W735 B73 Maize Gene Expression Atlas a Plant Ontology Use Case

Date: Saturday, January 14, 2012
Time: 11:25 AM
Room: Royal Palm Salon 5-6
Mary Schaeffer , USDA-ARS and University of Missouri, Columbia, MO
Ethalinda Cannon , Iowa State University, Ames, IA
Sudhansu Dash , Iowa State University, Ames, IA
John Van Hemert , Iowa State University, Ames, IA
Jack Gardiner , Iowa State University, Ames, IA
Bremen M Braun , USDA ARS, Ames, IA
Darwin A Campbell , USDA ARS, Ames, IA
Justin Preece , Oregon State University, Corvallis, OR
Carson M Andorf , USDA-ARS, Ames, IA
Scott M Birkett , Iowa State University, Ames, IA
Lisa C Harper , USDA-ARS and University of California-Berkeley, Albany, CA
Taner Z Sen , USDA -ARS and Iowa State University, Ames, IA
Roger Wise , USDA-ARS / Iowa State University, Ames, IA
Julie Dickerson , Iowa State Univeristy, Ames, IA
Carolyn J. Lawrence , USDA ARS and Iowa State University, Ames, IA
We report the curation path used to associate Plant Ontology (PO) terms to the B73 Maize Gene Atlas, a genome-wide transcription profile of 60 tissues representing 11 distinct organs over the life cycle of a maize plant [Sekhon et al (2011) Plant J 66:553-563 PMID 21299659] and currently accessible at MaizeGDB and PLEXdb. The annotation process began at MaizeGDB by integrating each tissue with maize specific terms for anatomy, growth and development. These terms had already been assigned Plant Ontology Accessions, largely from our early participation in the PO project.  The initial strategy was to infer the PO terms from this process. This worked very well for anatomy terms, and poorly for temporal (developmental) PO terms, which required direct annotation.  We then engaged in a highly interactive review process with the Plant Ontology team, using email, conference calls and the Source Forge Biomedical Ontologies Tracker. This ensured quality annotations of these data, and also resulted in some minor clarification of term definitions and term hierarchies at the PO.  At the same time, we updated MaizeGDB to reflect concurrent changes at PO in the representation of distinctive aspects of Poaceae and Zea reproductive structures. PO association files were prepared using gene model expression data updated to the current assembly, B73 reference genome_v2, and as a collaboration between MaizeGDB and PLEXdb (JVH, SD, RW, JD). These files were further enhanced by the inclusion of classical gene names, provided by CoGe (http://genomevolution.org/CoGe/). These PO associations  were  released Oct 2011, are accessible for download at plantontology.org,  and can be viewed in various browser modes both at PO and at MaizeGDB.  We thank SM Kaeppler  and R Buell  for making their data available to MaizeGDB  nearly a year prior to formal publication.  We gratefully acknowledge the USDA-ARS (MaizeGDB), the NSF (MaizeGDB, PLEXdb), and the National Corn Growers Association NCGA (MaizeGDB) for funding our work.