Sharing and archiving nucleic acid structure mapping data
- Philippe Rocca-Serra1,
- Stanislav Bellaousov2,
- Amanda Birmingham3,
- Chunxia Chen4,
- Pablo Cordero5,
- Rhiju Das5,
- Lauren Davis-Neulander4,
- Caia D.S. Duncan6,
- Matthew Halvorsen4,
- Rob Knight7,8,
- Neocles B. Leontis9,
- David H. Mathews2,
- Justin Ritz4,
- Jesse Stombaugh7,
- Kevin M. Weeks6,
- Craig L. Zirbel10 and
- Alain Laederach4,11
- 1Oxford e-Research Center, University of Oxford, OX1 3QG, Oxford, United Kingdom
- 2Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
- 3Thermo Fisher Scientific, Lafayette, Colorado 80026, USA
- 4Biology Department, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
- 5Biochemistry Department, Stanford University, Stanford, California 94305, USA
- 6Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
- 7Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
- 8Howard Hughes Medical Institute, Boulder, Colorado 80309, USA
- 9Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, USA
- 10Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, Ohio 43403, USA
Abstract
Nucleic acids are particularly amenable to structural characterization using chemical and enzymatic probes. Each individual structure mapping experiment reveals specific information about the structure and/or dynamics of the nucleic acid. Currently, there is no simple approach for making these data publically available in a standardized format. We therefore developed a standard for reporting the results of single nucleotide resolution nucleic acid structure mapping experiments, or SNRNASMs. We propose a schema for sharing nucleic acid chemical probing data that uses generic public servers for storing, retrieving, and searching the data. We have also developed a consistent nomenclature (ontology) within the Ontology of Biomedical Investigations (OBI), which provides unique identifiers (termed persistent URLs, or PURLs) for classifying the data. Links to standardized data sets shared using our proposed format along with a tutorial and links to templates can be found at http://snrnasm.bio.unc.edu.
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Footnotes
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↵11 Corresponding author.
E-mail alain{at}unc.edu.
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Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.2753211.
- Received March 28, 2011.
- Accepted April 23, 2011.
- Copyright © 2011 RNA Society
Freely available online through the RNA Open Access option.
