Querying neXtProt nanopublications and their value for insights on sequence variants and tissue expression
Querying neXtProt nanopublications and their value for insights on sequence variants and tissue expression
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DOI：
10.1016/j.websem.2014.05.001
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发表时间：
2014-12-01
影响因子：
2.5
通讯作者：
Loizou, Antonis
中科院分区：
文献类型：
--
作者：
Chichester, Christine;Gaudet, Pascale;Loizou, Antonis
了解个体之间的遗传差异如何影响蛋白质的调节，表达和最终功能是实现个人医疗承诺的重要一步。有几个技术障碍阻碍了生物学知识向与精准医学相关的应用的转变。数据集成的一个重要挑战是，新的生物序列（蛋白质，DNA）具有与互操作性相关的多个问题，可能会在已发布的数据中造成困境，特别是当不同的数据源似乎不一致时。因此，迫切需要以统一的方式促进信息整合的系统和方法，以允许无缝查询多种数据类型，其可以阐明例如蛋白质修饰和致病基因组变体之间的关系。我们的工作首次展示了如何使用语义技术来解决这些挑战，使用应用于neXtProt数据集的nanopublication模型，这是一个关于人类蛋白质信息的精选知识库。我们已经应用了nanopublication模型来演示对几个命名图的查询，包括与来自neXtProt的策划科学断言相关的出处信息。我们通过使用序列变异，翻译后修饰（PTM）和组织表达的用例显示，查询neXtProt纳米出版实施是一种扩展生物学见解的可靠方法。(C)2014爱思唯尔有限公司版权所有。
Understanding how genetic differences between individuals impact the regulation, expression, and ultimately function of proteins is an important step toward realizing the promise of personal medicine. There are several technical barriers hindering the transition of biological knowledge into the applications relevant to precision medicine. One important challenge for data integration is that new biological sequences (proteins, DNA) have multiple issues related to interoperability potentially creating a quagmire in the published data, especially when different data sources do not appear to be in agreement. Thus, there is an urgent need for systems and methodologies to facilitate the integration of information in a uniform manner to allow seamless querying of multiple data types which can illuminate, for example, the relationships between protein modifications and causative genomic variants. Our work demonstrates for the first time how semantic technologies can be used to address these challenges using the nanopublication model applied to the neXtProt data set, a curated knowledgebase of information about human proteins. We have applied the nanopublication model to demonstrate querying over several named graphs, including the provenance information associated with the curated scientific assertions from neXtProt. We show by way of use cases using sequence variations, post-translational modifications (PTMs) and tissue expression, that querying the neXtProt nanopublication implementation is a credible approach for expanding biological insight. (C) 2014 Elsevier B.V. All rights reserved.