PubChemRDF: towards the semantic annotation of PubChem compound and substance databases.
PubChemRDF: towards the semantic annotation of PubChem compound and substance databases.
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DOI：
10.1186/s13321-015-0084-4
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发表时间：
2015
影响因子：
8.6
通讯作者：
Bolton E
中科院分区：
文献类型：
--
作者：
Fu G;Batchelor C;Dumontier M;Hastings J;Willighagen E;Bolton E
PubChem是一个开放的化学结构，生物活性和生物医学注释库。语义网技术正在成为分发和集成科学数据的一种越来越重要的方法。将PubChem数据公开给语义Web服务可以帮助实现自动化数据集成和管理，以及促进可互操作的Web应用程序。这项工作是PubChemRDF项目系列之一，描述了将PubChem物质和化合物信息转换为资源描述框架（RDF）格式的方法。提供了基本的例子来演示它的使用。这项工作的目的是以具有成本效益的方式为研究人员提供两个新的主要好处。首先，我们的目标是消除固有的限制，使用基于Web的资源PubChem，允许研究人员使用现成的语义技术（即RDF三重存储和相应的SPARQL查询引擎）查询和分析PubChem数据的本地计算资源。其次，这项工作旨在通过将PubChem数据与现有的本体框架（包括化学信息本体、语义科学集成本体等）相关联，帮助改善PubChem数据与NCBI外部资源和跨科学领域的数据共享、分析和集成。为了从语义上描述PubChem档案中可用的信息，使用了预先存在的本体框架，而不是创建新的本体框架。描述了化合物和物质之间的语义关系、与化合物和物质相关联的化学描述符、化学品之间的相互关系以及物质的来源和属性元数据。PubChem化合物和物质的语义链接的示意图。本文的在线版本（doi：10.1186/s13321-015-0084-4）包含补充材料，可供授权用户使用。
PubChem is an open repository for chemical structures, biological activities and biomedical annotations. Semantic Web technologies are emerging as an increasingly important approach to distribute and integrate scientific data. Exposing PubChem data to Semantic Web services may help enable automated data integration and management, as well as facilitate interoperable web applications. This work, one of a series covering the PubChemRDF project, describes an approach to translate PubChem Substance and Compound information into Resource Description Framework (RDF) format. Basic examples are provided to demonstrate its use. The aim of this effort is to provide two new primary benefits to researchers in a cost-effective manner. Firstly, we aim to remove the inherent limitations of using the web-based resource PubChem by allowing a researcher to use readily available semantic technologies (namely, RDF triple stores and their corresponding SPARQL query engines) to query and analyze PubChem data on local computing resources. Secondly, this work intends to help improve data sharing, analysis, and integration of PubChem data to resources external to NCBI and across scientific domains, by means of the association of PubChem data to existing ontological frameworks, including CHEMical INFormation ontology, Semanticscience Integrated Ontology, and others. With the goal of semantically describing information available in the PubChem archive, pre-existing ontological frameworks were used, rather than creating new ones. Semantic relationships between compounds and substances, chemical descriptors associated with compounds and substances, interrelationships between chemicals, as well as provenance and attribute metadata of substances are described. Schematic representation of the semantic links for PubChem compounds and substances. The online version of this article (doi:10.1186/s13321-015-0084-4) contains supplementary material, which is available to authorized users.