Journal of Biomolecular NMR

, Volume 36, Issue 3, pp 147–155 | Cite as

A nomenclature and data model to describe NMR experiments

  • Rasmus H. Fogh
  • Wim F. Vranken
  • Wayne Boucher
  • Tim J. Stevens
  • Ernest D. Laue
Article

Abstract

Despite ongoing efforts in organising NMR information, there is no consistent and well-described generic standard for naming NMR experiments. The main reason for the absence of a universal naming system is that the information content of the coherence pathways is difficult to describe in full detail. We propose a system that describes the common and generic elements of the coherence pathways produced by pulse sequences. The system itself is formalised by an ‘NMR experiment protocol’ model, which is described in the Universal Modelling Language (UML) as part of the CCPN data model. Furthermore, normalized experiment names can be derived from this proposed model. We hope this article will stimulate discussion to organise the wealth of NMR experiments, and that by bringing this discussion into the public domain we can improve and expand our proposed system to include as much information and as many NMR experiments as possible.

Keywords

CCPN data model data standard experiment nomenclature experiment pathway NMR 

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Notes

Acknowledgements

The authors thank Daniel Nietlispach for very useful discussions to steer the model in the right direction. We are grateful for support from the Biochemistry and Biological Sciences Research Council, UK (Grants 8/B13014 and 8/B20259), and the European Community “Quality of Life and Management of Living Resources” program (Grants QLRI-CT-2001-00015 “TEMBLOR” and QLG2-CT-2000-01313 “NMRQUAL”).

Supplementary material

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Electronic supplementary material Supplementary material is available in the online version of this article at http://www.dx.doi.org/10.1007/s10858-006-9076-z and is accessible for authorized users.

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Copyright information

© Springer Science+Business Media B.V. 2006

Authors and Affiliations

  • Rasmus H. Fogh
    • 1
  • Wim F. Vranken
    • 2
  • Wayne Boucher
    • 1
  • Tim J. Stevens
    • 1
  • Ernest D. Laue
    • 1
  1. 1.Department of BiochemistryUniversity of CambridgeCambridgeUK
  2. 2.Macromolecular Structure DatabaseEuropean Bioinformatics Institute, HinxtonCambridgeUK

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