. The structure and composition of the two branches of the PO, describing plant anatomy and developmental stages, were extensively revised and expanded to describe all plants. Throughout the revision process, the curators worked with plant anatomy, computer science and linguistic experts to incorporate advances in ontology design and construction. These included the use of standardized formats, rigorously-defined terms and relationships between the vocabulary terms that a computer and a human can decipher, and references to external ontologies where appropriate. Definitions were created or re-written in the genus-differentia form for many existing terms, as well as for all new terms. Collaborative projects were undertaken with a number of other research groups, working on moss (Physcomitrella), banana, Cassava, maize, rice, sorghum, nightshade plants, legumes, etc. The PO organized outreach and education (K-12) activities to extend PO usage in gene expression and phenotype annotations, and improve awareness of the PO in Plant Biology research. The PO was very active in outreach, resulting in extensive collaboration with over 30 major online plant genomics resources which use the Plant Ontology as an integrated vocabulary for gene, mutant and phenotype, germplasm and/or bio-sample annotation. The current database hosts about 1500 vocabulary terms and about 2.25 million annotations to plant genes, varieties, genomic loci with associated agronomic traits, etc. Project websites: Main project website: www.plantontology.org Mirror websites: Hosted by iPlant Collaborative: http://iplant.plantontology.org Hosted by Japanese collaborators: Project Documents: http://wiki.plantontology.org/ Project data repository (Includes Ontologies and annotated datasets): http://palea.cgrb.oregonstate.edu/viewsvn/Poc/ Submit ontology requests: https://sourceforge.net/p/obo/plant-ontology-po-term-requests/ License: Distributed under the Creative Commons Attribution-NoDerivs 3.0 United States License. Based on a work at www.plantontology.org.

National Science Foundation (NSF)
Division of Integrative Organismal Systems (IOS)
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Diane Jofuku Okamuro
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Oregon State University
United States
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