The Plant Ontology: a tool for structural, developmental, and molecular plant biologists

TitleThe Plant Ontology: a tool for structural, developmental, and molecular plant biologists
Publication TypeConference Presentation
AuthorsWalls RL
Secondary TitleBotany 2010
Conference Date2010
Date PresentedJul. 31 - Aug. 4
Abstract

The Plant Ontology (PO: http://www.plantontology.org) was developed to accommodate functional annotation efforts by plant databases in particular and the plant research community in general. Participating databases such as TAIR, NASC, Gramene, and MaizeGDB, have been using the PO since 2003 to describe structure- and growth-stage-specific expression of genes, proteins, and phenotypes from mutants and natural variants. The PO consists of two interrelated ontologies: 1. Plant Structure and 2. Plant Growth and Developmental Stages. Each ontology consists of a structured vocabulary that includes both definitions of terms and relationships among terms. In addition, there are links to annotations for associated genes, literature references, and images. To date there are over 1100 terms in the PO and over 500,000 associations. The original scope of the PO was a few model angiosperm species (Zea mays, Arabidopsis thaliana, and Oryza sativa), but with the expansion of sequencing information from new genomes, the PO is also expanding. We are working to encompass all land plants, making new cross-taxon comparisons possible. Additional species-specific terms will accommodate annotations from Vitis, Helianthus, Populus, Gossypium, Rosaceae (Malus and Prunus), Fabaceae (Medicago and Glycine), Solanaceae (Solanum and Lycopersicum), and Poaceae (Triticum, Hordeum, Avena, Sorghum, and Brachypodium). Coverage of non-angiosperm plants includes bryophytes such as Physcomitrella, Marchantia, and Selaginella, pteridophytes, and gymnosperms. The main purpose of the PO is to facilitate cross database querying and to foster consistent use of vocabularies in annotation. With the addition of non-angiosperm terminology and the continued addition of reference images, the PO also provides a novel reference and teaching tool that can be used as a guide to plant structures, their relationships and parts, and common growth and development landmarks in the lifecycles of plants across multiple taxa. This presentation will provide an overview of the ontologies being developed, the annotation database, and their possible applications.