Journal of Biomolecular NMR

, Volume 63, Issue 2, pp 141–150 | Cite as

CONNJUR R: an annotation strategy for fostering reproducibility in bio-NMR—protein spectral assignment

  • Matthew Fenwick
  • Jeffrey C. Hoch
  • Eldon Ulrich
  • Michael R. Gryk
Article

Abstract

Reproducibility is a cornerstone of the scientific method, essential for validation of results by independent laboratories and the sine qua non of scientific progress. A key step toward reproducibility of biomolecular NMR studies was the establishment of public data repositories (PDB and BMRB). Nevertheless, bio-NMR studies routinely fall short of the requirement for reproducibility that all the data needed to reproduce the results are published. A key limitation is that considerable metadata goes unpublished, notably manual interventions that are typically applied during the assignment of multidimensional NMR spectra. A general solution to this problem has been elusive, in part because of the wide range of approaches and software packages employed in the analysis of protein NMR spectra. Here we describe an approach for capturing missing metadata during the assignment of protein NMR spectra that can be generalized to arbitrary workflows, different software packages, other biomolecules, or other stages of data analysis in bio-NMR. We also present extensions to the NMR-STAR data dictionary that enable machine archival and retrieval of the “missing” metadata.

Keywords

CONNJUR Data model Reproducibility Analysis NMR-STAR 

Notes

Acknowledgments

This research was funded by United States National Institutes of Health Grant GM-083072. The authors would like to thank Dr. Mark Maciejewski for kindly providing time-domain data of the Samp3 protein and Dr. Woonghee Lee for adding the reproducibility extensions to the NMRFam release of Sparky.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10858_2015_9964_MOESM1_ESM.pdf (64 kb)
Supplementary material 1 (PDF 64 kb)

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Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  • Matthew Fenwick
    • 1
  • Jeffrey C. Hoch
    • 1
  • Eldon Ulrich
    • 2
  • Michael R. Gryk
    • 1
  1. 1.Department of Molecular Biology and BiophysicsUConn HealthFarmingtonUSA
  2. 2.Department of BiochemistryUniversity of Wisconsin-MadisonMadisonUSA

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