Whole-plant growth stage ontology for angiosperms and its application in plant biology.
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.
Pujar
Anuradha
A
Department of Plant Breeding, Cornell University, Ithaca, New York 14853, USA.
Jaiswal
Pankaj
P
Kellogg
Elizabeth A
EA
Ilic
Katica
K
Vincent
Leszek
L
Avraham
Shulamit
S
Stevens
Peter
P
Zapata
Felipe
F
Reiser
Leonore
L
Rhee
Seung Y
SY
Sachs
Martin M
MM
Schaeffer
Mary
M
Stein
Lincoln
L
Ware
Doreen
D
McCouch
Susan
S
D017360:Arabidopsis / Q000254:growth & development*; D001901:Botany / Q000379:methods*; D018525:Germination; D012275:Oryza / Q000254:growth & development*; D018515:Plant Leaves; D018520:Plant Shoots; D012098:Reproduction; D012984:Software; D009626:Terminology as Topic; D003313:Zea mays / Q000254:growth & development*