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首页> 外文期刊>BMC Bioinformatics >Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data
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Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data

机译：Chem2Bio2RDF：用于化学基因组和系统化学生物学数据的链接和数据挖掘的语义框架

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Background 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 Results 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. Conclusions 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.
机译：背景技术近来，关于基因，蛋白质，遗传变异，化合物，疾病和药物的新数据源激增。这些数据源的集成以及跨越它们的模式的标识非常重要。诸如Bio2RDF和LODD之类的倡议已经解决了使用RDF分别链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纳入非常有限。结果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，该存储库被交叉链接到Bio2RDF和LODD。我们还创建了一个链接路径生成工具来促进SPARQL查询的生成，并创建了扩展的SPARQL功能来满足特定的化学/生物学搜索需求。我们证明了Chem2Bio2RDF在研究多药理学，鉴定潜在的多途径抑制剂以及不良药物反应途径的关联中的实用性。结论我们创建了一种新的语义系统化学生物学资源，并已证明其在多药理学，多途径抑制和药物不良反应-途径作图的特定实例中的潜在用途。我们还展示了用化学信息学和生物信息学功能扩展SPARQL的有用性。

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