Annotating Gene Expression in <i>Physcomitrella patens</i> using the Plant Ontology: Facilitating Cross-Taxa Comparisons

TitleAnnotating Gene Expression in Physcomitrella patens using the Plant Ontology: Facilitating Cross-Taxa Comparisons
Publication TypeConference Presentation
Presenting AuthorCooper LD
Secondary AuthorsWalls RL, Elser JL, Preece J, Smith B, Mungall CJ, Rensing S, Hiss M, Szövényi P, Lang D, Gandolfo MA, Stevenson DW, Jaiswal P
Conference NamePlant and Animal Genome XX Conference
Tertiary TitleNon-seed plants workshop
Conference LocationSan Diego, CA

The Plant Ontology (PO: is a structured vocabulary and database resource for all plant scientists that links plant anatomy, morphology and development to the rapidly expanding field of plant genomics. Recent changes in the PO include the addition of more than 80 new terms to accommodate non-seed plants, with an emphasis on those needed to annotate gene expression from the Physcomitrella patens genome. The primary purpose of the PO is to facilitate cross-database querying and to foster consistent use of vocabularies in annotation. The use of ontologies ensures consistent annotations within and across species, enabling both prediction of gene function and cross-species comparisons of gene expression. An essential, powerful feature of the PO is the set of links from terms to associated annotations, which are structure- or development-specific genes, proteins and phenotypes sourced from numerous plant genomics datasets. Currently, the PO includes over 2 million annotations associated with over 1,300 terms. We will give a brief tutorial on how to access the PO and associated data, and demonstrate the utility of linking Physcomitrella gene expression data to PO terms. 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.