A procedure for assessing GO annotation consistency
A procedure for assessing GO annotation consistency
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DOI：
10.1093/bioinformatics/bti1019
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发表时间：
2005-06-01
期刊：
影响因子：
5.8
通讯作者：
Blake, JA
中科院分区：
文献类型：
--
作者：
Dolan, ME;Ni, L;Blake, JA
动机：基因本体论(GO)被广泛用于注释基因和基因产品的分子属性。承担基因组功能注释的多个小组将其注释集贡献给GO数据库资源，这些数据随后被用于比较功能分析研究。尽管围棋馆长在分配围棋批注时遵循相同的协议和标准，但每个批注组遵循的具体程序可能会有所不同。由于应用不同的注释标准会冲淡比较分析的有效性，因此评估注释一致性的方法至关重要。开发一种广泛适用于GO注释一致性评估的方法是比较基因组学界的一个重要问题。结果：我们开发了一种评估不同注释组提供的GO注释一致性的方法。该方法是完全通用的，可以应用于比较任意两组围棋注释。这是评估跨物种围棋注释一致性的第一次尝试。我们的方法利用GO的层次结构来比较注释集，以比较同源基因对之间的GO注释。该方法生成关于每个同源对的注释一致性和不一致性的报告。我们介绍了通过比较小鼠和人类基因集的GO注释获得的结果。
Motivation: The Gene Ontology (GO) is widely used to annotate molecular attributes of genes and gene products. Multiple groups undertaking functional annotations of genomes contribute their annotation sets to the GO database resource and these data are subsequently used in comparative functional analysis research. Although GO curators adhere to the same protocols and standards while assigning GO annotations, the specific procedure followed by each annotation group can vary. Since differences in application of annotation standards would dilute the effectiveness of comparative analysis, methods for assessing annotation consistency are essential. The development of methodologies that are broadly applicable for the assessment of GO annotation consistency is an important issue for the comparative genomics community.Results: We have developed a methodology for assessing the consistency of GO annotations provided by different annotation groups. The method is completely general and can be applied to compare any two sets of GO annotations. This is the first attempt to assess cross-species GO annotation consistency. Our method compares annotation sets utilizing the hierarchical structure of the GO to compare GO annotations between orthologous gene pairs. The method produces a report on the annotation consistency and inconsistency for each orthologous pair. We present results obtained by comparing GO annotations for mouse and human gene sets.