Whole-plant growth stage ontology for angiosperms and its application in plant biology

Pujar, An., Jaiswal, P., Kellogg, E. A., Ilic, K., Vincent, L., Avraham, Sh., Stevens, P., Zapata, F., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L. D., Ware, D. H., McCouch, S. (October 2006) Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiology, 142 (2). pp. 414-428. ISSN 00320889

URL: https://www.ncbi.nlm.nih.gov/pubmed/16905665
DOI: 10.1104/pp.106.085720

Abstract

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. © 2006 American Society of Plant Biologists.

Item Type: Paper
Subjects: organism description > plant > Arabidopsis
bioinformatics > genomics and proteomics > annotation > gene expression profiling annotation
organism description > plant behavior
bioinformatics > genomics and proteomics > databases > databases
bioinformatics > genomics and proteomics > Mapping and Rendering > ontology
organism description > plant
CSHL Authors:
Communities: CSHL labs > Stein lab
CSHL labs > Ware lab
Depositing User: CSHL Librarian
Date: October 2006
Date Deposited: 09 Dec 2011 19:41
Last Modified: 23 Feb 2017 19:33
PMCID: PMC1586063
Related URLs:
URI: http://repository.cshl.edu/id/eprint/22879

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