Ontology-Based Prediction and Prioritization of Gene Functional Annotations
Ontology-Based Prediction and Prioritization of Gene Functional Annotations
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DOI：
10.1109/tcbb.2015.2459694
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发表时间：
2016-03-01
影响因子：
4.5
通讯作者：
Masseroli, Marco
中科院分区：
文献类型：
--
作者：
Chicco, Davide;Masseroli, Marco
基因及其蛋白质产物是生物体的基本分子单位。了解它们的功能是理解生理和病理生物过程以及开发新药和疗法的关键。基因或蛋白质与其功能的关联，通过生物分子术语或本体论的受控术语来描述，称为基因功能注释。通过术语和本体表达的非常多的和有价值的基因注释是可用的。然而，它们可能包含一些错误的信息，因为只有一部分注释由策展人审查。此外，考虑到生物分子知识的快速发展，它们从定义上讲是不完整的。在这种情况下，能够加快注释管理过程并可靠地建议新注释的计算方法非常重要。在这里，我们首先提出了一个计算管道，使用不同的语义和机器学习方法来预测新的基于本体的基因功能注释;然后，我们引入了一个新的语义优先级规则，根据它们正确的可能性对预测的注释进行分类。我们的测试和验证证明了我们的管道的有效性和预测注释的优先级，通过选择最有可能的流形预测注释，后来证实。
Genes and their protein products are essential molecular units of a living organism. The knowledge of their functions is key for the understanding of physiological and pathological biological processes, as well as in the development of new drugs and therapies. The association of a gene or protein with its functions, described by controlled terms of biomolecular terminologies or ontologies, is named gene functional annotation. Very many and valuable gene annotations expressed through terminologies and ontologies are available. Nevertheless, they might include some erroneous information, since only a subset of annotations are reviewed by curators. Furthermore, they are incomplete by definition, given the rapidly evolving pace of biomolecular knowledge. In this scenario, computational methods that are able to quicken the annotation curation process and reliably suggest new annotations are very important. Here, we first propose a computational pipeline that uses different semantic and machine learning methods to predict novel ontology-based gene functional annotations; then, we introduce a new semantic prioritization rule to categorize the predicted annotations by their likelihood of being correct. Our tests and validations proved the effectiveness of our pipeline and prioritization of predicted annotations, by selecting as most likely manifold predicted annotations that were later confirmed.