Improving the Sequence Ontology terminology for genomic variant annotation.
Improving the Sequence Ontology terminology for genomic variant annotation.
复制标题
DOI：
10.1186/s13326-015-0030-4
复制
发表时间：
2015
影响因子：
1.9
通讯作者：
Eilbeck K
中科院分区：
文献类型：
--
作者：
Cunningham F;Moore B;Ruiz-Schultz N;Ritchie GR;Eilbeck K
基因组变异格式 (GVF) 使用序列本体 (SO) 来实现序列变异的详细注释。注释包括用于序列改变类型、改变的基因组特征以及改变的影响的SO术语。 SO 维护和更新规范并提供底层本体结构。进行了需求分析，以收集当时 SO 版本中缺失的术语，但需要充分描述序列改变对一组变异基因组注释的影响。我们对 SO 进行了扩展和重构，以包含并定义所有描述变异对 Ensembl 变异数据库中参考基因组特征的影响的术语。新术语用于用 COSMIC 和 dbSNP 的一组变体来注释人类参考基因组。使用SO术语生成包含170,853个序列改变的GVF文件，以注释改变的种类、改变的效果和改变的参考特征。该数据集中出现了 4 种改变和 24 种效果。 （Ensembl Variation 注释了 34 个不同的 SO 结果项：http://www.ensembl.org/info/docs/variation/predicted_data.html）。我们解释了序列本体的更新，以描述变化对现有参考特征的影响。我们提供了一组使用此术语的注释以及定义良好的 GVF 规范。我们还对这个大型注释数据集进行了临时探索。
The Genome Variant Format (GVF) uses the Sequence Ontology (SO) to enable detailed annotation of sequence variation. The annotation includes SO terms for the type of sequence alteration, the genomic features that are changed and the effect of the alteration. The SO maintains and updates the specification and provides the underlying ontologicial structure. A requirements analysis was undertaken to gather terms missing in the SO release at the time, but needed to adequately describe the effects of sequence alteration on a set of variant genomic annotations. We have extended and remodeled the SO to include and define all terms that describe the effect of variation upon reference genomic features in the Ensembl variation databases. The new terminology was used to annotate the human reference genome with a set of variants from both COSMIC and dbSNP. A GVF file containing 170,853 sequence alterations was generated using the SO terminology to annotate the kinds of alteration, the effect of the alteration and the reference feature changed. There are four kinds of alteration and 24 kinds of effect seen in this dataset. (Ensembl Variation annotates 34 different SO consequence terms: http://www.ensembl.org/info/docs/variation/predicted_data.html). We explain the updates to the Sequence Ontology to describe the effect of variation on existing reference features. We have provided a set of annotations using this terminology, and the well defined GVF specification. We have also provided a provisional exploration of this large annotation dataset.