Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data

BMC Bioinformatics

Research Article

Bin Chen¹  David J Wild¹  Qian Zhu¹  Xiao Dong¹  Huijun Wang¹  Dazhi Jiao²  Ying Ding³ 

[1] School of Informatics and Computing, Indiana University, Bloomington, IN, USA;School of Informatics and Computing, Indiana University, Bloomington, IN, USA;School of Library and Information Science, Indiana University, Bloomington, IN, USA;School of Library and Information Science, Indiana University, Bloomington, IN, USA;

关键词: Oxybutynin;    Lepirudin;    Loxapine;    SPARQL Query;    Bromfenac;   

DOI  :  10.1186/1471-2105-11-255

 received in 2009-11-23, accepted in 2010-05-17,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundRecently 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 limitedResultsWe 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.ConclusionsWe 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.

【 授权许可】

Unknown   
© Chen et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.