Skip to main content

The ‘Open Discovery’ Challenge

  • Chapter
Book cover Literature-based Discovery

Part of the book series: Information Science and Knowledge Management ((ISKM,volume 15))

Abstract

One of the most exciting goals of literature-based discovery is the inference of new, previously undocumented relationships based upon an analysis of known relationships. Human ability to read and assimilate scientific information has long lagged the rate by which new information is produced, and the rapid accumulation of published literature has exacerbated this problem further. The idea that a computer could begin to take over part of the hypothesis formation process that has long been solely within the domain of human reason has been met with both skepticism and excitement, both of which are fully merited. Conceptually, it has already been demonstrated in several studies that a computational approach to literature analysis can lead to the generation of novel and fruitful hypotheses. The biggest barriers to progress in this field are technical in nature, dealing mostly with the shortcomings that computers have relative to humans in understanding the nature, importance and implications of relationships found in the literature. This chapter will discuss where current efforts have brought us in solving the open-discovery problem, and what barriers are limiting further progress.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Wren, J.D., et al., Knowledge discovery by automated identification and ranking of implicit relationships. Bioinformatics, 2004. 20(3): 389–398

    Article  Google Scholar 

  2. Valencia, A., Search and retrieve. Large-scale data generation is becoming increasingly important in biological research. But how good are the tools to make sense of the data? EMBO Rep, 2002. 3(5): 396–400

    Article  Google Scholar 

  3. Blagosklonny, M.V. and A.B. Pardee, Conceptual biology: unearthing the gems. Nature, 2002. 416(6879): 373

    Article  Google Scholar 

  4. Bray, D., Reasoning for results. Nature, 2001. 412(6850): 863

    Article  Google Scholar 

  5. Swanson, D.R., Fish oil, Raynaud’s syndrome, and undiscovered public knowledge. Perspect Biol Med, 1986. 30(1): 7–18

    Google Scholar 

  6. Swanson, D.R., Undiscovered public knowledge. Libr Q, 1986. 56: 103–118

    Article  Google Scholar 

  7. Swanson, D.R., Migraine and magnesium: eleven neglected connections. Perspect Biol Med, 1988. 31(4): 526–557

    Google Scholar 

  8. Swanson, D.R., Somatomedin C and arginine: implicit connections between mutually isolated literatures. Perspect Biol Med, 1990. 33(2): 157–186

    Google Scholar 

  9. Swanson, D.R. and N.R. Smalheiser, An interactive system for finding complementary literatures: a stimulus to scientific discovery. Artif Intell, 1997. 91: 183–203

    Article  MATH  Google Scholar 

  10. Smalheiser, N.R., Informatics and hypothesis-driven research. EMBO Rep, 2002. 3(8): 702

    Article  Google Scholar 

  11. Pratt, W. and M. Yetisgen-Yildiz. LitLinker: capturing connections across the biomedical literature. In Proceedings of the International Conference on Knowledge Capture (K-Cap’03), 2003, Florida

    Google Scholar 

  12. Srinivasan, P., Text mining: generating hypotheses from MEDLINE. J Am Soc Inf Sci Technol, 2004. 55(5): 396–413

    Article  Google Scholar 

  13. Wren, J.D., Extending the mutual information measure to rank inferred literature relationships. BMC Bioinformatics, 2004. 5(1): 145

    Article  Google Scholar 

  14. Wren, J.D., Using fuzzy set theory and scale-free network properties to relate MEDLINE terms. Soft Computing, 2006. 10(4): 374–381

    Article  Google Scholar 

  15. Jenssen, T.K., et al., A literature network of human genes for high-throughput analysis of gene expression. Nat Genet, 2001. 28(1): 21–28

    Article  Google Scholar 

  16. Rindflesch, T.C., et al., EDGAR: extraction of drugs, genes and relations from the biomedical literature. Pac Symp Biocomput, 2000. 517–528

    Google Scholar 

  17. Stapley, B.J. and G. Benoit, Biobibliometrics: information retrieval and visualization from co-occurrences of gene names in Medline abstracts. Pac Symp Biocomput, 2000. 529–540

    Google Scholar 

  18. Xenarios, I., et al., DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res, 2002. 30(1): 303–305

    Article  Google Scholar 

  19. Andrade, M.A. and P. Bork, Automated extraction of information in molecular biology. FEBS Lett, 2000. 476(1–2): 12–17

    Article  Google Scholar 

  20. Blaschke, C., et al., Automatic extraction of biological information from scientific text: protein–protein interactions. In Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, 1999, pp. 60–67

    Google Scholar 

  21. Burgunder, J.M., Pathophysiology of akinetic movement disorders: a paradigm for studies in fibromyalgia? Z Rheumatol, 1998. 57(Suppl 2): 27–30

    Article  Google Scholar 

  22. Wren, J.D. and H.R. Garner, Data-mining analysis suggests an epigenetic pathogenesis for Type II Diabetes. J Biomed Biotechnol, 2005. 2: 104–112

    Article  Google Scholar 

  23. Xenarios, I., et al., DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res, 2002. 30(1): 303–305

    Article  Google Scholar 

  24. Zanzoni, A., et al., MINT: a Molecular INTeraction database. FEBS Lett, 2002. 513(1): 135–140

    Article  Google Scholar 

  25. Wren, J.D., The emerging in-silico scientist: how text-based bioinformatics is bridging biology and artificial intelligence. IEEE Eng Med Biol Mag, 2004. 23(2): 87–93

    Article  Google Scholar 

  26. Boolell, M., et al., Sildenafil: an orally active type 5 cyclic GMP-specific phosphodiesterase inhibitor for the treatment of penile erectile dysfunction. Int J Impot Res, 1996. 8(2): 47–52

    Google Scholar 

  27. DuCharme, D.W., et al., Pharmacologic properties of minoxidil: a new hypotensive agent. J Pharmacol Exp Ther, 1973. 184(3): 662–670

    Google Scholar 

  28. Zappacosta, A.R., Reversal of baldness in patient receiving minoxidil for hypertension. N Engl J Med, 1980. 303(25): 1480–1481

    Google Scholar 

  29. Perez-Iratxeta, C., P. Bork, and M.A. Andrade, Association of genes to genetically inherited diseases using data mining. Nat Genet, 2002. 31(3): 316–319

    Google Scholar 

  30. Edgar, R., M. Domrachev, and A.E. Lash, Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res, 2002. 30(1): 207–210

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Wren, J.D. (2008). The ‘Open Discovery’ Challenge. In: Bruza, P., Weeber, M. (eds) Literature-based Discovery. Information Science and Knowledge Management, vol 15. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-68690-3_4

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-68690-3_4

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-68685-9

  • Online ISBN: 978-3-540-68690-3

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics