Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Emergent behavior of growing knowledge about molecular interactions

Nature Biotechnology volume 23, pages 1243–1247 (2005)Cite this article

A billion nonredundant molecular interactions lie buried in the biomedical literature. A text-mining approach could help scientists better exploit this knowledge.

In the time of Isaac Newton (1643–1727), a prominent scientist could follow advances in multiple fields of knowledge—as far apart from each other as mathematics, astronomy, physics, history and theology. It took a talent of Newton's caliber, of course, to contribute to several of them during one lifetime. Today, with thousands of biomedical journals published in English alone, even Sir Isaac would not have the luxury of systematically following all that happens in biology, let alone in multiple research fields. Currently, millions of active biomedical researchers are scattered around the globe, most focusing on a small fragment of the enormous biological universe. Consequently, knowledge acquisition and validation by scientific communities is bound to have large-scale properties that are normally hidden from individual scientists. These large-scale properties would reveal themselves only at the level of a meta-analysis of large volumes of data produced by numerous scientists. The practical importance of such meta-analyses—besides satisfying academic curiosity—lies in their potential for indicating hidden opportunities lurking in the currently accessible knowledge.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it

$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Hypothetical and actual modes of growth of the knowledge about molecular interactions.
Figure 2: 'Temperature' of a journal and its correlation with 'novelty' and impact factor.
Figure 3: Illustration of the existence of knowledge pockets: the facts produced in one subfield are largely invisible to other subfields.
Figure 4: Extrapolation-based estimate of the number of molecular relationships that can be extracted from the full-text research articles from the currently available biomedical and chemical journals, assuming that the currently available technology is used for information extraction.

References

  1. Friedman, C., Kra, P., Yu, H., Krauthammer, M. & Rzhetsky, A. Bioinformatics 17 (Suppl. 1), S74–82 (2001).

    Article  Google Scholar 

  2. Rzhetsky, A. et al. J. Biomed. Inform. 37, 43–53 (2004).

    Article  CAS  Google Scholar 

  3. Barabasi, A.L. et al. Physica A 311, 590–614 (2002).

    Article  Google Scholar 

  4. Guimera, R., Uzzi, B., Spiro, J. & Amaral, L.A. Science 308, 697–702 (2005).

    Article  CAS  Google Scholar 

  5. Barabasi, A.L. & Albert, R. Science 286, 509–512 (1999).

    Article  CAS  Google Scholar 

  6. http://www.isinet.com.

  7. Chen, C. Proc. Natl. Acad. Sci. USA 101 (Suppl. 1), 5303–5310 (2004).

    Article  CAS  Google Scholar 

  8. Price, D.J.D. Science 149, 510–515 (1965).

    Article  CAS  Google Scholar 

  9. Gilks, W.R., Richardson, S. & Spiegelhalter, D.J. (eds.) Markov Chain Monte Carlo In Practice (Chapman & Hall/CRC, New York, 1996).

    Google Scholar 

  10. Hastings, W.K. Biometrika 57, 97–109 (1970).

    Article  Google Scholar 

  11. Metropolis, S.C., Rosenbluth, A., Rosenbluth, M., Teller, A. & Teller, E. J. Chem. Phys. 21, 1087–1092 (1953).

    Article  CAS  Google Scholar 

  12. Krauthammer, M. et al. Bioinformatics 18 (Suppl. 1), S249–257 (2002).

    Article  Google Scholar 

  13. Draper, N.R. & Smith, H. Applied Regression Analysis (Wiley, New York, 1998).

    Book  Google Scholar 

Download references

Acknowledgements

We are grateful to Igor G. Feldman, Sidonie T. Jones, Lyn Dupré Oppenheim, James J. Russo, Rita Rzhetsky, Bengü Sezen and Kenneth C. Smith for numerous invaluable comments regarding earlier versions of this article, and to Harmen Bussemaker for the suggestion of naming the α-parameter 'temperature.' This study was supported by grants from the National Institutes of Health, the National Science Foundation, the Department of Energy and the Defense Advanced Research Projects Agency to A.R.

Author information

Authors and Affiliations

  1. Department of Biological Sciences, Columbia University, New York, 10032, New York, USA

    Murat Cokol & Andrey Rzhetsky

  2. Judith P. Sulzberger MD Columbia Genome Center, Columbia University, New York, 10032, New York, USA

    Murat Cokol, Ivan Iossifov, Chani Weinreb & Andrey Rzhetsky

  3. Department of Biomedical Informatics, Columbia University, New York, 10032, New York, USA

    Ivan Iossifov, Chani Weinreb & Andrey Rzhetsky

  4. Center for Computational Biology and Bioinformatics (C2B2), Columbia University, New York, 10032, New York, USA

    Andrey Rzhetsky

Authors
  1. Murat Cokol
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ivan Iossifov
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Chani Weinreb
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Andrey Rzhetsky
    View author publications

    You can also search for this author in PubMed Google Scholar

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Cokol, M., Iossifov, I., Weinreb, C. et al. Emergent behavior of growing knowledge about molecular interactions. Nat Biotechnol 23, 1243–1247 (2005). https://doi.org/10.1038/nbt1005-1243

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt1005-1243

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing