New York Botanical Garden, Bronx, 10458-5126, USA.
Am J Bot. 2012 Aug;99(8):1263-75. doi: 10.3732/ajb.1200222. Epub 2012 Jul 30.
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.
生物本体论是访问和分析快速增长的植物基因组和表型数据的重要工具。本体论提供了结构化的词汇表，以支持数据的一致聚合，以及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。
本文介绍了生物本体论是什么、为什么与植物学相关以及本体论开发原则等背景知识。它概述了与植物科学相关的本体论和相关资源，详细描述了植物本体论 (PO)。我们讨论了构建涵盖所有绿色植物（Viridiplantae）的本体论所面临的挑战。
本体论可以在以下四个关键领域推动植物科学的发展：（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。
生物本体论为基于共同植物学理解的比较植物生物学提供了灵活的框架。随着更多物种的基因组和表型数据的可用，我们预计数据的本体论术语注释将变得不那么集中，同时跨物种查询的需求将变得更加普遍，这将导致更多的植物科学研究人员转向本体论。
