Plant growth stages are identified as distinct morphological landmarks in a continuous developmental process. The terms
describing these developmental stages record the morphological appearance of the plant at a specific point in its life cycle. The
widely differing morphology of plant species consequently gave rise to heterogeneous vocabularies describing growth and
development. Each species or family specific community developed distinct terminologies for describing whole-plant growth
stages. This semantic heterogeneity made it impossible to use growth stage description contained within plant biology
databases to make meaningful computational comparisons. The Plant Ontology Consortium (http://www.plantontology.org)
was founded to develop standard ontologies describing plant anatomical as well as growth and developmental stages that can
be used for annotation of gene expression patterns and phenotypes of all flowering plants. In this article, we describe the
development of a generic whole-plant growth stage ontology that describes the spatiotemporal stages of plant growth as a set
of landmark events that progress from germination to senescence. This ontology represents a synthesis and integration of
terms and concepts from a variety of species-specific vocabularies previously used for describing phenotypes and genomic
information. It provides a common platform for annotating gene function and gene expression in relation to the developmental
trajectory of a plant described at the organismal level. As proof of concept the Plant Ontology Consortium used the plant
ontology growth stage ontology to annotate genes and phenotypes in plants with initial emphasis on those represented in The
Arabidopsis Information Resource, Gramene database, and MaizeGDB.This is the publisher’s final pdf. The published article is copyrighted by the American Society of Plant Biologists and can be found at: http://www.plantphysiol.org/
