Improving integrative searching of systems chemical biology data using semantic annotation
Improving integrative searching of systems chemical biology data using semantic annotation
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DOI：
10.1186/1758-2946-4-6
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发表时间：
2012-03-08
影响因子：
8.6
通讯作者：
Wild, David J.
中科院分区：
文献类型：
--
作者：
Chen, Bin;Ding, Ying;Wild, David J.
背景资料：系统化学生物学和化学基因组学被认为是现代生物医学研究中的关键综合学科，但需要对来自化学和生物学的大型、综合、异构数据集进行数据挖掘。我们以前开发了一个基于RDF的资源称为Chem2Bio2RDF，使查询这些数据使用SPARQL查询语言。虽然这项工作已被证明是有用的，作为这些学科的第一个主要资源之一，它的效用可以通过应用本体来注释RDF图中的节点和边来大大提高，从而能够发布更丰富的语义查询。结果：我们开发了一个广义的化学基因组学和系统化学生物学OWL本体，称为Chem2Bio2OWL，它描述了化合物，药物，蛋白质靶点，途径，基因，疾病和副作用，以及它们之间的关系。本体还包括数据来源。我们用它来注释我们的Chem2Bio2RDF数据集，使其成为一个丰富的语义资源。通过一系列的科学案例研究，我们展示了如何（i）简化构建SPARQL查询的过程，（ii）使有用的新类型的查询的数据和（iii）使智能推理和语义图挖掘在化学基因组学和系统化学生物学。
Background: Systems chemical biology and chemogenomics are considered critical, integrative disciplines in modern biomedical research, but require data mining of large, integrated, heterogeneous datasets from chemistry and biology. We previously developed an RDF-based resource called Chem2Bio2RDF that enabled querying of such data using the SPARQL query language. Whilst this work has proved useful in its own right as one of the first major resources in these disciplines, its utility could be greatly improved by the application of an ontology for annotation of the nodes and edges in the RDF graph, enabling a much richer range of semantic queries to be issued.Results: We developed a generalized chemogenomics and systems chemical biology OWL ontology called Chem2Bio2OWL that describes the semantics of chemical compounds, drugs, protein targets, pathways, genes, diseases and side-effects, and the relationships between them. The ontology also includes data provenance. We used it to annotate our Chem2Bio2RDF dataset, making it a rich semantic resource. Through a series of scientific case studies we demonstrate how this (i) simplifies the process of building SPARQL queries, (ii) enables useful new kinds of queries on the data and (iii) makes possible intelligent reasoning and semantic graph mining in chemogenomics and systems chemical biology.