Tools & Resources

Chem2Bio2RDF – A semantic systems chemical biology / chemogenomic network linking chemical compounds with genes, diseases, targets, pathways and adverse effects that allows cross-domain querying using SPARQL. Datasets are linked with the Chem2Bio2OWL ontology. Developed in conjunction with Prof. Ying Ding in the School of Library & Information Science. For more information, see the Chem2Bio2RDF website, the Chem2Bio2RDF Wiki, and our 2010 BMC Bioinformatics paper.


 ChemBioSpace Association Search – A tool for finding and ranking associations between any two drugs, diseases, genes, side effects or metabolic pathways. Click on the question mark in the top right hand corner for information about using this tool. A paper on this method is in press at PLoS One.


WENDI – a tool for finding non-obvious relationships between chemical compounds and biology that aggregates information from databases, extracted from the literature, and computational predictions. Funded by Eli Lilly. For more information, see our Journal of Cheminformatics paper.



 PlotViz – the SALSA HPC lab at IU developed a high dimensional visualization tool called PlotViz. We collaborated with the lab to enable its use on huge chemical datasets to allow contextualization of compounds and drugs in chemical similarity space. PlotViz is fully integrated with Chem2Bio2RDF (SPARQL querying) and WENDI. For more information see our ECMLS conference paper.



 ChemViz – a cheminformatics plug-in for Cytoscape developed by Dazhi Jiao as part of the Google Summer of Code



 PubChemSR – A desktop PC tool for downloading and extracting information from the PubChem database. For more information, see our Chemistry Central Journal paper.




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