02124nas a2200229   4500000000100000000000100001008004100002260000900043100001700052700001800069700001700087700001900104700002400123700001600147700002100163700001900184245009100203300000800294490000700302520157100309022001401880       2019                            d  c20191 aRamona Walls1 aLaurel Cooper1 aJustin Elser1 aMaria Gandolfo1 aChristopher Mungall1 aBarry Smith1 aDennis Stevenson1 aPankaj Jaiswal00aThe Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species.  a6310 v103 aThe Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation database (http://www.planteome.org) make plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution.  a1664-462X