Skip to main content

The Place of Literature-Based Discovery in Contemporary Scientific Practice

  • Chapter
Literature-based Discovery

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

Abstract

In this brief essay, we consider some of the lessons that we learned from our experience working with the Arrowsmith consortium that may have implications for the field of literature-based discovery (LBD) as a whole.

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. Smalheiser, N. R.: The Arrowsmith project: 2005 status report. In: Conference on Discovery Science 2005. Lecture Notes in Artificial Intelligence, vol. 3735, eds. A. Hoffmann, H. Motoda, and T. Scheffer, Springer, Berlin Heidelberg New York (2005) 26–43

    Google Scholar 

  2. Smalheiser, N. R., Torvik, V. I., Bischoff-Grethe, A., Burhans, L. B., Gabriel, M., Homayouni, R., Kashef, A., Martone, M. E., Perkins, G. A., Price, D. L., Talk, A. C., West, R.: Collaborative development of the Arrowsmith two-node search interface designed for laboratory investigators. J. Biomed. Discov. Collab. 1 (2006) 8

    Article  Google Scholar 

  3. Torvik, V. I., Smalheiser, N. R.: A quantitative model for linking two disparate sets of articles in Medline. Bioinformatics 23 (2007) 1658–1665

    Article  Google Scholar 

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

    Article  MATH  Google Scholar 

  5. Bekhuis, T.: Conceptual biology, hypothesis discovery, and text mining: Swanson’s legacy. Biomed. Digit. Libr. 3 (2006) 2

    Article  Google Scholar 

  6. Jensen, L. J., Saric, J., Bork, P.: Literature mining for the biologist: from information retrieval to biological discovery. Nat. Rev. Genet. 7 (2006) 119–129

    Article  Google Scholar 

  7. Weeber, M., Kors, J. A., Mons, B.: Online tools to support literature-based discovery in the life sciences. Brief. Bioinform. 6 (2005) 277–286

    Article  Google Scholar 

  8. Hristovski, D., Peterlin, B., Mitchell, J. A., Humphrey, S. M.: Using literature-based discovery to identify disease candidate genes. Int. J. Med. Inform. 74 (2005) 289–298

    Article  Google Scholar 

  9. Skeels, M. M., Henning, K., Yetisgen-Yildiz, M., Pratt, W.: Interaction Design for Literature-Based Discovery. Proceedings of the ACM International Conference on Human Factors in Computing Systems (CHI 2005), Portland, OR

    Google Scholar 

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

    Article  Google Scholar 

  11. Srinivasan, P., Libbus, B.: Mining MEDLINE for implicit links between dietary substances and diseases. Bioinformatics 20 Suppl 1 (2004) I290–I296

    Article  Google Scholar 

  12. Wren, J. D., Bekeredjian, R., Stewart, J. A., Shohet, R. V., Garner, H. R.: Knowledge discovery by automated identification and ranking of implicit relationships. Bioinformatics 20 (2004) 389–398

    Article  Google Scholar 

  13. Srinivasan, P.: Text Mining: Generating hypotheses from MEDLINE. J. Am. Soc. Inf. Sci. Technol. 55 (2004) 396–413

    Article  Google Scholar 

  14. Weeber, M., Vos, R., Klein, H., De Jong-Van Den Berg, L. T., Aronson, A. R., Molema, G.: Generating hypotheses by discovering implicit associations in the literature: a case report of a search for new potential therapeutic uses for thalidomide. J. Am. Med. Inform. Assoc. 10 (2003) 252–259

    Article  Google Scholar 

  15. Weeber, M., Vos, R., Baayen, R. H.: Using concepts in literature-based discovery: simulating Swanson’s Raynaud–fish oil and migraine–magnesium discoveries. J. Am. Soc. Inf. Sci. Technol. 52 (2001) 548–557

    Article  Google Scholar 

  16. Valdes-Perez, R. E.: Principles of human-computer collaboration for knowledge discovery in science. Artif. Intell. 107 (1999) 335–346

    Article  MATH  Google Scholar 

  17. Kostoff, R. N.: Science and technology innovation. Technovation 19 (1999) 593–604

    Article  Google Scholar 

  18. Smalheiser, N. R., Swanson, D. R.: Using ARROWSMITH: a computer-assisted approach to formulating and assessing scientific hypotheses. Comput. Methods Programs Biomed. 57 (1998) 149–153

    Article  Google Scholar 

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

    Article  Google Scholar 

  20. Smalheiser, N. R., Swanson, D. R.: Assessing a gap in the biomedical literature: magnesium deficiency and neurologic disease. Neurosci. Res. Commun. 15 (1994) 1–9

    Google Scholar 

  21. Smalheiser, N. R., Manev, H., Costa, E.: RNAi and Memory: Was McConnell on the right track after all? Trends Neurosci. 24 (2001) 216–218

    Article  Google Scholar 

  22. Smalheiser, N. R.: Predicting emerging technologies with the aid of text-based data mining: the micro approach. Technovation 21 (2001) 689–693

    Article  Google Scholar 

  23. Swanson, D. R., Smalheiser, N. R., Bookstein, A.: Information discovery from complementary literatures: categorizing viruses as potential weapons. J. Am. Soc. Inf. Sci. Technol. 52 (2001) 797–812

    Article  Google Scholar 

  24. Smalheiser, N. R.: Bath toys: a source of gastrointestinal infection. N. Engl. J. Med. 350 (2003) 521

    Article  Google Scholar 

  25. Fuller, S. S., Revere, D., Bugni, P. F., Martin, G. M.: A knowledgebase system to enhance scientific discovery: Telemakus. Biomed. Digit. Libr. 1 (2004) 2

    Article  Google Scholar 

  26. Kostoff, R. N., Braun, T., Schubert, A., Toothman, D. R., Humenik, J. A.: Fullerene data mining using bibliometrics and database tomography. J. Chem. Inf. Comput. Sci. 40 (2000) 19–39

    Google Scholar 

  27. Smalheiser, N. R., Torvik, V. I.: Mammalian microRNAs derived from genomic repeats. Trends Genet. 21 (2005) 322–326

    Article  Google Scholar 

  28. Smalheiser, N. R., Torvik, V. I.: Alu elements within human mRNAs are probable microRNA targets. Trends Genet. 22 (2006) 532–536

    Article  Google Scholar 

  29. Petukhova, O. A., Mittenberg, A. G., Kulichkova, V. A., Kozhukharova, I. V., Ermolaeva, I. uB., Gauze, L. N., Konstantinova, I. M.: A new class of small RNP (alpha-RNP) containing antisense RNA in K-562 cells. IV. The coordinated regulation of the expression of Alu-containing mRNA and alpha-RNA during differentiation. Ontogenez 28 (1997) 437–444

    Google Scholar 

  30. Daskalova, E., Baev, V., Rusinov, V., Minkov, I.: Sites and mediators of network miRNA-based regulatory interactions. Evol. Bioinform. Online 2 (2006) 99–116

    Google Scholar 

  31. Swanson D. R.: Intervening in the life cycles of scientific knowledge. Libr. Trends 41 (1993) 606–631

    Google Scholar 

  32. Swanson D. R.: Migraine and magnesium: eleven neglected connections. Perspect. Biol. Med. 31 (1998) 526–557

    Google Scholar 

  33. Swanson D. R.: Fish oil, Raynaud’s syndrome, and undiscovered public knowledge. Perspect. Biol. Med. 30 (1996) 7–18

    Google Scholar 

  34. Swanson, D. R., Smalheiser, N. R., Bookstein, A.: Information discovery from complementary literatures: categorizing viruses as potential weapons. J. Am. Soc. Inf. Sci. Technol. 52 (2001) 797–812

    Article  Google Scholar 

  35. Homayouni, R., Heinrich, K., Wei, L., Berry, M. W.: Gene clustering by latent semantic indexing of MEDLINE abstracts. Bioinformatics 21 (2005) 104–115

    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

Smalheiser, N.R., Torvik, V.I. (2008). The Place of Literature-Based Discovery in Contemporary Scientific Practice. 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_2

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-68690-3_2

  • 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