The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant
The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant
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DOI：
10.1104/pp.106.092825
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发表时间：
2007-02-01
期刊：
影响因子：
7.4
通讯作者：
Rhee, Seung Y.
中科院分区：
文献类型：
--
作者：
Ilic, Katica;Kellogg, Elizabeth A.;Rhee, Seung Y.
植物表型的正式描述以及基因表达和蛋白质定位数据的标准化注释需要准确描述植物解剖学和形态学的统一术语。这有利于跨物种比较研究以及表型和表达模式的定量比较。一个主要缺点是不同物种的出版物和基因组数据库中用于描述植物解剖学和形态学的术语多种多样。相同的术语有时适用于不同分类群中的不同植物结构。相反，相似的结构由其物种特定术语命名。为了解决这个问题，我们创建了植物结构本体（PSO），这是开花植物解剖学和形态学的第一个通用本体表示。 PSO 面向广泛的植物研究界，包括实验室科学家、基因组数据库管理员和生物信息学家。 PSO 的初始版本集成了拟南芥 (Arabidopsis thaliana)、玉米 (Zea mays) 和水稻 (Oryza sativa) 的现有本体；该本体的最新版本包含与豆科、茄科、其他谷类作物和杨树（杨属）相关的术语。拟南芥信息资源、诺丁汉拟南芥库存中心、Gramene、MaizeGDB 和 SOL Genomics Network 等数据库正在使用 PSO 来描述基因的表达模式以及突变体和自然变体的表型，并定期向植物本体数据库提供新的注释。 PSO 还用于专门的公共数据库，例如 BRENDA、GENEVESTIGATOR、NASCArrays 等。可以使用植物本体浏览器查询和检索来自参与数据库的 10,000 多个基因注释和表型描述。 PSO 以及贡献的基因关联可以在 www.plantontology.org 上获得。
Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that accurately describes plant anatomy and morphology. This facilitates cross species comparative studies and quantitative comparison of phenotypes and expression patterns. A major drawback is variable terminology that is used to describe plant anatomy and morphology in publications and genomic databases for different species. The same terms are sometimes applied to different plant structures in different taxonomic groups. Conversely, similar structures are named by their species-specific terms. To address this problem, we created the Plant Structure Ontology (PSO), the first generic ontological representation of anatomy and morphology of a flowering plant. The PSO is intended for a broad plant research community, including bench scientists, curators in genomic databases, and bioinformaticians. The initial releases of the PSO integrated existing ontologies for Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and rice (Oryza sativa); more recent versions of the ontology encompass terms relevant to Fabaceae, Solanaceae, additional cereal crops, and poplar (Populus spp.). Databases such as The Arabidopsis Information Resource, Nottingham Arabidopsis Stock Centre, Gramene, MaizeGDB, and SOL Genomics Network are using the PSO to describe expression patterns of genes and phenotypes of mutants and natural variants and are regularly contributing new annotations to the Plant Ontology database. The PSO is also used in specialized public databases, such as BRENDA, GENEVESTIGATOR, NASCArrays, and others. Over 10,000 gene annotations and phenotype descriptions from participating databases can be queried and retrieved using the Plant Ontology browser. The PSO, as well as contributed gene associations, can be obtained at www.plantontology.org.