Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2019 Feb;73(1-2):5-9.
doi: 10.1007/s10858-018-0220-3. Epub 2018 Dec 22.

NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments

Eldon L Ulrich  1 , Kumaran Baskaran  1 , Hesam Dashti  1 , Yannis E Ioannidis  2 , Miron Livny  3 , Pedro R Romero  1 , Dimitri Maziuk  1 , Jonathan R Wedell  1 , Hongyang Yao  1 , Hamid R Eghbalnia  1 , Jeffrey C Hoch  4 , John L Markley  5
Affiliations
Review

NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments

Eldon L Ulrich et al. J Biomol NMR. 2019 Feb.

Abstract

The growth of the biological nuclear magnetic resonance (NMR) field and the development of new experimental technology have mandated the revision and enlargement of the NMR-STAR ontology used to represent experiments, spectral and derived data, and supporting metadata. We present here a brief description of the NMR-STAR ontology and software tools for manipulating NMR-STAR data files, editing the files, extracting selected data, and creating data visualizations. Detailed information on these is accessible from the links provided.

Keywords: Archival data; Biomolecules; Data specification; Experiment description; Experimental conditions; NMR-STAR; Nuclear magnetic resonance spectroscopy; Ontology; Python; R environment; Visualization of data.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
First two tiers in the NMR-STAR ontology for BMRB. The STAR dictionary tree is an interactive tool for inspecting the NMR-STAR ontology and assessing the most appropriate construct for the user’s application. The NMR-STAR ontology is under constant evolution with community feedback to reflect advancements in NMR techniques. An interactive version is available from the BMRB website with tools that enable searching by category or tag
See this image and copyright information in PMC

References

    1. Bahrami A, Assadi AH, Markley JL, Eghbalnia HR. Probabilistic interaction network of evidence algorithm and its application to complete labeling of peak lists from protein NMR spectroscopy. PLoS Comput Biol. 2009;5:e1000307. doi: 10.1371/journal.pcbi.1000307. - DOI - PMC - PubMed
    1. Berjanskii MV, Wishart DS. The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts. Nucleic Acids Res. 2007;35:W531–W537. doi: 10.1093/nar/gkm328. - DOI - PMC - PubMed
    1. Cornilescu G, Delaglio F, Bax A. Protein Backbone Angle Restraints From Searching a Database for Chemical Shift and Sequence Homology. J Biomol NMR. 1999;13:289–302. doi: 10.1023/A:1008392405740. - DOI - PubMed
    1. d’Auvergne EJ, Gooley PR. Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J Biomol NMR. 2008;40:121–133. doi: 10.1007/s10858-007-9213-3. - DOI - PMC - PubMed
    1. d’Auvergne EJ, Gooley PR. Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J Biomol NMR. 2008;40:107–119. doi: 10.1007/s10858-007-9214-2. - DOI - PMC - PubMed

MeSH terms

LinkOut - more resources