Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data.
Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data.
复制标题
DOI：
10.1186/1471-2105-11-255
复制
发表时间：
2010-05-17
影响因子：
3
通讯作者：
Wild DJ
中科院分区：
文献类型：
--
作者：
Chen B;Dong X;Jiao D;Wang H;Zhu Q;Ding Y;Wild DJ
最近，关于基因、蛋白质、遗传变异、化合物、疾病和药物的新数据来源激增。这些数据源的集成和跨越它们的模式的识别是至关重要的。诸如Bio2RDF和LODD之类的倡议已经解决了使用RDF分别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的存储库，这些存储库交叉链接到Bio2RDF和LODD中。我们还创建了一个链接路径生成工具来促进SPARQL查询的生成，并创建了扩展的SPARQL函数来满足特定的化学/生物搜索需求。我们展示了Chem2Bio2RDF在研究多药理学、鉴定潜在的多途径抑制剂以及途径与药物不良反应的关联方面的效用。我们已经创建了一个新的语义系统化学生物学资源，并已经证明了它在多药理学，多途径抑制和药物不良反应-途径映射的具体例子中的潜在用途。我们还演示了用化学信息学和生物信息学功能扩展SPARQL的有用性。
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.
登录
查看更多内容
DOI：
10.1021/ci010132r
发表时间：
2002-11-01
期刊：
JOURNAL OF CHEMICAL INFORMATION AND COMPUTER SCIENCES
影响因子：
--
作者：
Durant, JL;Leland, BA;Nourse, JG
通讯作者：
Nourse, JG
影响因子：
5.8
作者：
Holland, R. C. G.;Down, T. A.;Pocock, M.;Prlic, A.;Huen, D.;James, K.;Foisy, S.;Draeger, A.;Yates, A.;Heuer, M.;Schreiber, M. J.
通讯作者：
Schreiber, M. J.
DOI：
10.1073/pnas.171311298
发表时间：
2001-08-14
影响因子：
11.1
作者：
Gong, GZ;Waris, G;Siddiqui, A
通讯作者：
Siddiqui, A
影响因子：
5.8
作者：
Andrews, RC;Rooyackers, O;Walker, BR
通讯作者：
Walker, BR
影响因子：
9.5
作者：
Chen, Huajun;Ding, Li;Chen, Jake Y.
通讯作者：
Chen, Jake Y.