Beyond the data deluge: Data integration and bio-ontologies
Beyond the data deluge: Data integration and bio-ontologies
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DOI：
10.1016/j.jbi.2006.01.003
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发表时间：
2006-06-01
影响因子：
4.5
通讯作者：
Bult, Carol J.
中科院分区：
文献类型：
--
作者：
Blake, Judith A.;Bult, Carol J.
生物医学研究日益成为一门数据驱动的科学。新技术支持生成序列、序列变体、转录本和蛋白质的基因组规模数据集；支撑生物医学和疾病理解的遗传因素。旨在管理这些数据的信息系统以及来自这些数据分析的功能见解（生物学知识）对于挖掘大型异构数据集以寻找新的生物学相关模式、生成用于实验验证的假设以及最终构建生物系统如何工作的模型至关重要。生物本体论在支持有效解释基因组规模数据集的两种关键方法方面发挥着重要作用：数据集成和比较基因组学。迄今为止，诸如基因本体之类的生物本体主要作为结构化受控术语和数据聚合器在社区基因组数据库中使用。在本文中，我们使用基因本体（GO）和小鼠基因组信息学（MGI）数据库作为用例来说明生物本体对数据集成和比较基因组学的影响。尽管本体论对生物知识的数字分类产生了深远的影响，但新的生物医学研究以及生物信息的扩展和变化性质限制了生物本体论支持知识发现的动态推理的发展。 (c) 2006 Elsevier Inc. 保留所有权利。
Biomedical research is increasingly a data-driven science. New technologies support the generation of genome-scale data sets of sequences, sequence variants, transcripts, and proteins; genetic elements underpinning understanding of biomedicine and disease. Information systems designed to manage these data, and the functional insights (biological knowledge) that come from the analysis of these data, are critical to mining large, heterogeneous data sets for new biologically relevant patterns, to generating hypotheses for experimental validation, and ultimately, to building models of how biological systems work. Bio-ontologies have an essential role in supporting two key approaches to effective interpretation of genome-scale data sets: data integration and comparative genomics. To date, bio-ontologies such as the Gene Ontology have been used primarily in community genome databases as structured controlled terminologies and as data aggregators. In this paper we use the Gene Ontology (GO) and the Mouse Genome Informatics (MGI) database as use cases to illustrate the impact of bio-ontologies on data integration and for comparative genomics. Despite the profound impact ontologies are having on the digital categorization of biological knowledge, new biomedical research and the expanding and changing nature of biological information have limited the development of bio-ontologies to support dynamic reasoning for knowledge discovery. (c) 2006 Elsevier Inc. All rights reserved.