Gene Ontology: Pitfalls, Biases, and Remedies
Gene Ontology: Pitfalls, Biases, and Remedies
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DOI：
10.1007/978-1-4939-3743-1_14
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发表时间：
2017-01-01
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影响因子：
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通讯作者：
Dessimoz, Christophe
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文献类型：
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作者：
Gaudet, Pascale;Dessimoz, Christophe
基因本体论(GO)是一个令人敬畏的资源，但关于它有几个考虑因素对于理解数据和正确解释它是必不可少的。围棋足够简单，可以在不深入了解其结构或如何开发的情况下使用，这既是一个优势，也是一个弱点。在这一章中，我们讨论了一些常见的对本体论的误解和注释。更好地理解Go中的陷阱和偏见应该有助于用户最大限度地利用这一非常丰富的资源。我们还回顾了一些常见的关于围棋的误解和误导性假设，包括数据不完备性的影响，注释限定符的重要性，以及与不同本体关系相关的传递性或缺乏传递性。我们还讨论了几个可能混淆聚合分析(如基因浓缩分析)的偏差。对于这些陷阱和偏见，我们建议采取补救措施和最佳实践。
The Gene Ontology (GO) is a formidable resource, but there are several considerations about it that are essential to understand the data and interpret it correctly. The GO is sufficiently simple that it can be used without deep understanding of its structure or how it is developed, which is both a strength and a weakness. In this chapter, we discuss some common misinterpretations of the ontology and the annotations. A better understanding of the pitfalls and the biases in the GO should help users make the most of this very rich resource. We also review some of the misconceptions and misleading assumptions commonly made about GO, including the effect of data incompleteness, the importance of annotation qualifiers, and the transitivity or lack thereof associated with different ontology relations. We also discuss several biases that can confound aggregate analyses such as gene enrichment analyses. For each of these pitfalls and biases, we suggest remedies and best practices.