School of Informatics and Computing, Indiana University, Bloomington, IN, USA.
BMC Bioinformatics. 2010 May 17;11:255. doi: 10.1186/1471-2105-11-255.
Recently there has been an explosion of new data sources about genes, proteins, genetic variations, chemical compounds, diseases and drugs. Integration of these data sources and the identification of patterns that go across them is of critical interest. Initiatives such as Bio2RDF and LODD have tackled the problem of linking biological data and drug data respectively using RDF. Thus far, the inclusion of chemogenomic and systems chemical biology information that crosses the domains of chemistry and biology has been very limited
We have created a single repository called Chem2Bio2RDF by aggregating data from multiple chemogenomics repositories that is cross-linked into Bio2RDF and LODD. We have also created a linked-path generation tool to facilitate SPARQL query generation, and have created extended SPARQL functions to address specific chemical/biological search needs. We demonstrate the utility of Chem2Bio2RDF in investigating polypharmacology, identification of potential multiple pathway inhibitors, and the association of pathways with adverse drug reactions.
We have created a new semantic systems chemical biology resource, and have demonstrated its potential usefulness in specific examples of polypharmacology, multiple pathway inhibition and adverse drug reaction--pathway mapping. We have also demonstrated the usefulness of extending SPARQL with cheminformatics and bioinformatics functionality.
最近，有关基因、蛋白质、遗传变异、化学化合物、疾病和药物的新数据源呈爆炸式增长。整合这些数据源并识别跨越它们的模式是至关重要的。Bio2RDF 和 LODD 等计划分别使用 RDF 解决了连接生物数据和药物数据的问题。到目前为止，跨越化学和生物学领域的化学基因组学和系统化学生物学信息的包含非常有限。
我们通过聚合来自多个化学基因组学存储库的数据创建了一个名为 Chem2Bio2RDF 的单一存储库，这些数据被交叉链接到 Bio2RDF 和 LODD 中。我们还创建了一个链接路径生成工具，以方便 SPARQL 查询生成，并创建了扩展的 SPARQL 函数来满足特定的化学/生物学搜索需求。我们演示了 Chem2Bio2RDF 在调查多药理学、识别潜在的多途径抑制剂以及将途径与药物不良反应相关联方面的实用性。
我们创建了一个新的语义系统化学生物学资源，并通过多药理学、多途径抑制和药物不良反应-途径映射的具体示例展示了其潜在的有用性。我们还演示了扩展 SPARQL 以结合化学信息学和生物信息学功能的有用性。
