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A Cheminformatic Toolkit for Mining Biomedical Knowledge

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Abstract

Purpose

Cheminformatics can be broadly defined to encompass any activity related to the application of information technology to the study of properties, effects and uses of chemical agents. One of the most important current challenges in cheminformatics is to allow researchers to search databases of biomedical knowledge, using chemical structures as input.

Materials and Methods

An important step towards this goal was the establishment of PubChem, an open, centralized database of small molecules accessible through the World Wide Web. While PubChem is primarily intended to serve as a repository for high throughput screening data from federally-funded screening centers and academic research laboratories, the major impact of PubChem could also reside in its ability to serve as a chemical gateway to biomedical databases such as PubMed.

Conclusion

This article will review cheminformatic tools that can be applied to facilitate annotation of PubChem through links to the scientific literature; to integrate PubChem with transcriptomic, proteomic, and metabolomic datasets; to incorporate results of numerical simulations of physiological systems into PubChem annotation; and ultimately, to translate data of chemical genomics screening efforts into information that will benefit biomedical researchers and physician scientists across all therapeutic areas.

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Acknowledgements

This work was supported by NIH grants RO1-GM078200 and P20-HG003890 to G.R.R and K.S. We would like to thank Kazu Saitou, Jungkap Park and Xinyuan Zhang for help with the illustrations and graphics.

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Authors and Affiliations

  1. Department of Pharmaceutical Sciences, University of Michigan College of Pharmacy, 428 Church Street, Ann Arbor, MI, 48109, USA

    Gus R. Rosania

  2. Department of Medicinal Chemistry, University of Michigan College of Pharmacy, Ann Arbor, MI, USA

    Gordon Crippen

  3. Department of Chemical Engineering, University of Michigan School of Engineering, Ann Arbor, MI, USA

    Peter Woolf

  4. Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA

    David States

  5. Department of Statistics, University of Michigan, Ann Arbor, MI, USA

    Kerby Shedden

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  1. Gus R. Rosania
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Correspondence to Gus R. Rosania.

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Rosania, G.R., Crippen, G., Woolf, P. et al. A Cheminformatic Toolkit for Mining Biomedical Knowledge. Pharm Res 24, 1791–1802 (2007). https://doi.org/10.1007/s11095-007-9285-5

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  • DOI: https://doi.org/10.1007/s11095-007-9285-5

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