Pharmaceutical Research

, Volume 24, Issue 10, pp 1791–1802

A Cheminformatic Toolkit for Mining Biomedical Knowledge

  • Gus R. Rosania
  • Gordon Crippen
  • Peter Woolf
  • David States
  • Kerby Shedden
Expert Review

DOI: 10.1007/s11095-007-9285-5

Cite this article as:
Rosania, G.R., Crippen, G., Woolf, P. et al. Pharm Res (2007) 24: 1791. doi:10.1007/s11095-007-9285-5



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.


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.

Key words

bioactivity fingerprints bioinformatics chemical genetics chemical genomics chemical space cheminformatics data mining high throughput screening mathematical modeling QSAR 

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Gus R. Rosania
    • 1
  • Gordon Crippen
    • 2
  • Peter Woolf
    • 3
  • David States
    • 4
  • Kerby Shedden
    • 5
  1. 1.Department of Pharmaceutical SciencesUniversity of Michigan College of PharmacyAnn ArborUSA
  2. 2.Department of Medicinal ChemistryUniversity of Michigan College of PharmacyAnn ArborUSA
  3. 3.Department of Chemical EngineeringUniversity of Michigan School of EngineeringAnn ArborUSA
  4. 4.Department of Human GeneticsUniversity of Michigan Medical SchoolAnn ArborUSA
  5. 5.Department of StatisticsUniversity of MichiganAnn ArborUSA

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