Standard representations for chemical information

  • John M. Barnard
Conference paper

Abstract

This paper will give a brief historical survey of the development of standard notations for chemical structures, including structure diagrams, nomenclature and line notations. The more recent development of standard computer formats for the representation of chemical structures and associated data will then be discussed, and the paper will conclude with a summary of the present state, and future prospects, of a standard connection table format for the exchange of data.

Keywords

Mercury Manifold Polypeptide Cyclohexane Hyde 

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References

  1. 1.
    Flood, W.E., The Origins of Chemical Names’. London: Oldbourne (1963).Google Scholar
  2. 2.
    Gordon, J.E. and Brockwell, J.C., ‘Chemical Inference 1. Formalization for the Language of Organic Chemistry: Generic Structural Formulas’, Journal of Chemical Information and Computer Sciences 23 117–134 (1983).Google Scholar
  3. 3.
    Rush, J.E. ‘Handling Chemical Structure Information’, Annual Review of Information Science and Technology 13 209–62 (1978).Google Scholar
  4. 4.
    Godly, E. ‘Towards Standard Representations of Chemical Structure’, Chemical Structure Association Newsletter (2) 11–13 (1983).Google Scholar
  5. 5.
    Chemical Substance Index Names’. Chemical Abstracts Index Guide, Appendix IV. American Chemical Society (1989). [Also available separately as ‘Naming and Indexing Chemical Substances for Chemical Abstracts’, CAS Reprint 298.]Google Scholar
  6. 6.
    Nickon, A. and Silversmith, E.F., ‘Organic Chemistry: the Name Game’, Oxford: Pergamon (1987).Google Scholar
  7. 7.
    International Union of Pure and Applied Chemistry, Commission on the Nomenclature of Inorganic Chemistry, ‘The Nomenclature of Inorganic Chemistry. 2nd Edition’, Pure and Applied Chemistry 28 1–110 (1971).Google Scholar
  8. 8.
    International Union of Pure and Applied Chemistry, Commission on the Nomenclature of Organic Chemistry, ‘The Nomenclature of Organic Chemistry. Sections A, B, C, D, E, F and H’, Oxford: Pergamon (1979).Google Scholar
  9. 9.
    Lees, R. and Smith, A.F. (editors), ‘Chemical Nomenclature Usage’, Chichester: Ellis Horwood (1983).Google Scholar
  10. a.
    Loening, K.L., ‘Standardization of Chemical Nomenclature’ (pp. 53–57)Google Scholar
  11. b.
    Godly, E.W., ‘Standardization of Chemical Nomenclature in Government Legislation and Documentation’ (pp. 58–68)Google Scholar
  12. c.
    Egan, H., ‘The Role of the United Kingdom in Chemical Nomenclature’ (pp. 69-73)Google Scholar
  13. 10.
    Wiswesser, W.J., ‘Historic Development of Chemical Notations’, Journal of Chemical Information and Computer Sciences 25 258–263 (1985).Google Scholar
  14. 11.
    International Union of Pure and Applied Chemistry. Commission on Codification, Ciphering and Punched Card Techniques, ‘Rules for IUP AC Notation for Organic Compounds’, Longmans (1961).Google Scholar
  15. 12.
    Smith, E.G. and Baker, P.A., ‘The Wiswesser Line-Formula Chemical Notation’, 3rd Edition, Philadelphia: Chemical Information Management Inc. (1972).Google Scholar
  16. 13.
    Baker, P.A. (ed.), ‘The Wiswesser Line-Formula Chemical Notation. Amended Rules 1985’, Chemical Structure Association (1985).Google Scholar
  17. 14.
    Loening, K.L., ‘Poster Session: Conventions, Practices and Pitfalls in Drawing Chemical Structures’, in Chemical Structures. The International Language of Chemistry, ed. W.A. Warr, pp. 413–423. Heidelberg: Springer-Verlag (1988).Google Scholar
  18. 15.
    Cahn, R.S., Ingold, C.K. and Prelog, V. ‘Specification of Molecular Chirality’, Angewandte Chemie International Edition in English 5 385–415 (1966).Google Scholar
  19. 16.
    Prelog, V. and Helmchen, G., ‘Basic Principles of the CIP- System and Proposals for a Revision’, Angewandte Chemie International Edition in English 21 567–583 (1982).CrossRefGoogle Scholar
  20. 17.
    Ash, J.E., ‘Connection Tables and their Role in a System’, in Chemical Information Systems, ed. J.E. Ash and E. Hyde. Chichester: Ellis Horwood (1975).Google Scholar
  21. 18.
    Barnard, J.M., Towards a Standard Interchange Format for Chemical Structure Data’, in Proceedings of the 12th International Online Information Meeting, pp. 605–609, Oxford: Learned Information (1988).Google Scholar
  22. 19.
    Protein Databank File Record Formats’. Department of Chemistry, Brookhaven National Laboratory, Upton, NY 11973 (1979).Google Scholar
  23. 20.
    Brown, I.D., ‘Standard Crystallographic File Structure’, Acta Crystallographica A39 216–224 (1983).Google Scholar
  24. 21.
    Gund, P., Barry, D.C., Blaney, J.M., Cohen, N.C., ‘Guidelines for Publications in Molecular Modelling Related to Medicinal Chemistry’, Journal of Medicinal Chemistry 31 2230–2234 (1988).CrossRefGoogle Scholar
  25. 22.
    Bebak, H., Buse, C., Donner, W.T., Hoever, P., Jacob, H., Klaus, H., Pesch, J., Rmelt, J., Schilling, P., Woost, B. and Zirz, C. ‘The Standard Molecular Data Format (SMD Format) as an Integration Tool in Computer Chemistry’ Journal of Chemical Information and Computer Science 29 1–5 (1989).Google Scholar
  26. 23.
    Gasteiger, J., Hendriks, B.M.P., Hoever, P., Jochum, C., Somberg, H. JCAMP-CX. A Standard Exchange Format for Chemical Structure Information in Computer Readable Form\ Applied Spectroscopy (in press).Google Scholar
  27. 24.
    McDonald, R.S., Wilks, P.A., ‘JCAMP-DX: A Standard Form for Exchange of InfraRed Spectra in Computer-Readable Form’, Applied Spectroscopy 42 151–162 (1988).CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 1989

Authors and Affiliations

  • John M. Barnard
    • 1
  1. 1.Barnard Chemical Information LtdStannington, SheffieldUK

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