SPINS: Standardized ProteIn NMR Storage. A data dictionary and object-oriented relational database for achiving protein NMR spectra

Michael C. Baran, Hunter N.B. Moseley, Gurmukh Sahota, Gaetano T. Montelione

Research output: Contribution to journalReview articlepeer-review

17 Scopus citations

Abstract

Modern protein NMR spectroscopy laboratories have a rapidly growing need for an easily queried local archival system of raw experimental NMR datasets. SPINS (Standardized ProteIn Nmr Storage) is an object-oriented relational database that provides facilities for high-volume NMR data archival, organization of analyses, and dissemination of results to the public domain by automatic preparation of the header files required for submission of data to the BioMagResBank (BMRB). The current version of SPINS coordinates the process from data collection to BMRB deposition of raw NMR data by standardizing and integrating the storage and retrieval of these data in a local laboratory file system. Additional facilities include a data mining query tool, graphical database administration tools, and a NMRStar v2.1.1 file generator. SPINS also includes a user-friendly internet-based graphical user interface, which is optionally integrated with Varian VNMR NMR data collection software. This paper provides an overview of the data model underlying the SPINS database system, a description of its implementation in Oracle, and an outline of future plans for the SPINS project.

Original languageEnglish
Pages (from-to)113-121
Number of pages9
JournalJournal of Biomolecular NMR
Volume24
Issue number2
DOIs
StatePublished - Oct 1 2002

Bibliographical note

Funding Information:
We thank J. Aramini, J. Everett, D. Monleon, R. Paranji, C. Rios, T. Szyperski, and G.V.T. Swapna, along with J. Markley and E. Ulrich of the BioMa-gResBank for helpful discussions, suggestions, and advise. This work was supported by grants from the Protein Structure Initiative of National Institutes of Health (P50 GM62413) and The New Jersey Commission on Science and Technology (2042-007-13).

Keywords

  • Integrated analysis process
  • NMR spectra archive
  • Oracle database
  • Structural genomics

ASJC Scopus subject areas

  • Biochemistry
  • Spectroscopy

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