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

Anuradha Pujar, Pankaj Jaiswal, Elizabeth A. Kellogg, Katica Ilic, Leszek Vincent, Shulamit Avraham, Peter Stevens, Felipe Zapata, Leonore Reiser, Seung Y. Rhee, Martin M. Sachs, Mary Schaeffer, Lincoln Stein, Doreen Ware, Susan McCouch

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)414-428
Number of pages15
JournalPlant physiology
Volume142
Issue number2
DOIs
StatePublished - Oct 1 2006

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Angiosperms
plant biology
Angiospermae
developmental stages
plant growth
Growth
phenotype
Vocabulary
gene expression
plant morphology
Phenotype
terminology
information sources
trajectories
life cycle (organisms)
growth and development
Databases
genes
Gene Expression
Arabidopsis

ASJC Scopus subject areas

  • Physiology
  • Genetics
  • Plant Science

Cite this

Pujar, A., Jaiswal, P., Kellogg, E. A., Ilic, K., Vincent, L., Avraham, S., ... McCouch, S. (2006). Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant physiology, 142(2), 414-428. https://doi.org/10.1104/pp.106.085720

Whole-plant growth stage ontology for angiosperms and its application in plant biology. / Pujar, Anuradha; Jaiswal, Pankaj; Kellogg, Elizabeth A.; Ilic, Katica; Vincent, Leszek; Avraham, Shulamit; Stevens, Peter; Zapata, Felipe; Reiser, Leonore; Rhee, Seung Y.; Sachs, Martin M.; Schaeffer, Mary; Stein, Lincoln; Ware, Doreen; McCouch, Susan.

In: Plant physiology, Vol. 142, No. 2, 01.10.2006, p. 414-428.

Research output: Contribution to journalArticle

Pujar, A, Jaiswal, P, Kellogg, EA, Ilic, K, Vincent, L, Avraham, S, Stevens, P, Zapata, F, Reiser, L, Rhee, SY, Sachs, MM, Schaeffer, M, Stein, L, Ware, D & McCouch, S 2006, 'Whole-plant growth stage ontology for angiosperms and its application in plant biology', Plant physiology, vol. 142, no. 2, pp. 414-428. https://doi.org/10.1104/pp.106.085720
Pujar A, Jaiswal P, Kellogg EA, Ilic K, Vincent L, Avraham S et al. Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant physiology. 2006 Oct 1;142(2):414-428. https://doi.org/10.1104/pp.106.085720
Pujar, Anuradha ; Jaiswal, Pankaj ; Kellogg, Elizabeth A. ; Ilic, Katica ; Vincent, Leszek ; Avraham, Shulamit ; Stevens, Peter ; Zapata, Felipe ; Reiser, Leonore ; Rhee, Seung Y. ; Sachs, Martin M. ; Schaeffer, Mary ; Stein, Lincoln ; Ware, Doreen ; McCouch, Susan. / Whole-plant growth stage ontology for angiosperms and its application in plant biology. In: Plant physiology. 2006 ; Vol. 142, No. 2. pp. 414-428.
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