A nomenclature and data model to describe NMR experiments
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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.
KeywordsCCPN data model data standard experiment nomenclature experiment pathway NMR
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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”).
- Bax A., Clore G.M., Driscoll P.C., Gronenborn A.M., Ikura M., Kay L.E. (1990a) J. Magn. Reson. 87:620–627Google Scholar
- Bax A., Ikura M., Kay L.E., Torchia D.A., Tschudin R. (1990b) J. Magn. Reson. 86:304–318Google Scholar
- Braunschweiler L., Ernst R.R. (1983) J. Magn. Reson. 53:521–528Google Scholar
- Frenkiel T., Bauer C., Carr M.D., Birdsall B., Feeney J. (1990) J. Magn. Reson. 90:420–425Google Scholar
- Grzesiek S., Bax A. (1992) J. Magn. Reson. 96:432–440Google Scholar
- Grzesiek S., Bax A. (1993a) J. Biomol. NMR 3:185–204Google Scholar
- Kay L.E., Ikura M., Tschudin R., Bax A. (1990b) J. Magn. Reson. 89:496–514Google Scholar
- Norwood T.J., Boyd J., Heritage J.E., Soffe N., Campbell I.D. (1990) J. Magn. Reson. 87:488–501Google Scholar
- Otting G., Wuthrich K. (1989) J. Magn. Reson. 85:586–594Google Scholar
- Powers R., Gronenborn A.M., Marius Clore G., Bax A. (1991) J. Magn. Reson. 94:209–213Google Scholar
- Sklenar V., Peterson R.D., Rejante M.R., Feigon J. (1993a) J. Biomol. NMR 3:721–727Google Scholar
- Vuister G.W., Boelens R., Kaptein R. (1988) J. Magn. Reson. 80:176–185Google Scholar