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SpinLIMS


 Introduction

  SpinLIMS is a relational database comprising several entities or "tables" developed by MySQL. To make the database extensible, SpinLIMS client software was developed to incorporate a simple registration system. SpinLIMS contains numerous reference spectra of small molecules to macromolecules recorded in solid state and solution state (polar and nonpolar solvent systems) that can be applied to mixture analysis of various samples. Overall, there are 34 data tables in SpinLIMS, as well as tables for managing the information from NMR experiments. In addition to HSQC in D2O (705 spectra) and 2D-Jres in D2O (623 spectra), SpinLIMS has several newly added spectra from CP-MAS (35 spectra), HSQC in MeOD (947 spectra) and DMSO (171 spectra), and 2D-Jres in MeOD (357 spectra). SpinMacro, InterAnalysis, SpinAssign, and SpinCouple are connected to the MySQL server via a local network in InterSpin. As a result, the re-implemented SpinAssign and SpinCouple facilitate chemical shift searches in MeOD. SpinAssign also facilitates searches in DMSO/pyridine solvent.


  Schematic diagram of SpinLIMS.
(a) SpinLIMS is a relational database based on NMR spectra and molecular information. Thirty-four tables store a variety of information: for example, "metabolitename" is compound name, "metabolite" is compound, "atom" is atom, "nucleus" is nuclide, "cs_assign" is assignment of chemical shift, "cs" is chemical shift, "Jval" is J values, "hc_pk" is HSQC peaks ("h_pk" for 1H-1D NMR, "c_pk" for 13C-1D NMR), "pkshape" is peak linear type, "hj_pk" is 2D-Jres peak, "spectrum" is spectrum, "pulse" is NMR pulse sequence type, "solvent" is solvent (register as "none" in case of solid), "stdref" is reference compound.
(b) SpinLIMS services are provided to users from the MySQL server via InterSpin.

 Entity-relationship diagram


  Diagram showing the relationship among core entities (tables) on the SpinLIMS database.


  The complete relationship among all entities (tables).
For a given query, each table contains the following data: "hc_pk" is HSQC peaks; "hj_pk" is 2D-Jres peaks; "h_pk" is 1H-1D NMR peaks; "c_pk" is 13C-1D NMR peaks; "spectrum" is the spectrum; "spectrum_type" is the type of spectrum; "pulse" is the NMR pulse sequence; "solvent" is the solvent; "stdref" is the standard compound; "baseurl" is the base URL for raw spectrum; "pkshape" is the peak shape; "pktype" is the type of peak; "cs" is chemical shifts; "jval" is J values; "cs_assign" is one-atom assignment for one chemical shift; "support" is evidence of assignment; "metabolite" is metabolite; "atom" is atom; "nucleus" is nucleus; "metabolitename" is the name of metabolite; "shiyaku" is the compound number; "Shiyakubasyo" is the storage location of compound; "organization" is the organization who measured the data; "limsuser" is the user who registered the data; "reserve" is the measuring reservation; "tag" is the tag for clustering compound, metabolite, and spectrum; "tag_met" is the tag for metabolite; "tag_cs" is the tag for chemical shift; "tag_jval" is the tag for J value; "limsuserref" is the reference user for sampled_by, nmr_by, processed_by of spectrum table, and reserved_by of reserve table; "tag_feature" is a feature to tag related spectra, for example, for tasting data, etc.; "bin" is the bin for spectrum; "bspectrum" is the binning spectrum; and "tag_spc" is the tag for spectrum.


           

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