The Plant Ontology: Linking Genomic and Phenomic Data Across Plant Taxa

TitleThe Plant Ontology: Linking Genomic and Phenomic Data Across Plant Taxa
Publication TypeConference Presentation
Presenting AuthorCooper LD
Secondary AuthorsWalls RL, Gandolfo MA, Stevenson DW, Smith B, Elser JL, Preece J, Mungall CJ, Jaiswal P
Conference NamePlant and Animal Genome XX Conference
Tertiary TitlePlant Phenotypes Workshop
Conference LocationSan Diego, CA

The Plant Ontology (PO: consists of over 1,300 rigorously-defined ontology terms and their relations that describe plant anatomy, morphology and developmental stages. Approximately 400 new plant anatomy terms have been recently added to enhance the framework for cross-species comparisons and to accommodate work in economically important plant species such as Musa and Eucalyptus, along with an additional 80 new terms needed to describe gene expression in the moss Physcomitrella patens and other non-vascular plants. In addition, the PO provides associations between the ontology terms and a variety of plant genomics resources including characterized genes, proteins, mRNA sequences, germplasm resources and QTLs. Currently, the PO includes freely accessible web links to over 2 million such annotations from maize, Arabidopsis, rice, strawberry, tomato and eggplant (along with other members of the Solanaceae family) and P. patens, with additional associations to grape, potato, cotton and many other plant species being added soon. Terms from the PO can be combined with ones from other ontologies such as the TO (Trait Ontology) and GO (Gene Ontology) to describe plant phenotypes. The combination of ontology terms and the annotation of diverse gene expression and phenotype data sets facilitates diverse analyses, including assessing the similarity between genes of inter- or intra-specific origin and the exploration of structural homologies among organs, tissues and cell types. In this presentation, we will provide an overview of the Plant Ontology and its resources and present a comparison of phenotypes across species, based on the orthology of gene expression profiles and the ontological relations among plant structures.