Chem2Bio2RDF and tool outages

NOTICE FEB 24 2012: Due to a water cooling emergency at Indiana University, server machines may have to be brought down at short notice. This may result in Chem2Bio2RDF and the other tools being down for extended periods of time over the next 3-4 days.

New eBook

Introducing Cheminformatics - intensive self-study guide http://slg.djwild.info

New cheminformatics learning materials now available

New cheminformatics educational materials are now available at http://icep.wikispaces.com including updated wiki pages on introductory cheminformatics, a first tutorial video on 2D structure representation, and a low-cost intensive introductory self-study guide.

New Drug Discovery Today paper on Systems Chemical Biology

Systems chemical biology and the Semantic Web: what they mean for the future of drug discovery research.

Wild DJ, Ding Y, Sheth AP, Harland L, Gifford EM, Lajiness MS.

Systems chemical biology, the integration of chemistry, biology and computation to generate understanding about the way small molecules affect biological systems as a whole, as well as related fields such as chemogenomics, are central to emerging new paradigms of drug discovery such as drug repurposing and personalized medicine. Recent Semantic Web technologies such as RDF and SPARQL are technical enablers of systems chemical biology, facilitating the deployment of advanced algorithms for searching and mining large integrated datasets. In this paper, we aim to demonstrate how these technologies together can change the way that drug discovery is accomplished.


http://www.sciencedirect.com/science/article/pii/S1359644611004764

Cheminformatics & Chemogenomics featured in Genome Technology Magazine

The November issue of Genome Technology Magazine has an article featuring our work developing integrated semantic resources for drug discovery: http://www.genomeweb.com/pfizer-funds-chemogenomics-drug-discovery-web-resource-indiana-university

Press release - Pfizer grant for chemogenomics research

Original release at: http://newsinfo.iu.edu/news/page/normal/15623.html

BLOOMINGTON, Ind. -- An Indiana University data mining expert will use a grant from Pfizer to create a public resource exploring connections between chemical compounds and their biological activities.

IU Bloomington School of Informatics and Computing Professor David Wild will use large-scale semantic Web-based data mining and network methods to seek to uncover previously undiscovered historical links between chemical compounds, drugs, biological pathways, targets, genes and diseases.

Pfizer has awarded Wild $140,000 to conduct the chemogenomics study and to facilitate research relating to the discovery of new therapies and treatments.

"This research is significant because it will for the first time provide a large-scale public chemogenomics resource with integrated data mining tools," Wild said. "Biomedical researchers will be able to use this to seek to find new important biological relationships and to help discover new drugs."

The field of chemogenomics, often described in a wider sense as "systems chemical biology," is rapidly emerging as a way of helping discover new disease therapies and uncovering new uses for existing drugs.

Wild's lab has already created Chem2Bio2RDF, a prototype semantic resource Web-based program that integrates vast quantities of public chemical and biological data on compounds, drugs, genes, pathways, diseases, side-effects and scholarly publications, along with some initial tools for mining the data.

That resource and its associated tools already show promise for important potential biomedical applications, including predicting off-target and multi-target interactions of drugs and chemical compounds, finding potential applications of existing drugs to new therapeutic areas, and discovery of currently unknown desirable biological effects of existing chemical compounds.

"Professor Wild and his research team are developing innovative solutions to some very complex data mining problems in associating chemical structure to biological activities across numerous databases relevant to drug discovery," said Jeff Howe, senior director in Pfizer's Computational Sciences Center of Emphasis. "We are pleased to support his leading-edge research on semantic Web-based data mining for chemogenomics and systems chemical biology."

Peter Luke, senior director of R&D Business Development at Pfizer, said the support was an example of a growing willingness to create opportunities for collaborations between industry and academia.

"As pre-competitive research through open innovation with academic institutions becomes even more important within the pharmaceutical Industry, we are pleased to fund this research, which is yet another example of partnering with institutions to facilitate novel science programs," Luke said.

About the Indiana University School of Informatics
Founded in 2000 as the first school of its kind in the United States, the Indiana University School of Informatics is dedicated to research and teaching across a broad range of computing and information technology, with emphases on science, applications and societal implications. The school includes the School of Informatics at IUPUI and the School of Informatics and Computing at Bloomington, where programs include computer science and informatics. The school administers a variety of bachelor and masters degree programs in computer science and informatics, as well as Ph.D. programs in computer science, and the first-ever Ph.D. in informatics. The school is dedicated to excellence in education and research, to partnerships that bolster economic development and entrepreneurship, and to increasing opportunities for women and underrepresented minorities in computing and technology. For more information, visit http://www.soic.indiana.edu.

Cheminformatics Postdoc wins award for scientific excellence

Qian Zhu, a postdoctoral fellow working with David Wild, has been named a winner of the fall 2010 CINF Scholarship for Scientific Excellence (see http://acscinf.org/html/sciexcel.html). The scholarship, awarded by the Division of Chemical Information (CINF) of the American Chemical Society (ACS) was given at the 240th ACS National Meeting in Boston, based on a competitive poster presentation on Qian's work in a Lilly-funded project to develop a tool called WENDI for finding non-obvious links between chemical structures and biological effects. This work was recently published in a Journal of Cheminformatics article (http://www.jcheminf.com/content/2/1/6)