Ontologies as integrative tools for plant science.
Ontologies as integrative tools for plant science.
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DOI：
10.3732/ajb.1200222
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发表时间：
2012-08
影响因子：
3
通讯作者：
Stevenson DW
中科院分区：
文献类型：
--
作者：
Walls RL;Athreya B;Cooper L;Elser J;Gandolfo MA;Jaiswal P;Mungall CJ;Preece J;Rensing S;Smith B;Stevenson DW
生物本体论是获取和分析快速增长的植物基因组和表型数据的基本工具。本体提供结构化词汇表以支持一致的数据聚合，并提供用于自动分析和推理的语义框架。它们是语义网的关键组成部分。本文介绍了什么是生物本体，为什么它们与植物学相关，以及本体发展的原则。它包括与植物科学相关的本体论和相关资源的概述，以及植物本体论（PO）的详细描述。我们讨论了建立一个涵盖所有绿色植物（绿植物）的本体的挑战。本体论可以在四个关键领域促进植物科学的发展：(1)比较遗传学、基因组学、表型组学和发育；(2)分类学和系统学；(3)语义应用；(4)教育。生物本体论为比较植物生物学提供了一个灵活的框架，基于共同的植物学理解。随着更多物种的基因组和表型数据的可用性，我们预计用本体论术语标注数据将变得不那么集中，同时，跨物种查询的需求将变得更加普遍，导致更多的植物科学研究人员转向本体论。
Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the semantic web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Ontologies can advance plant science in four keys areas: (1) comparative genetics, genomics, phenomics, and development; (2) taxonomy and systematics; (3) semantic applications; and (4) education. Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies.
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