An Interval-Based Index Structure for Structure Elucidation in Chemical Databases

  • Sven Helmer
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4529)


We propose to adapt an interval-based index structure, Relational Interval trees, to support the process of determining the structure of an unknown chemical compound. Important information for retrieving relevant substructures that make up a compound can only be described in an imprecise way, resulting in interval-based values specifying chemical shifts. The access method was implemented on top of a commercial database system and evaluated experimentally. The results of these experiments show that Relational Interval trees are an efficient way of indexing data needed for structure elucidation.


Structure Elucidation Nuclear Magnetic Resonance Spectroscopy Interval Tree Point Query Vector Approach 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. 1.
    Diallo, M.S., Faulon, J.L., Goddard, W.A., Johnson, J.H.: Binding of Hydrophobic Organic Compounds to Dissolved Humic Substances: A Predictive Approach Based on Computer Assisted Structure Elucidation, Atomistic Simulations and Flory-Huggins Solution Theory. In: Humic Substances: Structures, Models and Functions, Royal Society of Chemistry (2001)Google Scholar
  2. 2.
    Dunkel, R., Mayne, C.L., Pugmire, R.J., Grant, D.M.: Computerized analysis of two-dimensional double quantum NMR spectra. In: Symposium on Advances in Computer Simulation and Artificial Intelligence in Analytical Chemistry (April 1990)Google Scholar
  3. 3.
    Funatsu, K., Susuta, Y., Sasaki, S.I.: Application of the automated structure elucidation system (CHEMICS) to the chemistry of natural products. Pure and Appl. Chem. 61(3), 609–612 (1989)CrossRefGoogle Scholar
  4. 4.
    Kriegel, H.P., Pötke, M., Seidl, T.: Managing intervals efficiently in objectrelational databases. In: Proc. of 26th Int. Conf. on Very Large Data Bases (VLDB), pp. 407–418 (2000)Google Scholar
  5. 5.
    Manber, U.: Introduction to Algorithms: A Creative Approach. Addison Wesley, New York (1989)zbMATHGoogle Scholar
  6. 6.
    Preparata, F.P., Shamos, M.I.: Computational Geometry: An Introduction. Springer, Heidelberg (1993)Google Scholar
  7. 7.
    Roberts, C.S.: Partial-match retrieval via the method of superimposed codes. Proc. of the IEEE 67(12), 1624–1642 (1979)CrossRefGoogle Scholar
  8. 8.
    Wikipedia. NMR spectroscopy,
  9. 9.
    Will, M., Fachinger, W., Richert, J.: Fully automated structured elucidation - a spectroscopist’s dream comes true. J. Chem. Inf. Comput. Science 36(2), 221–227 (1996)CrossRefGoogle Scholar

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© Springer Berlin Heidelberg 2007

Authors and Affiliations

  • Sven Helmer
    • 1
  1. 1.University of London, Birkbeck College, LondonUnited Kingdom

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