Whole-plant growth stage ontology for angiosperms and its application in plant biology
Whole-plant growth stage ontology for angiosperms and its application in plant biology
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DOI：
10.1104/pp.106.085720
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发表时间：
2006-10-01
期刊：
影响因子：
7.4
通讯作者：
McCouch, Susan
中科院分区：
文献类型：
--
作者：
Pujar, Anuradha;Jaiswal, Pankaj;McCouch, Susan
植物生长阶段被认为是连续发育过程中独特的形态标志。描述这些发育阶段的术语记录了植物在其生命周期的特定时刻的形态外观。植物物种的形态差异很大，因此产生了描述生长和发育的异质词汇。每个物种或科特定群落都开发了不同的术语来描述整个植物的生长阶段。这种语义异质性使得不可能使用植物生物学数据库中包含的生长阶段描述来进行有意义的计算比较。植物本体联盟 (http://www.plantontology.org) 的成立是为了开发描述植物解剖学以及生长和发育阶段的标准本体，可用于注释所有开花植物的基因表达模式和表型。在本文中，我们描述了通用全植物生长阶段本体论的发展，该本体论将植物生长的时空阶段描述为一组从发芽到衰老的标志性事件。该本体论代表了以前用于描述表型和基因组信息的各种物种特定词汇中的术语和概念的综合和整合。它提供了一个通用平台，用于注释与在有机体水平上描述的植物发育轨迹相关的基因功能和基因表达。作为概念证明，植物本体联盟使用植物本体生长阶段本体来注释植物中的基因和表型，最初重点关注拟南芥信息资源、Gramene 数据库和 MaizeGDB 中代表的基因和表型。
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.