This is the initial draft of the msi-nmr-ontology binned under 'webimported' OBI and BFO classes. This is a primary discussion- and test-version to encourage nmr term development. As a secondary role this ontology serves as a testbed to evaluate the BFO top level ontology , modularization and the owl-import and referencing mechanism. The nmr ontology is developed by the ontology working group (http://msi-ontology.sourceforge.net/) of the msi-metabolomicssociety (msi-workgroups.sf.net). 18.10.2006 v.0.1 msi-owg, http://msi-ontology.sourceforge.net/ Daniel Schober, Susanna-Assunta Sansone Contact via MSI OWG mailing list (mailto:msi-workgroups-ontology@lists.sourceforge.net) NMR en Free, no licenses needed Keywords: NMR, nuclear magnetic resonance, metabolomics, metabolomics investigation, metabolomics experiment Important top level classes: NMR_instrument, NMR_instrument_configuration, NMR_parameter_set, NMR_vendor, NMR_software, data_processing_method, NMR_spectrum, NMR-data-set, NMR_probe Intended application: data annotation, reporting requirements usage: in development In alphabetical order: Andy Tseng (Human Serum Metabolome Project, Un of Manchester, UK), Bertram Ludaescher (UCDavis Genome Center, US), Chris Taylor (EBI and HUPO-PSI), Daniel Schober (EBI and HUPO-PSI), Dennis Rubtsov (Un of Cambridge, UK), Helen Jenkins (Un of Wales, Aberystwyth, UK), Irena Spasic (Center for Integrative Systems Biology, Manchester, UK), Larissa Soldatova (University of Wales, Aberystwyth, UK), Lori Querengasser (Un of Alberta, CA), Martin Scholz (UCDavis Genome Center, US), Matej Oresic (VTT Technical Research Centre of Finland, FI), Oliver Fiehn (UCDavis Genome Center, US), Philippe Rocca-Serra (EBI and MGED), Susanna-Assunta Sansone (EBI, HUPO-PSI and MGED)) owl-DL NMR-instrument specific component of metabolomics investigations This controlled vocabular (taxonomy) contains mainly Descriptors relevant to the experimental conditions of the Nuclear Magnetic Resonance (NMR) component in a metabolomics investigation. pre-processing_parameter_set defneed def: A reference to information on the provenance of the NMR sample. synonym: NMR sample reference NMR_sample_reference Frydman_encoding defneed UltraShield defneed machine configuration instrument setting Daniel Schober Move to OBI. An instrument configuration is the process of setting the possible parameters of an instrument in order to archive a certain intended goal. instrument configuration An instrument configuration is the process of setting the possible parameters of an instrument in order to archive a certain intended goal. 061108 It is not clear if this domain independent class should be moved to OBI. Free An instrument configuration is the description for the setting of an instrument or a machine in order to archive a certain intended goal or task. ArMet OM instrument_configuration unstable This class should capture differrent instrument settings on the machine used in response to diverse analytical approaches. projected_spectrum tempdef: The data matrix a spectrum consists of can be projected from a higher dimension onto a lower dimension, e.g. a 3D NMR spectrum can be converted (projected) into a 2D NMR spectrum. defprov: Daniel Schober Bruker_NMR_probe defneed TODO: May need no definition. Paravision quality_check_result tempdef: A quality check result is the usefull outcome of a quality check. defprov: Daniel Schober water_suppression_parameter defneed NMR_magnet def: A magnet which induces a certain frequency (MHz) and which has a certain bore diameter. altdef: The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the nmr acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss. 17O defneed clsdel: was under study_report ?result defneed polynomial_fitting first_order_phase_correction defneed NMR_data_pre-processing_parameter_set defneed synonym: NMR data pre-processing parameter set AURELIA console TODO: same as or part of acquisition computer? def: A component of an NMR instrument that controls the activities of the other components. tempdef: An immanent important, non-obligatory part of any NMR data set. defprov: Daniel Schober synonym: cardinal part of NMR data set cardinal_part_of_NMR_data_set JEOL_NMR_probe defneed 2H TODO: Do we need definitions here? def: A post-processing method that divides a pre-processed NMR spectrum into a series of buckets (or bins) along the x-axis, and then integrates the spectral intensity within each bucket. altdef: A type of automated integration which occurs across pre-defined regions for a spectrum. bucketing Ultrastabilized two_dimensional_NMR_acquisition_parameter_set defneed synonym: 2D NMR acquisition parameter set GEMINI 19F SampleTrack one_dimensional_carr_purcell_meiboom_gill tempdef: A modification of Carr-Purcell RF pulse sequence with 90° phase shift in the rotating frame of reference between the 90° pulse and the subsequent 180° pulses to reduce accumulating effects of imperfections in the 180° pulses. Suppression of effects of pulse error accumulation can alternatively be achieved by alternating phases of the 180° pulses by 180°. defprov: Daniel Schober synonym: 1D_CPMG atom_environment_encoding def: A scheme for producing a numerical representation of the environment of an atom. INOVA TopSpin_1.3 DISCOVERY def: The Discovery™ is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing network defprov: tecmag website spinning_rate def: The rate at which an item of analysis material is spun. def: Having been excited by the RF pulse, the nuclei turn back ("relax") to their initial state ( the initial equilibrium population) within usually several seconds when the induced magnetization decays. Since the precession of the nuclei is free and due to the decay of the induced magnetization the whole process is termed Free Induction Decay (FID). Usually, several FIDs are co-added in order to improve the signal-to-noise ratio of a spectrum. The summed up FID is then once subjected to a mathematical operation (Fourier transform) which results in an NMR spectrum. synonym: 2D_FID two_dimensional_free_induction_decay one_dimensional_NMR_acquisition_parameter_set defneed synonym: 1D NMR acquisition parameter set defneed y-axis_unit NMR_Suite tempdef: The end value for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum. x_end_value data_pre-processing defneed defneed Hadamard_encoding NMR_quality_check_result def: A result of an NMR quality check. synonym: NMR quality check result presat defneed synonym: presaturation calibration_compound def: The compound that produced the peak used to reference a spectrum during data pre-processing. tecmag flip-back_watergate defneed defneed synonym: 1D spectrum one_dimensional_spectrum 13C data_post-processing def: Automatic or manual procedures performed upon pre-processed NMR data sets that aim to summarise them or annotate them with speculative values. 11B magic_angle_spinning_rotor defneed synonym: MAS_rotor def: The process of producing a spectrum from raw data. synonym: NMR data pre-processing NMR_data_pre-processing defneed magnetic_field_strength states-time_proportional_phase incrementation def: A method for quadrature detection. synonym: S-TPPI decoupled_nucleus def: An indication of whether the nucleus being studied is the acquitsition nucleus. data_transformation def: A method for transforming the time-based acquisition data into frequency-based data. chemical_shift_standard def: A compound that is added to an NMR sample to enable the alignment of spectra. The power of NMR is that for most nuclei the NMR frequency changes very slightly with different molecular environment or chemical bonding. These shifts are very small, on the order of 1 part in 10+9. This is referred to as "Chemical Shift." Tables of chemical shifts are tabulated and used to determine molecular structure. Combining NMR chemical shift information with other NMR information such as peak integration, coupling constants and Nuclear Overhauser Enhancement (NOE) can result in complete three-dimensional molecular structures of molecules in solution without using X-ray crystallography. quality_control_method tempdef: A quality control method is a method, which is applied to ensure or to verify for a good quality outcome. defprov: Daniel Schober tempdef: An integral data transformation that re-expresses a function in terms of sinusoidal basis functions, i.e. as a sum or integral of sinusoidal functions multiplied by some coefficients ("amplitudes"). defprov: Daniel Schober fourier_transformation tempdef: The sample-tube holds the nmr sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter. tube additional_axis_unit def: The unit of measurement of the second dimension of a 2D NMR dataset. defneed TODO: May need no definition. Bruker_NMR_software 29Si ECX data_processing_method def: A method or algorithm that converts an input data set into an output data set in a tracable and useful manner. def: A strategy for normalising a data set. normalisation_strategy gaussian_broadening defneed jump_and_return tempdef: A jump and return pulse sequence method is a water suppression method that uses a defined pulse sequences to make fast exchanging protons visible. synonym: jump and return pulse sequence defneed synonym: 2D spectrum two_dimensional_spectrum 31P AMX buffer def: A compound added to a sample to alter its pH value. CapNMR_Probe def: A reference to a description of a pulse sequence in the literature. pulse_sequence_literature_reference def: An Instrument which is used to carry out a NMR analysis of some sample. synonym: NMR instrument NMR_instrument def: A reference to a file of data pre-processing parameters produced by the machine. processing_parameter_set_file_reference def: A parameter to a window function. window_function_parameter defneed Bruker_autosampler def: A sequence of excitation pulses. pulse_sequence def: The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit. defprov: Bruker website B-ACS NMR_spectral_projection_parameter_set def: The data processing parameters that describe a method of translating a 2D NMR pre-processed spectrum into a 1D NMR spectrum. synonym: NMR spectral projection parameter set ECA WaveWat def: A computational method that archieves water suppression via wavlet multi resolution analysis. def: A complex datatype (or complex value) is a datatype that is not a primitive one (like string or integer) and that references to more primitive values. Often, these are called reference data types. Complex datatypes can belong to the object data type. Data types that define sets of complex values include Array, Date, Error, Function, and XML and others. complex_datatype sample_introduction_method def: A method of introduction of an NMR sample to an NMR instrument. JEOL_NMR_software def: A description of the post-processing strategy used to convert a pre-processed NMR spectrum into a suitable data format for chemometric analysis. synonym: NMR spectrum post-processing parameter set TODO: altsprcls: process, not clear wether set is plural (list) or process. NMR_spectrum_post-processing_parameter_set x_start_value def: The starting value for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum. altdef: The initial time or frequency a FID or spectrum is recorded from. def: A reference to a file containing a specfication of the shape of an excitation pulse. shaped_pulse_file_reference quality_check_compound_signal def: The compound that produced a peak that is measured to assess the quality of a data set. MR_Resources NMR_analysis def: The analysis of one NMR sample at one time by NMR producing one raw dataset (a FID). synonym: NMR analysis def: Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation. The SampleJet utilizes the modern-day industry standard for sample arrangements—the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement. defprov: Bruker website SampleJet tempdef: A quality check is a quality control method, which is applied to data after they have been processed. It is applied to get information about the quality of the data processing methods. defprov: Daniel Schober quality_check zero_order_phase_correction def: A parameter used to mix real and imaginary part of an NMR spectrum that the real part of the spectrum is in pure absorption mode. altdef: The number of degrees that a central peak must be moved in order to achieve an absorptive mode line width. defneed line_sharpening hankel_singular_value_decomposition def: This Method removes the residual water and its side lobes, thereby reducing the baseline for the metabolites of interest and allowing subsequent data analysis using more sophisticated nonlinear least squares algorithms. synonym: HSVD echo_anti-echo defneed defneed peak-picked_spectrum TODO: has spectral post processing parameter. defneed NMR_instrument_parameter_set NMR_sample_holder def: A NMR sample holder is the part of an NMR instrument, which carries the nmr probe,sample tube and the nmr sample. Varian_NMR_instrument def: A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers. acquisition_computer NMR_solvent def: A compound added to a sample to an NMR sample to align the spectrometer frequency. synonym: NMR solvent JEOL_NMR_instrument Bruker_MATCH def: The Bruker Multiple Adjustable Tube Clamp Holder MATCH™ system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications. The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube. defprov: Bruker website synonym: Bruker Multiple Adjustable Tube Clamp Holder AVANCE_II_spectrometer TODO: May need no definition defneed defneed convolution Bruker_NMR_instrument defneed line_broadening defneed MERCURY defneed NMR_software cardinal_part_of_NMR_instrument def: A part of an NMR instrument which is cardinally important and hence obligatory and compulsatory for the proper intended function of the instrument. synonym: cardinal part of NMR instrument def: Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile “single point of failure” that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency. altdef: The instrument that transmits and recieves radiofrequency to and from the NMR sample. NMR_probe tecmag_console literature_reference defneed sine_squared defneed defneed NMR_imaging_probe water_suppression_method tempdef: A technique used to suppress the water peak in a spectrum. Suppression of the strong solvent signal is necessary in order to obtain high signal to noise for the peaks of the sample under investiogation, e.g. protein peaks. defprov: Daniel Schober Delta defneed synonym: sb shifted_bell dwell_time def: A digital sampling interval. alsprcls: time_interval Micro_Imaging_probe defneed sine defneed Hyphenation tempdef: A sample introduction parameter is a parameter that describes the particular method of introducing the sample under investigation into the nmr instrument. sample_introduction_parameter JS_Research JEOL CryoProbe def: The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis: Significant S/N gains (with moderately salty samples also) Short pulse widths Short ring down times Linear behavior in power response Gradient capability CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and higher All high resolution probes have a lock circuit All high resolution probes have Z-gradient defprov: Bruker website def: A software artifact used during spectral post-processing. spectrum_post-processing_software post-processing_algorithm def: An algorithm for achieving a post-processed spectrum. APOLLO defneed Doty_Scientific defneed symmetrise def: In today's fast-paced research environment, NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean™ system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material. defprov: Bruker website Bruker_AutoClean water_suppression_enhanced_through_T1_effects tempdef: An improved water-suppression technique called WET (water suppression enhanced through T1 effects), developed from a Bloch equation analysis of the longitudinal magnetization over the T1 and B1 ranges of interest, achieves T1- and B1-insensitive suppression with four RF pulses, each having a numerically optimized flip angle. Once flip angles have been optimized for a given sequence, time-consuming flip-angle adjustments during clinical examinations are eliminated. defprov: Daniel Schober synonym: WET Metabolic_Profiler def: An algorithm is a procedure (a finite set of well-defined instructions) for accomplishing some task which, given an initial state, will terminate in a defined end-state. defprov:wiki algorithm spectral_denoising def: A method for eliminating or reducing the noise in a spectrum. AUREMOL def: The list of parameters that describe the settings used to process a 2D J-resolved NMR spectrum. altdeft: The set of variables associated with adjusting the spectrum in the frequency domain to phase, baseline correct and integrate a spectrum. synonym: NMR 2D J-resolved processing parameter set NMR_two_dimensional_J-resolved_processing_parameter_set sample_temperature_in_magnet def: The temperature of an NMR sample whilst in the magnet of an NMR instrument. sample_temperature def: In some cases, it is necessary or advisable to control the temperature of the sample at some value other than ambient. The sample may be only slightly solubility at room temperatures, or it may be desirable to control some aspect of the dynamics of the system. In such cases, a default temperature, or some means of selecting this parameter, can be built into the experiment. def: An investigation of the component parts of a whole and their relations in making up the whole. defprov: Google define altdef: A systematic approach to problem solving. Complex problems are made simpler by separating them into more understandable elements. This involves the identification of purposes and facts, the statement of defensible assumptions, and the formulation of conclusions. analysis tecmag_EAGLE_probe def: The Eagle™ is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz widebore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers. defprov: website def: The intensity of an electric, magnetic, or other field. field_strength NMR_tube_washing_system defneed def: A method of flattening the baseline of a spectrum. baseline_correction states defneed def: The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data. defprov: Bruker website synonym: Bruker Efficient Sample Transfer NMR Bruker_BEST_NMR pulse_sequence_file_reference def: A reference to a file containing a specification of a pulse sequence. SampleRail def: This system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system. The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back defprov: website quantum_momentum_field_gradient tempdef: Quantum Moment/Field Gradient interaction or relaxation mechanism. defprov: Daniel Schober synonym: QF 1H def: The nucleus of the element Hydrogen, a proton. rem1: The nucleus most often studied in NMR metabolomics. excitation_sculpting def: A specific technique used to suppress the solvent signal in a spectrum. altdef:: A type of pulse sequence (or part of it) used to suppress a frequency (most commonly solvent). file_reference defneed shifted_sine_bell tenpdef: A function used to multiply a FID by to produce a desired amount of line broadening and spectral resolution. defprov: Daniel Schober synonym: ssb defneed watergate NMR_quality_check_parameter_set tempdef: A nuclear magnetic resonance spectroscopy quality check parameter set is a parameter set used for the quality check method for an NMR analysis synonym: NMR quality check parameter set def: The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats. defprov: Bruker website NMR_Case optional_part_of_NMR_instrument def: Part of an NMR instrument which is not cardinally important and hence optional / facultative for the proper intended function of the instrument. synonym: optional part of NMR instrument clsdel: ontologically there is no such universal which characteristic is a possible (!) state of being a part of something... TODO: Discuss "obligatory_part_of". two_dimensional_hadamard_total_correlation_spectroscopy defneed synonym: 2D_hadamard_TOCSY tecmag_NMR_instrument irradiation_frequency def: The frequency of the RF radiation used to irradiate an NMR sample. liquid_NMR_probe Acorn_NMR_Inc time_proportional_phase incrementation defneed synonym: TPPI AC NMR_data_pre-processing_parameter_set_by_dimension def: The set of variables dependent on a given pulse sequence for a given dimension that will be optimised in order to acquire a spectrum. synonym: NMR data pre-processing parameter set by dimension def: Samples that are neither solid nor liquid, being of biological, chemical, and/or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Bruker’s high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject/insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g., 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used. defprov: Bruker website altdef: High resolution MAS (hr-MAS) provides an easy means of obtaining high resolution spectra for a variety of samples that would otherwise result in poorly resolved spectra. The addition of an hr-MAS probe and a MAS pneumatic unit to a standard high resolution spectrometer is all that is needed to open the gate to the world of hr-MAS spectroscopy and gain access to a vast amount of highly interesting samples. synonyms: High resolution MAS, hr-MAS high_resolution_magic_angle_spin_probe acquisition_nucleus def: The nucleus of an element or isotope that is being studied during an NMR analysis. Common NMR requirements include direct 1D and 2D proton-only NMR, direct observation of 13C NMR with 1H decoupling, direct observation of other nuclei such as 19F, 31P, 29Si, 31P, 27Al, and 15N (with or without 1H decoupling), triple resonance NMR (especially inverse triple resonance such as 1H observe, 13C and 15N decouple), and inverse 2D and 3D experiments such as HMQC and HMBC. spectrum_post-processing defneed NMR_instrument_configuration def: The configuration of an NMR Instrument. synonym: NMR_instrument_configuration def: The process of producing an annotated spectrum from a pre-processed spectrum. synonym: NMR spectral post processing NMR_spectral_post-processing Wilmad defneed solid_NMR_probe NMR_spectrum tempdef: A frequency sorted array of the NMR signal frequency components. Nuclei with different resonance frequencies will show up as peaks at different corresponding frequencies in the spectrum, or 'lines'. synonym: NMR spectrum nuclear_overhauser_and_exchange_spectroscopy-presat tempdef: The presat for an nuclear overhauser and exchange spectroscopy experiment. A 2D method used to map NOE correlations between protons within a molecule. The nuclear Overhauser effect (NOE) causes changes in peak areas, as a secondary effect of decoupling. defprov: Daniel Schober synonym: NOESY-presat post-acquisition_water_suppression_method tempdef: A data processing technique used to suppress the water peak in a spectrum in order to get clearer results. defprov: Daniel Schober defneed tilt ninety_degree_pulse_duration def: The duration of the excitation pulse needed to rotate the magnetisation vector by 90 degrees. synonym: 90 degree pulse duration peak_picking defneed one_dimensional_free_induction_decay def: Having been excited by the RF pulse, the nuclei turn back ("relax") to their initial state ( the initial equilibrium population) within usually several seconds when the induced magnetization decays. Since the precession of the nuclei is free and due to the decay of the induced magnetization the whole process is termed Free Induction Decay (FID). Usually, several FIDs are co-added in order to improve the signal-to-noise ratio of a spectrum. The summed up FID is then once subjected to a mathematical operation (Fourier transform) which results in an NMR spectrum. synonym: 1D_FID defneed radon_encoding def: The axis onto which the spectrum was projected. projection_axis defneed synonym: 1D diffusion edited one_dimensional_diffusion_edited coherence_pathway_rejection tempdef: A water suppression method which is used to suppress the natural water signal in a gradient selection experiment (e.g. echo/antiecho), where the water coherence is not "refocused" by the refocus gradient (therefore, is not selected). defprov: Daniel Schober encoding_method tempdef: A data processing method which compresses a data file for a specific purpose. defprov: Daniel Schober Varian tempdef: Total Correlation Spectroscopy. A 2D homonuclear correlation experiment used to analyse scalar (J) coupling networks between protons. TOCSY is able to relay magnetisation between spins, A-B-C-D.., and can therefore show correlations amongst spins that are not directly coupled (eg A-C and A-D) but exist within the same spin system. defprov: Daniel Schober synonym:2D_TOCSY two_dimensional_total_correlation_spectroscopy quality_check_peak_feature def: A feature of a peak that is measured to assess the quality of a data set. def: One dimensional (referring to a FID, pre-processed spectrum, or post-processed spectrum). synonym: 1D one_dimensional def: A reference is a label which refers to data elsewhere, as opposed to containing the data itself. Accessing the value that a reference refers to is called dereferencing it. References are fundamental in constructing many data structures and in exchanging information between different parts of programs and databases. reference 15N def: A data set that was generated within, from or for an NMR experiment. synonym: NMR data set NMR_data_set tempdef: The process of configuring an NMR instrument for 1D NMR analysis. defprov: Daniel Schober synonym: 1D NMR configuration one_dimensional_NMR_configuration TODO: Definition depends on sprcls. def: The exponential function used to multiply a FID by to produce a desitred amount of line broadening. exponential_multiplication CAT acquisition_parameter_set_file_reference def: A reference to the file of acquisition parameters produced by a machine. two_dimensional_NMR_configuration tempdef: The process of configuring an NMR instrument for 2D NMR analysis. defprov: Daniel Schober synonym: 2D NMR configuration TODO: depends on superclass view. number_of_data_points tempdef: The number of data points in a data set. TODO: Def not aristotelian. defneed flow_probe TODO: Belongs in Ref Ontol. defneed vendor tempdef: A chemical compound is a small object which reacts chemically and is usually a molecule or composed out of molecules. defprov: Daniel Schober TODO: May be imported from other Ontology. chemical_compound def: A reference to a file containing the raw FID. synonym: FID_file_reference free_induction_decay_file_reference def: A post-processed NMR spectrum in which the y-values of the datapoints have been summed based on periodic ranges of the x-axis values. bucketed_spectrum TODO: has spectral post processing parameter def: The ratio of the mass or volume of a solute to the mass or volume of the solution or solvent. concentration projection_method A method of spectral projection. tempdef:GFT NMR allows for rapid multidimensional FT NMR spectral information gathering, avoiding sampling limitations without compromising on the precision of chemicalshift. defprov: ttp://www.nsm.buffalo.edu/Research/GFT/szyperski_publications_1st_page/Szyperski%2067.pdf synonym: GFT-projection G_matrix_fourier_transform_projection tempdef: A jump and return 1-1 pulse sequence method is a jump and return method that uses one 90 degree pulse and one 90 degree return puls to make fast exchanging protons visible, first described by Plateau,P. and Gueron,M. (1982) J. Am. Chem. Soc., 104, 7310–7311. Compared to the 1-3-3-1 method it has a lower receiver gain and the dispersive tail of water interferes with the signals of interest. jump_and_return_1-1 NMR_cryo_probe defneed def: The parts-per-million value of the peak used to reference a spectrum. calibration_reference_shift High_resolution_probe def:BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features. defprov: Bruker website synonym: HR Probe def: Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes. defprov: Bruker website synonym: flow_HR-probe flow_high_resolution_probe UNITY relaxation_delay def: The delay between repeat scans to allow nuclei to relax back to their steady state. 1mm_MicroProbe def: Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include: up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount) excellent solvent suppression properties virtually no salt effect discrete samples in tubes that can be sealed and stored automation accessory for sample preparation and handling available defprov: Bruker website VXR TODO:Exclusion guided definition. tempdef: A non FT based method for converting from the time to the frequency domain. non-fourier_transformation solid_magic_angle_spinning_probe def: Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei. defprov: Bruker website synonym: solid_MAS_probe defneed TODO: May not need definition due to its instance character. Bruker tempdef:A jump and return 1-3-3-1 pulse sequence method is a jump and return method that uses a 1-3-3-1 pulse sequence to make fast exchanging protons visible. Compared to the 1-1 method it has better water suppression (higher receiver gain) capabilities, but with offset-dependent phase distortion (unsuitable for 2D). jump_and_return_1-3-3-1 window_function_method def: A function applied to a FID to increase the signal-to-noise ratio or the resolution. maximum_intensity_projection defneed def: A frequency used during Hadamard encoding. hadamard_frequency tempdef: In one dimensional NMR, as the multiplets from different chemically shifted nuclei overlap, spectral assignments become too difficult. In order to resolve the chemical shift and spin-spin coupling parameters along the different axis, 2D and 3D J-resolved NMR spectroscopies are used. defprov: Daniel Schober synonym: 2D J-resolved two_dimensional_J-resolved NMR_instrument_acquisition_parameter_set def: The list of parameters that describe the instrument settings used for the acquisition of a spectrum. altdef: The set of variables dependent on a given pulse sequence that will be optimised in order to acquire a spectrum. synonym: NMR instrument acquisition parameter set def: The units of measure for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum. altdef: The units used to represent either time domain (for a FID) or the frequency domain (for a spectrum). x-axis_unit autosampler def: An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. altdef: The autosampler is an automatic sample changer. def: The temperature of an item of analysis material whilst in an autosampler. sample_temperature_in_autosampler defneed Bruker_NMR_magnet altspcls: process ??? method defneed UltraShield_Plus AMIX_VIEWER_&_AMIX-TOOLS def: The ATM option for AVANCE spectrometers is available for: Double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90° pulsewidths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems. defprov: Bruker website synonym: High Resolution Probes with Automatic Tuning and Matching HR_Probes_with_ATM def: The process of ensuring the quality of the raw data that results from an NMR analysis. synonym: NMR quality check NMR_quality_check sample tempdef: A sample is a role that is played by an object of interest in an investigation used to obtain generalizable information about the sample source. defprov: Daniel Schober NMR_plattform TODO: What is the differrence to NMR instrument? defneed NMR_parameter_set defneed def: The number of repeat scans performed and summed to create the data set for an NMR sample. number_of_scans def: A software artifact used during data pre-processing. data_pre-processing_software NMR_sample def: A sample that has been prepared for chemical analysis by NMR. NMR samples are usually liquid solutions contained in glass tubes. NMR solution sample volume ranges from 50ul to 5ml depending on the NMR probe. Sample concentrations of solute for 1H NMR are usually in the range of 100ug to 5g, with 10 to 50mg being typical. NMR is not a chemical trace analysis technique. The NMR signal of solids and gases can be recorded but to measure solid-state NMR additional specialized hardware is required. synonym: NMR sample NMR_vendor defneed Capillary_LC-NMR def: .A projection method that sums the intensities of a pre-processed 2D J-resolved NMR spectrum to obtain a projected spectrum. altdef: The adding of spectra together to produce a composite avergaed spectrum. summation_projection def: The number of scans whose data is not summed to create the data set for an NMR sample, but that are carried out to establish the steady-state of relaxation for the nuclei. number_of_steady_state_scans ??? How to model "hoch 2"? US_2 _deleted_classes environment