Annotating the Maize B73 Gene Expression Atlas – A Plant Ontology Use Case for Genomics Data Curation

TitleAnnotating the Maize B73 Gene Expression Atlas – A Plant Ontology Use Case for Genomics Data Curation
Publication TypeConference Poster
Presenting AuthorCooper LD
Secondary AuthorsSchaeffer M, Walls RL, Elser JL, Preece J, Smith B, Mungall CJ, Gandolfo MA, Stevenson DW, Jaiswal P
Conference NameBiocuration 2012
Conference LocationWashington DC, USA
Year2012
Conference DatesApril 2012
Abstract

The Plant Ontology (www.plantontology.org) 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 (www.maizegdb.org), 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 (www.plexdb.org). The curation path used to associate the PO terms to the maize gene atlas began at MaizeGDB, by mapping each microarray tissue sample to Plant

URLhttp://pir.georgetown.edu/biocuration2012.html/index.html