Using the Plant Ontology to improve the interoperability of genomic and phenomic data sets

TitleUsing the Plant Ontology to improve the interoperability of genomic and phenomic data sets
Publication TypeConference Presentation
AuthorsWalls RL
Secondary AuthorsCooper L, Gandolfo MA, Stevenson DW, Smith B, Elser JL, Preece J, Mungall CJ, Jaiswal P
Conference Name

Plant Genomes & Biotechnology: from Genes to Networks

Conference Date2011
Date PresentedNov. 30 - Dec 3

The Plant Ontology (PO: is a structured vocabulary (ontology) consisting of terms, attributes, and relations that describe anatomy, morphology, and development stages of green plants. In addition, the PO provides access to genes and phenotypes that have been associated with ontology terms via the annotation of samples from specific tissues and developmental stages. The PO is an essential, powerful tool for the annotation of diverse gene-expression and phenotype data sets that can be used to assess the similarity between genes of inter- or intra-specific origin and to explore structural homologies among organs, tissues and cell types. The PO facilitates computational reasoning, based on ontological relationships and biological context, allowing researchers to probe the complex relationships among data sets for gene expression, phenotypes, gene-gene interactions, and molecular functions (via the Gene Ontology). For example, the logical definitions and relationships in the PO can be used to deduce that ‘petal’ in dicots and ‘lemma’ in monocot grasses are both subtypes of ‘phyllome’ (leaf-like structures) and that both are associated with ‘flower’ (‘petal’ is part_of ‘flower’ and ‘lemma’ is part_of ‘inflorescence’ which has_part ‘flower’). Researchers can use the association data in the PO to compare the expression patterns of orthologous genes in these structures in maize and Arabidopsis, or to determine if similar phenotypes in the two structures are linked to orthologous genes. Currently, the PO includes over 2 million annotations from maize, Arabidopsis,strawberry, rice, solanaceous crops (such as tomato), and the moss Physcomitrella patens. These annotations are associated with over 1,400 ontology terms. Almost 400 new anatomical terms have been added to the PO recently, to enhance the framework for cross-species comparisons and accommodate work in future agricultural models such as Musa and Eucalyptus. Approximately 80 new terms were added specifically for non-vascular plants, with an emphasis on those needed to describe gene expression in P. patens. In this presentation, we will provide an overview of the Plant Ontology and its resources and present a pilot study comparing inter-specific gene expression profiles, based on the orthology of genes and ontological relations among plant structures.

Conference Location

Cold Spring Harbor Laboratory