Annotating the Maize B73 Gene Expression Atlas in the Plant Ontology- A Tool for Plant Genomics.

TitleAnnotating the Maize B73 Gene Expression Atlas in the Plant Ontology- A Tool for Plant Genomics.
Publication TypeConference Presentation
Presenting AuthorJaiswal P
Secondary AuthorsCooper L, Schaeffer M, Walls RL, Elser JL, Preece J, Smith B, Mungall CJ, Gandolfo MA, Stevenson DW
Conference Name54th Annual Maize Genetics Conference
Conference LocationPortland, OR

The Plant Ontology ( 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. The primary purpose of the PO is to facilitate cross-database querying and to foster consistent use of vocabularies in annotation. An essential feature of the PO is the set of freely accessible web links from terms to associated annotations, which are structure- or development-specific genes, proteins, and phenotypes sourced from numerous plant genomics datasets. In collaboration with MaizeGDB (, we have recently added approximately 1.5 million new associations between maize (Zea mays) gene models and Plant Ontology terms. These associations are based on a large NimbleGen microarray data set profiling genome-wide transcription patterns in 60 tissues, representing 11 distinct organs over the life cycle of a maize plant of the inbred line B73 (Sekhon, et al, Plant Journal, 2011). The microarray data was associated with  35,000 maize gene models developed from the recent sequencing of its genome and updated to the current assembly, B73 RefGen_v2, as a collaboration between MaizeGDB and PLEXdb ( PO association files in gaf 2.0 format ( were further enhanced by the inclusion of classical gene names, mapped by CoGe ( The maize gene atlas associations were made public in the Plant Ontology Release #16 in October 2011. They are available for download, and can be viewed in various browser modes, both at the PO and at MaizeGDB. The addition of the maize gene atlas annotations to the PO represents an example of how ontologies provide access to large genomics data sets. Currently, the PO includes over 2 million such annotations from 17 species associated with over 1,300 terms. Other recent additions include annotations to cotton (Gossypium) and the moss Physcomitrella patens, with plans for the future inclusion of grape (Vitis) and potato (Solanum). The PO is a valuable resource for both research and teaching that can be used as a guide to plant structures and growth and developmental landmarks in life cycles of plants across many taxa.