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The Plant Ontology: A Database for Plant Genomics

TitleThe Plant Ontology: A Database for Plant Genomics
Publication TypeConference Presentation
AuthorsCooper, L
Secondary TitlePlant Biology 2010
Conference Date2010
Date Presented2010

As data is generated from the various plant genome and comparative genomics projects, the working vocabulary from group to group and species to species can be disparate. To enable researchers across species to draw conclusions from known or predicted experiments, we are developing controlled vocabularies (ontologies) to describe plant morphologies, anatomical structures, and growth and developmental stages. Since the inception of the Plant Ontology (PO) database in 2003, plant biologists have been able to annotate and describe tissue and/or growth stage specific expression of proteins, genes, and phenotypes that were observed in experiments by utilizing PO terms in the database. There are currently over 1,100 terms documented in the PO, with over 500,000 associations, of which over 85% have been added within the last year. Currently, we are in the process of expanding the coverage of PO to non-angiosperm plants to include mosses (Physcomitrella), Lycopods (Selaginella), pteridophytes (ferns) and gymnosperms (conifers and cycads). We are also adding additional species-specific terms to accommodate annotations from Vitaceae (grape), Rosaceae (apple, cherry), Fabaceae (Medicago and soybean), Compositeae (sunflower), Solanaceae (potato, tomato), Poaceae (wheat, barley, oat, Sorghum and Brachypodium), Salicaceae (poplar) and Malvaceae (cotton). The development of the PO is coordinated with the development of the Gene Ontology (GO), and together these resources can be used to provide a comprehensive picture of the function, location and phenotypic effects of genes and gene products. The Plant Ontology project is funded by the National Science Foundation, USA and includes collaborations with groups from around the world.

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