nuclear magnetic resonance CV
type: Ontology
imports: bfo.owl
rights: Creative Commons Public Domain Mark 1.0
maintainer: http://www.metabolomics-msi.org/ http://phenomenal-h2020.eu/home/ http://www.cosmos-fp7.eu/WP2
documenter: Daniel Schober
bug-database: https://github.com/nmrML/nmrML/issues
audience: This CV is to be used by metabolomics researchers, or basically any chenomics or proteomics researchers who apply the nmrML xml to store their NMRraw data in a vendor agnostic manner. But nmrML can also be used to capture experimental results and (limited) basic metadata like molecule to spectral feature assignments.
definition: This artefact is an MSI-approved controlled vocabulary primarily developed under COSMOS EU and PhenoMeNal EU governance. The nmrCV is supporting the nmrML XML format with standardized terms. nmrML is a vendor agnostic open access NMR raw data standard. Its primaly role is analogous to the mzCV for the PSI-approved mzML XML format. It uses BFO2.0 as its Top level. This CV was derived from two predecessors (The NMR CV from the David Wishart Group, developed by Joseph Cruz) and the MSI nmr CV developed by Daniel Schober at the EBI. This simple taxonomy of terms (no DL semantics used) serves the nuclear magnetic resonance markup language (nmrML) with meaningful descriptors to amend the nmrML xml file with CV terms. Metabolomics scientists are encouraged to use this CV to annotrate their raw and experimental context data, i.e. within nmrML. The approach to have an exchange syntax mixed of an xsd and CV stems from the PSI mzML effort. The reason to branch out from an xsd into a CV is, that in areas where the terminology is likely to change faster than the nmrML xsd could be updated and aligned, an externally and decentrallised maintained CV can accompensate for such dynamics in a more flexible way. A second reason for this set-up is that semantic validity of CV terms used in an nmrML XML instance (allowed CV terms, position/relation to each other, cardinality) can be validated by rule-based proprietary validators: By means of cardinality specifications and XPath expressions defined in an XML mapping file (an instances of the CvMappingRules.xsd ), one can define what ontology terms are allowed in a specific location of the data model.
version info: 1.1.0
location: https://github.com/nmrML/nmrML/tree/master/ontologies
deprecated: http://www.metabolomicscentre.ca/nmrML/msi-nmr.obo
contributor: Catherine Deborde
coverage: Nuclear magnetic resonance (NMR) data annotation as required by the msi sanctioned open access nmrML XML format developed by the COSMOS EU project.
mailing-list: https://groups.google.com/forum/#!forum/nmrml/join
contributor: Daniel Jacob
has_obo_format_version: 1.2
creation date: 2017-10-19T10:11:26Z
contributor: Reza Salek
contributor: Michael Wilson
IAO_0000232: In case we like to be able to convert this owl CV back into the obo format, we should only use DL/owl constructs that are supported by obo. Hence, editors of this CV should take care not to use any higher descriptrion logics semantics, i.e. cardinality restrictions or defined terms using constructors. We should start to build the taxonomic backbone first and later connect the main axis via relations. If we want to use restrictions, we should only use existential quantifiers as the OBO format does not support universal quantification. List of terms required by current XSD (August 2013): these were bookmarked in CV (annotation property) and are visible in the new nmrTab: CVTerm occurrences: buffer-->buffer solvent-->solvent concentration standard type-->calibration compound , what is chemical shift reference ? What calibration_reference_shift under calibration compound ? concentration standard name we here see a use-mention problem arising for the CV. The xsd should probably change here to avoid this. encoding method (Quadrature detection method) is this the same as encoding method ? sample container-->NMR_sample_holder (spectrum) y axis type-->coordinate system descriptor post acquisition solvent suppression method Two usages in xsd, but with differrent type ? -->solvent suppression method calibration compound Two usages in xsd, but with differrent type ?-->calibration compound data transformation method-->data transformation method (spectral) projection method-->projection method spectral denoising method-->spectral denoising method window function method-->window function method baseline correction method-->baseline correction sample type-->NMR sample CVParam occurrences: file content-->data file content software type-->software source file type-->data file attribute (needs refactoring) instrument configuration type-->instrument configuration processing method type-->data processing method CVParamType occurrences: chemical shift standard-->chemical shift standard s…
auto-generated-by: OBO-Edit 2.2
comment: This version (1.1.0) uses the Basic Formal Ontology (BFO) as its top level ontology. We might at some point close the resulting semantic gap by using OBI and IAO as intermediate bridges.
saved-by: dschober
contributor: Joseph Cruz
format: OWL MIME type application/rdf+xml (Rather flat CV in OWL syntax. Taxonomic backbone with few relations used. No OWL DL complexity such as cardinalities, blank nodes, nested class definitions. The Semantic Validator used an OBO converted file format due to historic reasons. The OBO file is auto-generated-by the OWL API (version 3.4.2).)
contributor: Philippe Rocca-Serra
IAO_0000112: http://nmrml.org/examples/
created by: Daniel Schober
contributor: Steffen Neumann
default language: en
contributor: Daniel Schober
contributor: Since this is a prolonged effort spanning a larger time period, there naturally were many people involved in the creation over the years and during different times. People involved in the term creation from ID >1400000 : This part of the NMR ontology was originally developed by the ontology working group (http://msi-ontology.sourceforge.net/) of the msi-metabolomicssociety (msi-workgroups.sf.net): Daniel Schober (EBI) Chris Taylor (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) Philippe Rocca-Serra (EBI and MGED Society) Susanna-Assunta Sansone (EBI) People involved in the term creation from ID<1400000: Joseph Cruz Daniel Schober Michael Wilson Reza Salek Daniel Jacob David Wishart Terms with IDs ID<1400000 that were NOT asserted in the original Wishart obo file were created by Daniel Schober (COSMOS WP2). Its IDs were autogenerated with the Protege ID generator. Other people that substantially helped in revising the latest and Cosmos governed CV additions were: Michael Wilson, Wishart Group, Edmonton, Alberta, Canada Daniel Jacob, INRA, Bordeaux, France Annick Moing, INRA, Bordeaux, France Catherine Deborde, INRA, Bordeaux, France Reza Salek, EBI, Hinxton, UK Philippe Rocca-Serra, University of Oxford, Oxford, UK Andrea Porzel, IPB-Halle, Germany and the COSMOS WP2 team A paper describing the overall nmrML data standard and CV has been accepted by Analytical Chemistry (Manuscript ID: ac-2017-02795f.R1), title `nmrML: a community supported open data standard for the description, storage, and exchange of NMR data`, author(s): Schober, Daniel; Jacob, Daniel; Wilson, Michael; Cruz, Joseph; Marcu, Ana; Grant, Jason; Moing, Annick; Deborde, Catherine; de Figueiredo, Luis; Haug, Kenneth; Rocca-Serra, Philippe; Easton, John; Ebbels, Timothy; Hao, Jie; Ludwig, Christian; Günther, Ulrich; Rosato, A…
implements: https://github.com/nmrML/nmrML
contributor: Annick Moing
version IRI: nmrCV.owl

definition
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_obo_format_version
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

entity
type: Class

process
type: Class
subclass of: entity

realizable entity
type: Class
subclass of: entity

quality
type: Class
subclass of: entity

object
type: Class
subclass of: entity

generically dependent continuant
type: Class
subclass of: entity

integer32
type: Class
subclass of: byte format
coverage: For 1r/1i spectra and for Bruker, this term describe an array of integers (32bits).

sample number
type: Class
subclass of: sample attribute
definition: A reference number relevant to the sample under study.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000001

Axiom
annotated source: sample number
annotated property: definition
annotated target: A reference number relevant to the sample under study.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: sample number
annotated property: database_cross_reference
annotated target: value-type:xsd:string

long64
type: Class
subclass of: byte format
coverage: For 1r/1i spectra and for Bruker, this term describe an array of longs (64bits).

sample state information
type: Class
subclass of: sample attribute
definition: The chemical phase of a pure sample, or the state of a mixed sample.
has_obo_namespace: NMR
id: NMR:1000003

Axiom
annotated source: sample state information
annotated property: definition
annotated target: The chemical phase of a pure sample, or the state of a mixed sample.
database_cross_reference: MSI:NMR

sample mass information
type: Class
subclass of: sample attribute
definition: Total mass of sample used.
database_cross_reference: value-type:xsd:float
has_obo_namespace: NMR
id: NMR:1000004

Axiom
annotated source: sample mass information
annotated property: definition
annotated target: Total mass of sample used.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: sample mass information
annotated property: database_cross_reference
annotated target: value-type:xsd:float

sample volume
type: Class
subclass of: sample attribute
definition: Total volume of solution used.
database_cross_reference: value-type:xsd:float
has_obo_namespace: NMR
id: NMR:1000005

Axiom
annotated source: sample volume
annotated property: definition
annotated target: Total volume of solution used.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: sample volume
annotated property: database_cross_reference
annotated target: value-type:xsd:float

sample concentration
type: Class
subclass of: sample attribute
definition: Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used.
database_cross_reference: value-type:xsd:float
has_obo_namespace: NMR
id: NMR:1000006

Axiom
annotated source: sample concentration
annotated property: definition
annotated target: Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: sample concentration
annotated property: database_cross_reference
annotated target: value-type:xsd:float

quadrature detection
type: Class
subclass of: NMR data processing
comment: One of the problems that should be apparent after observing the spectrum and the FID is that it is not possible to determine if the frequency is positive or negative. The instrument uses a spectrometer frequency and all signal frequencies are measured relative to the spectrometer frequency. If a molecule produces two signals, one at 300,000,001 Hz and another at 299,999,999 Hz, and the spectrometer frequency is 300,000,000 Hz, the first signal is at +1 Hz and the second is at -1 Hz. Electronically the lower frequency signals are very easy frequency to detect, transmit, amplify and sample. The complication with this rotating frame of reference is that a single detector can not distinguish positive and negative frequencies. This problem is why quadrature detection is important. Quadrature detection uses two detector channels separated by 90 degrees. These are referred to as the real channel and the imaginary channel. Using these two channels, it is possible to distinguish positive and negative frequencies. This section shows how the quadrature signal is processed to obtain an NMR spectrum. The Fourier transform produces a complex number with a real and an imaginary component. The Re function extracts the real spectrum and the Im function extracts the imaginary spectrum from the complex number.

contact role
type: Class
subclass of: contact attribute

data file attribute
type: Class
subclass of: generically dependent continuant

NMR instrument type
type: Class
subclass of: instrument attribute

1D spectrum coordinate system descriptor
type: Class
subclass of: NMR spectrum descriptor

pre-acquisition solvent suppression
type: Class
subclass of: data transformation

peak processing
type: Class
subclass of: frequency domain data processing

Hexafluorobenzene
type: Class
subclass of: concentration standard
subclass of: NMR solvent

Chloroform-d
type: Class
subclass of: NMR solvent
has_exact_synonym: CDCl3

heavy water
type: Class
subclass of: NMR solvent
consider: CHEBI:41981
has_exact_synonym: D2O

sample pH
type: Class
subclass of: pH

post buffer pH
type: Class
subclass of: pH

apodization
type: Class
subclass of: time domain data processing
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: http://www.scs.illinois.edu/nmr/handouts/general_pdf/ugi034.pdf
definition: Apodization is an umbrella term that is used to refer to signal processing covering the manipulation of the FID to either increase signal-to-noise (S/N) or resolution. it is usually possible to gain either S/N or resolution, but not both. Apodization is usually performed by applying a window function to the FID

metabolomics database identifier
type: Class
subclass of: external reference identifier
source: http://www.metabolomicssociety.org/databases
comment: PRS: rename 'reference' to 'identifier'

Metabolights identifier
type: Class
subclass of: metabolomics database identifier

acetonitrile
type: Class
subclass of: 1H spectrum reference compound

1,4-Dioxane
type: Class
subclass of: 1H spectrum reference compound
subclass of: 13C spectrum reference compound

1H spectrum reference compound
type: Class
subclass of: chemical shift standard

2,2-Dimethyl-2-silapentane-5-sulfonate
type: Class
subclass of: 1H spectrum reference compound
has_exact_synonym: DSS

sodium acetate
type: Class
subclass of: 1H spectrum reference compound

tetramethylsilane
type: Class
subclass of: 1H spectrum reference compound
subclass of: 13C spectrum reference compound
has_exact_synonym: TMS

13C spectrum reference compound
type: Class
subclass of: chemical shift standard

NMR instrument model
type: Class
subclass of: instrument attribute
definition: Instrument model name not including the vendor's name.
has_obo_namespace: NMR
id: NMR:1000031

Axiom
annotated source: NMR instrument model
annotated property: definition
annotated target: Instrument model name not including the vendor's name.
database_cross_reference: MSI:NMR

instrument customization
type: Class
subclass of: instrument attribute
definition: Free text description of a single customization made to the instrument; for several modifications, use several entries.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000032

Axiom
annotated source: instrument customization
annotated property: definition
annotated target: Free text description of a single customization made to the instrument; for several modifications, use several entries.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: instrument customization
annotated property: database_cross_reference
annotated target: value-type:xsd:string

Chloroform-d1
type: Class
subclass of: 13C spectrum reference compound
subclass of: 2H spectrum reference compound

keyword
type: Class
subclass of: reference

tetramethylammonium bromide
type: Class
subclass of: 13C spectrum reference compound
subclass of: 15N spectrum reference compound

15N spectrum reference compound
type: Class
subclass of: chemical shift standard

ammonia (liquid)
type: Class
subclass of: 15N spectrum reference compound

ammonium bromide
type: Class
subclass of: 15N spectrum reference compound

1,4-morpholine
type: Class
subclass of: 15N spectrum reference compound

nitromethane
type: Class
subclass of: 15N spectrum reference compound

pyridine
type: Class
subclass of: 15N spectrum reference compound

sodium nitrate
type: Class
subclass of: 15N spectrum reference compound

post-acquisition solvent suppression
type: Class
subclass of: spectral denoising
has_exact_synonym: solvent filtering

decoupling method
type: Class
subclass of: NMR acquisition parameter
definition: Nuclear magnetic resonance decoupling (NMR decoupling for short) is a special method used in nuclear magnetic resonance (NMR) spectroscopy where a sample to be analyzed is irradiated at a certain frequency or frequency range to eliminate fully or partially the effect of coupling between certain nuclei. NMR coupling refers to the effect of nuclei on each other in atoms within a couple of bonds distance of each other in molecules. This effect causes NMR signals in a spectrum to be split into multiple peaks which are up to several hertz frequency from each other. Decoupling fully or partially eliminates splitting of the signal between the nuclei irradiated and other nuclei such as the nuclei being analyzed in a certain spectrum. NMR spectroscopy and sometimes decoupling can help determine structures of chemical compounds.
source: http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_decoupling

homonuclear decoupling
type: Class
subclass of: decoupling method

heteronuclear decoupling
type: Class
subclass of: decoupling method

emulsion
type: Class
subclass of: liquid
definition: State if the sample is in emulsion form.
has_obo_namespace: NMR
id: NMR:1000047

Axiom
annotated source: emulsion
annotated property: definition
annotated target: State if the sample is in emulsion form.
database_cross_reference: MSI:NMR

gas
type: Class
subclass of: sample state information
definition: State if the sample is in gaseous form.
has_obo_namespace: NMR
id: NMR:1000048

Axiom
annotated source: gas
annotated property: definition
annotated target: State if the sample is in gaseous form.
database_cross_reference: MSI:NMR

liquid
type: Class
subclass of: sample state information
definition: State if the sample is in liquid form.
has_obo_namespace: NMR
id: NMR:1000049

Axiom
annotated source: liquid
annotated property: definition
annotated target: State if the sample is in liquid form.
database_cross_reference: MSI:NMR

solid
type: Class
subclass of: sample state information
definition: State if the sample is in solid form.
has_obo_namespace: NMR
id: NMR:1000050

Axiom
annotated source: solid
annotated property: definition
annotated target: State if the sample is in solid form.
database_cross_reference: MSI:NMR

solution
type: Class
subclass of: liquid
definition: State if the sample is in solution form.
has_obo_namespace: NMR
id: NMR:1000051

Axiom
annotated source: solution
annotated property: definition
annotated target: State if the sample is in solution form.
database_cross_reference: MSI:NMR

suspension
type: Class
subclass of: liquid
definition: State if the sample is in suspension form.
has_obo_namespace: NMR
id: NMR:1000052

Axiom
annotated source: suspension
annotated property: definition
annotated target: State if the sample is in suspension form.
database_cross_reference: MSI:NMR

sample batch information
type: Class
subclass of: sample attribute
definition: Sample batch lot identifier.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000053

Axiom
annotated source: sample batch information
annotated property: definition
annotated target: Sample batch lot identifier.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: sample batch information
annotated property: database_cross_reference
annotated target: value-type:xsd:string

broad band decoupling
type: Class
subclass of: decoupling method

off resonance decoupling
type: Class
subclass of: decoupling method

specific decoupling
type: Class
subclass of: decoupling method
has_exact_synonym: band-selective decoupling
has_exact_synonym: narowband decoupling

angle of sinusoid
type: Class
subclass of: window function parameter

31P spectrum reference compound
type: Class
subclass of: chemical shift standard

phosphoric acid
type: Class
subclass of: 31P spectrum reference compound
has_exact_synonym: H3PO4

phosphorus
type: Class
subclass of: 31P spectrum reference compound
has_exact_synonym: P4

trimethyl phosphate
type: Class
subclass of: 31P spectrum reference compound
has_exact_synonym: (CH3O)3PO

triphenylphosphine
type: Class
subclass of: 31P spectrum reference compound
has_exact_synonym: P(C6H5)3

triphenylphosphine oxide
type: Class
subclass of: 31P spectrum reference compound
has_exact_synonym: O=P(C6H5)3

co-dissolved internal reference
type: Class
subclass of: chemical shift reference

synthetic reference signal
type: Class
subclass of: chemical shift reference

residual solvent signal
type: Class
subclass of: chemical shift reference

FID zero filling
type: Class
subclass of: time domain data processing

data extrapolation using linear prediction
type: Class
subclass of: FID zero filling

multiplying FID by window function
type: Class
subclass of: time domain data processing

FID fourier transformation
type: Class
subclass of: time domain data processing
definition: The mathematical conversion of time-resolved FID raw data into frequency resolved NMR spectra (frequency-resolved NMR data) by means of fourier transformation of coordinate systems.

phase correction
type: Class
subclass of: frequency domain data processing
has_exact_synonym: phasing
has_exact_synonym: spectral phasing

peak integration
type: Class
subclass of: peak processing

peak alignment
type: Class
subclass of: peak processing

peak shape fitting
type: Class
subclass of: peak fitting

spectral referencing
type: Class
subclass of: frequency domain data processing

sodium trimethylsilyl-propionate
type: Class
subclass of: 13C spectrum reference compound
source: Pohl, L.; Eckle, M. (1969). "Sodium 3-(trimethylsilyl)tetradeuteriopropionate, a new water-soluble standard for 1H.N.M.R.". Angewandte Chemie, International Edition in English 8 (5): 381. doi:10.1002/anie.196903811
has_exact_synonym: TMSP
has_exact_synonym: trimethylsilyl propanoic acid

linear scaling
type: Class
subclass of: scaling
comment: used to be 'linear scaling algorithm'

scaling
type: Class
subclass of: frequency domain data processing
comment: used to be called 'scaling algorithm'

non-linear scaling
type: Class
subclass of: scaling
comment: used to be postfixed with algorithm

total spectral area scaling
type: Class
subclass of: linear scaling

probabilistic quotient normalization
type: Class
subclass of: linear scaling
source: Dieterle F, Ross A, Schlotterbeck G, Senn H: Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomics. Anal Chem 2006, 78(13):4281-90.

scaling by generalized logarithmic transformation
type: Class
subclass of: non-linear scaling
has_exact_synonym: glog scaling

pareto scaling
type: Class
subclass of: non-linear scaling

autoscaling
type: Class
subclass of: non-linear scaling

2D J-resolved spectrum
type: Class
subclass of: NMR spectrum
subclass of: 2D spectrum
has_exact_synonym: JRES spectrum

MetaboLab software
type: Class
subclass of: open source NMR software
source: http://www.biomedcentral.com/1471-2105/12/366#B2

Metaboquant software
type: Class
subclass of: open source NMR software

rNMR software
type: Class
subclass of: open source NMR software

open source NMR software
type: Class
subclass of: NMR software

commercial NMR software
type: Class
subclass of: NMR software

NMRLab software
type: Class
subclass of: open source NMR software
source: Günther U, Ludwig C, Rüterjans H: NMRLAB - advanced NMR data processing in Matlab., J Magn Reson 2000, 145(2):201-208.

NMRPipe software
type: Class
subclass of: open source NMR software
source: Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A: NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 1995, 6(3):277-293.

matNMR software
type: Class
subclass of: open source NMR software
source: van Beek JD: matNMR: a flexible toolbox for processing, analyzing and visualizing magnetic resonance data in Matlab. J Magn Reson 2007, 187:19-26.

concentration of chemical compound
type: Class
subclass of: chemical compound attribute

manual phase correction
type: Class
subclass of: phase correction

automatic phase correction
type: Class
subclass of: phase correction

DC offset correction
type: Class
subclass of: phase correction

Gibbs multiplication
type: Class
subclass of: frequency domain data processing
source: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-366

skyline projection
type: Class
subclass of: spectral projection

shifted sine window function
type: Class
subclass of: sine window function
has_exact_synonym: shifted sine apodization

sinc window multiplication of FID (1D)
type: Class
subclass of: window function for apodization
has_exact_synonym: SINC
has_exact_synonym: Sinc window multiplication

SEM window function
type: Class
subclass of: window function for apodization
source: http://www.sciencedirect.com/science/article/pii/S0003267008000950
bug-database: https://github.com/nmrML/nmrML/issues/36
has_exact_synonym: combined sine-bell–exponential window function

trapezoid window function
type: Class
subclass of: window function for apodization
has_exact_synonym: TRAP
has_exact_synonym: trapezoid apodization
comment: Functional form ( 0:t1 linear increase from 0.0 to 1.0, t1:size-t2 1.0 -t2: linear decrease from 1.0 to 0.0 / Parameters ( * data Array of spectral data., * t1 Left ramp length., * t2 Right ramp length., * inv Set True for inverse apodization.

shifted gaussian window function
type: Class
subclass of: Gaussian window function

baseline correction using spline function
type: Class
subclass of: baseline correction

heteronuclear single quantum coherence spectrum
type: Class
subclass of: 2D spectrum
has_exact_synonym: HSQC NMR spectrum

Zangger-Sterk pulse sequence
type: Class
subclass of: NMR pulse sequence

pure shift 1D Zangger-Sterk pulse sequence
type: Class
subclass of: Zangger-Sterk pulse sequence
source: http://nmr.chemistry.manchester.ac.uk/

oneshot pulse sequence
type: Class
subclass of: NMR pulse sequence
source: http://nmr.chemistry.manchester.ac.uk/

pure shift oneshot pulse sequence
type: Class
subclass of: oneshot pulse sequence
source: http://nmr.chemistry.manchester.ac.uk/

perfect echo watergate pulse sequence
type: Class
subclass of: NMR pulse sequence
source: http://nmr.chemistry.manchester.ac.uk/
has_exact_synonym: PE Watergate pulse sequence

NMR Star 3.1 file format
type: Class
subclass of: NMR software data format

NMR Star 2.1 file format
type: Class
subclass of: NMR software data format

3D spectrum
type: Class
subclass of: NMR spectrum by dimensionality
has_exact_synonym: three dimensional spectrum

4D spectrum
type: Class
subclass of: NMR spectrum by dimensionality
has_exact_synonym: four dimensional spectrum

NMR spectrum by dimensionality
type: Class
subclass of: NMR spectrum

homonuclear chemical shift spectrum
type: Class
subclass of: NMR spectrum

heteronuclear chemical shift spectrum
type: Class
subclass of: NMR spectrum

Bruker instrument model
type: Class
subclass of: NMR instrument model
definition: Bruker instrument model.
has_obo_namespace: NMR
id: NMR:1000122

Axiom
annotated source: Bruker instrument model
annotated property: definition
annotated target: Bruker instrument model.
database_cross_reference: MSI:NMR

homonuclear exchange spectroscopy spectrum
type: Class
subclass of: NMR spectrum

heteronuclear exchange spectroscopy spectrum
type: Class
subclass of: NMR spectrum

homonuclear J-resolved spectrum
type: Class
subclass of: 2D J-resolved spectrum

heteronuclear J-resolved spectrum
type: Class
subclass of: 2D J-resolved spectrum

calibration test spectrum
type: Class
subclass of: NMR spectrum by processing step

NMR star software
type: Class
subclass of: open source NMR software

Felix software
type: Class
subclass of: commercial NMR software
source: http://www.felixnmr.com/

PIPP software
type: Class
subclass of: NMR software

TALOS+ software
type: Class
subclass of: NMR software

CYANA software
type: Class
subclass of: open source NMR software
source: http://www.cyana.org/wiki/index.php/Main_Page

XPLOR-NIH software
type: Class
subclass of: NMR software
source: http://nmr.cit.nih.gov/xplor-nih/

computed concentration
type: Class
subclass of: concentration of chemical compound
editorial note: request these in UO ?

XEASY software
type: Class
subclass of: open source NMR software
source: http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/XEASY

sparky software
type: Class
subclass of: open source NMR software

CARA software
type: Class
subclass of: open source NMR software
source: http://nmr-software.blogspot.de/2007/04/cara.html

Wattos software
type: Class
subclass of: open source NMR software

MADNMR software
type: Class
subclass of: NMR software

Pronto software
type: Class
subclass of: NMR software

TRIAD NMR software
type: Class
subclass of: NMR software

library based computed concentration
type: Class
subclass of: computed concentration

Lorenzian estimated concentration
type: Class
subclass of: computed concentration
has_exact_synonym: Lorenzian (-Integration) (Modeled Area) Estimated Concentration
comment: https://docs.google.com/spreadsheets/d/1egsLQWoQuCxAYPr9MIo-F0A5K9RCbJSC8yWZyYq_fiQ/edit

measured area based concentration
type: Class
subclass of: computed concentration
has_exact_synonym: Measured Area (Integration) based Concentration

time-domain amplitude computed concentration
type: Class
subclass of: computed concentration

group time delay compensation
type: Class
subclass of: time domain data processing
definition: This is independent of the bruker acquisition parameter named "GRPDLY" (Group Delay), but this is a "shift" applied on the fid to calibrate its zero

scaling by forward linear prediction
type: Class
subclass of: data extrapolation using linear prediction

back calculation of first points by linear-prediction
type: Class
subclass of: data extrapolation using linear prediction

scaling by mirror image linear prediction
type: Class
subclass of: data extrapolation using linear prediction

digital filtering
type: Class
subclass of: NMR acquisition parameter

3D strip plot generation
type: Class
subclass of: plot and graph generation
IAO_0000119: Daniel Schober
source: http://jjhelmus.github.io/nmrglue/current/jbnmr_examples/s11_strip_plots.html
definition: A spectrum vizualization method for 3D nmr spectra, assisting assignments for large sequential molecules, i.e. Proteins. The first two axis in the plot represent the ppms along the two acquisition nuclei, and a third dimension captures the sequential molecule order for the third nucleus.

Batman software
type: Class
subclass of: open source NMR software

JEOL instrument model
type: Class
subclass of: NMR instrument model

tecmag instrument model
type: Class
subclass of: NMR instrument model

automatic baseline recognition
type: Class
subclass of: baseline correction
source: Bao et al. (2013) A new automatic baseline correction method based on iterative method, J. Magn. Res. 218:35-43
source: Golotvin & Williams (2000), Improved baseline recognition and modeling of FT NMR spectra, J. Magn. Res. 146:122-125

Trimethylsilyl propionate
type: Class
subclass of: 1H spectrum reference compound
has_exact_synonym: TSP

TMIC lab pulse sequence
type: Class
subclass of: NMR pulse sequence
has_exact_synonym: pulse sequence from Wishart lab library

probe gradient strength
type: Class
subclass of: field strength

NMR acquisition computer operating system
type: Class
subclass of: NMR software
coverage: e.g. Linux or Windows, ...

NMR autosampler software
type: Class
subclass of: NMR software
coverage: e.g. Bruker Biospin ICON-NMR

Bruker Biospin ICON-NMR software
type: Class
subclass of: NMR autosampler software

buffer pH
type: Class
subclass of: pH

field frequency lock
type: Class
subclass of: sample attribute
coverage: e.g. heavy water (D2O)
has_exact_synonym: lock frequency

concentration standard
type: Class
subclass of: calibration compound
has_exact_synonym: quantitation standard

NMR acquisition software
type: Class
subclass of: NMR software

CIMR MI standard
type: Class
subclass of: minimum information standard

signal line width check
type: Class
subclass of: NMR quality check

signal line width at five percent intensity check
type: Class
subclass of: signal line width check

NMR spectrum descriptor
type: Class
subclass of: generically dependent continuant

pulse width
type: Class
subclass of: pulse parameter

hard pulse width
type: Class
subclass of: pulse width

sweep width
type: Class
subclass of: NMR acquisition parameter
has_exact_synonym: spectrum width

number of data points
type: Class
subclass of: 1D spectrum coordinate system descriptor
has_exact_synonym: number of data points in spectrum
has_exact_synonym: number of first dimension data points

x end value
type: Class
subclass of: 1D spectrum coordinate system descriptor
definition: 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.

y-axis type
type: Class
subclass of: 1D spectrum coordinate system descriptor

center of bin on x-axis
type: Class
subclass of: binned spectrum descriptor
has_exact_synonym: bucket x center

spectral quantitation algorithm
type: Class
subclass of: binned spectrum descriptor
has_exact_synonym: NMR spectrum quantification method

NMRProcFlow software
type: Class
subclass of: open source NMR software
definition: The NMRProcFlow open source software provides a complete set of tools for processing (e.g. Bucketing) and visualization of 1D NMR data, the whole within an interactive interface based on a spectra visualization.

Bayesil software
type: Class
subclass of: open source NMR software
definition: Bayesil is a web system that automatically identifies and quantifies metabolites using 1D 1H NMR spectra of ultra-filtered plasma, serum or cerebrospinal fluid. The NMR spectra must be collected in a standardized fashion for Bayesil to perform optimally. Bayesil first performs all spectral processing steps, including Fourier transformation, phasing, solvent filtering, chemical shift referencing, baseline correction and reference line shape convolution automatically. It then deconvolutes the resulting NMR spectrum using a reference spectral library, which here contains the signatures of more than 60 metabolites. This deconvolution process determines both the identity and quantity of the compounds in the biofluid mixture.
source: Ravanbakhsh S, Liu P, Bjorndahl TC, Mandal R, Grant JR, Wilson M, Eisner R, Sinelnikov I, Hu X, Luchinat C, Greiner R, Wishart DS. (2015) Accurate, Fully-Automated NMR Spectral Profiling for Metabolomics. PLoS ONE 10(5): e0124219.

nmrML Assign
type: Class
subclass of: Bayesil software
definition: nmrML-Assign is a web server for creating an nmrML file from a FID and a structure. The FID is first automatically processed with Bayesil. The resulting interactive spectrum allows assigning peaks to specific atoms in the structure and the assignments are saved in the nmrML format. For more information about nmrML please visit nmrML.org. nmrML-Assign works with 1H and 13C NMR spectra in Bruker or Agilent/Varian format.
comment: Uses JspectraView Software

doublet feature
type: Class
subclass of: multiplicity feature
has_exact_synonym: d

triplet feature
type: Class
subclass of: multiplicity feature
has_exact_synonym: t

quatruplet feature
type: Class
subclass of: multiplicity feature
has_exact_synonym: q

cluster of peaks across samples
type: Class
subclass of: data file content
definition: a set of peaks that are highly correlated in a series of samples
coverage: a feature request by Daniel Jacob inserted at IBP hackathon

simulated spectrum
type: Class
subclass of: NMR spectrum by processing step

pulse parameter
type: Class
subclass of: parameter

JEOL FID format
type: Class
subclass of: FID format

doublet of doublets feature
type: Class
subclass of: multiplicity feature
has_exact_synonym: dd

ABX multiplet pattern
type: Class
subclass of: multiplet feature
definition: AMX, ABX and ABC patterns, and various related spin systems are very common in Proton NMR of organic molecules.When two of the protons of an AMX pattern approach each other to form an ABX pattern, the characteristic changes in intensities of a strongly coupled system (leaning) are seen, and, as the size of J approaches the value of νAB more complicated changes arise, so that the pattern can no longer be analyzed correctly by first order methods.

singlet feature
type: Class
subclass of: multiplicity feature
has_exact_synonym: s

quintet feature
type: Class
subclass of: multiplicity feature
has_exact_synonym: qi

doublet of triplets
type: Class
subclass of: multiplicity feature
has_exact_synonym: dt

triplet of douplets
type: Class
subclass of: multiplicity feature
has_exact_synonym: td

triplet of triplets
type: Class
subclass of: multiplicity feature
has_exact_synonym: tt

NMR spectrum by pulse sequence
type: Class
subclass of: NMR spectrum

NMR spectrum by processing step
type: Class
subclass of: NMR spectrum

2D spectrum coordinate system descriptor
type: Class
subclass of: NMR spectrum descriptor

y-axis value type
type: Class
subclass of: 2D spectrum coordinate system descriptor
see also: the subclasses come from the Rubtsov specification

power value type
type: Class
subclass of: y-axis value type

magnitude value type
type: Class
subclass of: y-axis value type

real value type
type: Class
subclass of: y-axis value type

imaginary value type
type: Class
subclass of: y-axis value type

complex value types
type: Class
subclass of: y-axis value type

spectral projection axis
type: Class
subclass of: NMR spectrum descriptor

f1 axis
type: Class
subclass of: spectral projection axis

f2 axis
type: Class
subclass of: spectral projection axis

NMR Format converter
type: Class
subclass of: NMR software

BML-NMR identifier
type: Class
subclass of: metabolomics database identifier

creatinine
type: Class
subclass of: concentration standard
comment: will be further specified via a concentration value

2D pulse sequence
type: Class
subclass of: NMR pulse sequence

data simulation
type: Class
subclass of: data transformation
comment: used to be labeled 'NMR spectrum simulation'

dynamic nuclear polarization NMR
type: Class
subclass of: NMR instrument type
has_exact_synonym: DNP NMR
has_exact_synonym: dynamic nuclear polarization enhanced NMR system

chemical shift
type: Class
subclass of: NMR spectrum descriptor
definition: Chemical shift is the resonance frequency of a nucleus related to a chemical shift standard. in ppm along x-axis
source: http://en.wikipedia.org/wiki/Chemical_shift

nmr signal intensity
type: Class
subclass of: NMR spectrum descriptor
definition: an information object that describes the strength of the NMR signal

baseline correction using polynomial function
type: Class
subclass of: baseline correction

first transient of the tnnoesy-presaturation pulse sequence
type: Class
subclass of: 2D pulse sequence

Varian acquisition parameter file
type: Class
subclass of: acquisition parameter file

procpar
type: Class
subclass of: Varian processing parameter file

acqus
type: Class
subclass of: Bruker acquisition parameter file

Bruker acquisition parameter file
type: Class
subclass of: acquisition parameter file

peak feature
type: Class
subclass of: NMR spectrum descriptor
has_obo_namespace: NMR
id: NMR:1000231

global
type: Class
subclass of: Varian acquisition parameter file

Varian autosampler
type: Class
subclass of: autosampler

Varian SMS 50
type: Class
subclass of: Varian autosampler

Varian probe
type: Class
subclass of: NMR probe

5mm HCN probe
type: Class
subclass of: Varian liquid cold probe

Varian liquid cold probe
type: Class
subclass of: Varian probe

reference compound NMR spectrum
type: Class
subclass of: NMR spectrum
comment: e.g as in HMDB

Mestrelab software
type: Class
subclass of: NMR software

ACD spectrus software
type: Class
subclass of: NMR software

Mat NMR 3 software
type: Class
subclass of: NMR software

NMRLab software
type: Class
subclass of: software

Spinworks NMR software
type: Class
subclass of: software

NMR software vendor
type: Class
subclass of: software vendor

Spinworks
type: Class
subclass of: NMR software vendor

iNMR software
type: Class
subclass of: NMR software

NMR pipe
type: Class
subclass of: NMR software

cule NMR software
type: Class
subclass of: NMR software

Matlab to nmrML converter
type: Class
subclass of: NMR Format converter
source: Git: nmrML\tools\Parser_and_Converters\Matlab
comment: By Batman/ Tim Ebbels Group

Bruker processing parameter file
type: Class
subclass of: processing parameter file

procs
type: Class
subclass of: Bruker processing parameter file

Varian processing parameter file
type: Class
subclass of: processing parameter file

Madison Metabolomics Consortium Database MMCD identifier
type: Class
subclass of: metabolomics database identifier
source: http://mmcd.nmrfam.wisc.edu/
comment: PRS: rename 'identifyer' to 'identifier'

Bigg metabolomics database identifier
type: Class
subclass of: metabolomics database identifier
source: http://bigg.ucsd.edu/

Lorentz Gaussian window function
type: Class
subclass of: window function for apodization
has_exact_synonym: Lorentz-to-Gauss apodization
comment: Functional form: gm(x_i) = exp(e - g*g) Where: e = pi*i*g1 g = 0.6*pi*g2*(g3*(size-1)-i) Parameters: * data Array of spectral data. * g1 Inverse exponential width. * g2 Gaussian broaden width. * g3 Location of gauss maximum. * inv Set True for inverse apodization.

traf window function
type: Class
subclass of: window function for apodization
has_exact_synonym: TRAF
has_exact_synonym: Transform of Reverse Added FIDs
definition: A Window function described by Daniel Traficante in their original paper.

trafs window function
type: Class
subclass of: window function for apodization
has_exact_synonym: TRAFS

peak fitting
type: Class
subclass of: peak processing

peak assignment
type: Class
subclass of: peak processing

deconvolution
type: Class
subclass of: peak processing

chemical shift sorting
type: Class
subclass of: frequency domain data processing
definition: A method of sorting multiple spectra by position of chemical shift peaks. This method is used in Batman and improves the fit for shifted/overlapped peaks.

fid file
type: Class
subclass of: Bruker FID file

Varian FID file
type: Class
subclass of: FID file

Bruker FID file
type: Class
subclass of: FID file

ERVA-based bucketing
type: Class
subclass of: bucketing
source: Jacob D. et al (2013) Analytical and Bioanalytical Chemistry, 405, 5049-5061
comment: Taking advantage of the concentration variability of each compound in a series of samples, buckets are linked together into clusters based on significant correlations.This is done i.g. in ERVA-based bucketing

cluster of peaks
type: Class
subclass of: binned spectrum descriptor

Match NMR tube
type: Class
subclass of: Bruker tube

shaped tube
type: Class
subclass of: Bruker tube

Shigemi tube
type: Class
subclass of: NMR sample tube

standard tube
type: Class
subclass of: Bruker tube

Bruker tube
type: Class
subclass of: NMR sample tube

JEOL magnet
type: Class
subclass of: NMR magnet

JEOL ECS magnet
type: Class
subclass of: JEOL magnet

JEOL ECA magnet
type: Class
subclass of: JEOL magnet

JEOL ECX magnet
type: Class
subclass of: JEOL magnet

Varian NMR software
type: Class
subclass of: commercial NMR software

VnmrJ software
type: Class
subclass of: Varian NMR software

Wilmad tube
type: Class
subclass of: NMR sample tube

4mm Match tube
type: Class
subclass of: Match NMR tube

2.5mm Match tube
type: Class
subclass of: Match NMR tube

3mm Match tube
type: Class
subclass of: Match NMR tube

5mm Match tube
type: Class
subclass of: Match NMR tube

1mm Match tube
type: Class
subclass of: Match NMR tube

1.7mm Match tube
type: Class
subclass of: Match NMR tube

2mm Match tube
type: Class
subclass of: Match NMR tube

4.25mm Match tube
type: Class
subclass of: Match NMR tube

3mm standard tube
type: Class
subclass of: standard tube

5mm standard tube
type: Class
subclass of: standard tube

1mm standard tube
type: Class
subclass of: standard tube

1.7mm standard tube
type: Class
subclass of: standard tube

Wilmad economy tube
type: Class
subclass of: Wilmad tube

Wilmad precision tube
type: Class
subclass of: Wilmad tube

Norell tube
type: Class
subclass of: NMR sample tube

JEOL FID file
type: Class
subclass of: FID file

nmRIO
type: Class
subclass of: NMR Format converter
source: Git: nmrML\tools\Parser_and_Converters\R
comment: R statistics to nmrML. Developed by Steffen Neumann, IPB-Halle.de

rNMR-IO
type: Class
subclass of: NMR Format converter
source: Git: nmrML\tools\Parser_and_Converters\R\rNMR-IO

Vendor2nmrML_Java
type: Class
subclass of: NMR Format converter
definition: Based on both nmrML.xsd (XML Schema Definition) and CV params (such as ontologies nmrCV, UO, CHEBI ...), a converter written in Java was developed that automatically generates nmrML files, from raw files of the major NMR vendors. The choice of Java was guided by i) the JAXB framework (Java Architecture for XML Binding), ii) its OS-platform independence and iii) strengthened by the existence of a useful java library (i.e [nmr-fid-tool](https://github.com/LuisFF/nmr-fid-tool)) for further processing and visualisation of the resulting nmrML data. As nmrML intents to gather and integrate several types of data and corresponding metadata in a single file, it is necessary to process each data source separately. Thus, two command tools were developed. The first one, nmrMLcreate allows to create a new nmrML file, based on available Bruker or Varian/Agilent raw files. The second one, nmrMLproc allows to add and fill in additional sections corresponding to the data processing step.
source: Git: nmrML\tools\Parser_and_Converters\Java\converter
comment: Developed by Daniel Jacob at INRA Bordeaux. The recommended converter for Bruker and Varian/Agilent vendor format conversion.

Varian magnet
type: Class
subclass of: NMR magnet
has_exact_synonym: Agilent magnet

premium compact narrow bore magnet
type: Class
subclass of: Varian magnet

premium shielded narrow bore magnet
type: Class
subclass of: Varian magnet

premium shielded wide bore magnet
type: Class
subclass of: Varian magnet

modified Gaussian window function
type: Class
subclass of: Gaussian window function
has_exact_synonym: modified gaussian apodization
comment: Functional form: gmb(x_i) = exp(-a*i - b*i*i) Parameters: * data Array of spectral data. * a Exponential term. * b Gaussian term. * inv Set True for inverse apodization.

exponentially damped J-modulation window function
type: Class
subclass of: window function for apodization
has_exact_synonym: exponentially damped J-modulation apodization
comment: Functional form: jmod(x_i) = exp(-e)*sin( pi*off + pi*(end-off)*i/(size-1)) Parameters: * data Array of spectral data. * e Exponential term. * off Start of modulation in fraction of pi radians. * end End of modulation in fraction of pi radians. * inv Set True for inverse apodization

shifted sine bell window function
type: Class
subclass of: sine window function
has_exact_synonym: shifted sine-bell apodization
comment: Functional form: sp(x_i) = sin( (pi*off + pi*(end-off)*i/(size-1) )**pow Parameters: * data Array of spectral data. * start Start of Sine-Bell as percent of vector (0.0 -> 1.0) * end End of Sine-Bell as percent of vector (0.0 -> 1.0 ) * pow Power of Sine-Bell * inv Set True for inverse apodization.

triangle window function
type: Class
subclass of: window function for apodization
has_exact_synonym: triangle apodization
comment: Functional form: 0:loc linear increase/decrease from lHi to 1.0 loc: linear increase/decrease from 1.0 to rHi Parameters: * data Array of spectral data. * loc Location of apex, "auto" sets to middle. * lHi Left side starting height. * rHi Right side starting height. * inv Set True for inverse apodization.

acquisition log file
type: Class
subclass of: data file
definition: The acquisition log file is a created during an acquisition and could useful for debugging an acquisition that has gone awry.

PynmrML
type: Class
subclass of: NMR Format converter
source: Git: nmrML\tools\Parser_and_Converters\python
comment: A Python based vendor to nmrML converter developed by MIchael Wilson at TMIC Edmonton.

MetaboAnalyst software
type: Class
subclass of: NMR software
definition: A web server designed to permit comprehensive metabolomic data analysis, visualization and interpretation. It supports a wide range of complex statistical calculations and high quality graphical rendering functions that require significant computational resources.
comment: Jianguo Xia, Igor V. Sinelnikov, Beomsoo Han and David S. Wishart, MetaboAnalyst 3.0—making metabolomics more meaningful, Nucl. Acids Res. (1 July 2015) 43 (W1): W251-W257. doi: 10.1093/nar/gkv380

acqu2s
type: Class
subclass of: Bruker acquisition parameter file

acqu3s
type: Class
subclass of: Bruker acquisition parameter file

proc2s
type: Class
subclass of: Bruker processing parameter file

proc3s
type: Class
subclass of: Bruker processing parameter file

NMR spectrum file
type: Class
subclass of: data file

Bruker NMR spectrum file
type: Class
subclass of: NMR spectrum file

1R file
type: Class
subclass of: Bruker NMR spectrum file

title file
type: Class
subclass of: Bruker processing parameter file

XEASY software
type: Class
subclass of: NMR software
definition: A new program package, XEASY, was written for interactive computer support of the analysis of NMR spectra for three-dimensional structure determination of biological macromolecules. XEASY was developed for work with 2D, 3D and 4D NMR data sets. It includes all the functions performed by the precursor program EASY, which was designed for the analysis of 2D NMR spectra, i.e., peak picking and support of sequence-specific resonance assignments, cross-peak assignments, cross-peak integration and rate constant determination for dynamic processes.
source: Christian Bartels, Tai-he Xia, Martin Billeter, Peter Güntert, Kurt Wüthrich, The program XEASY for computer-supported NMR spectral analysis of biological macromolecules, J Biomol NMR (1995) 6: 1. doi:10.1007/BF00417486

NMR spectrum vizualisation software
type: Class
subclass of: NMR software

JspectraView software
type: Class
subclass of: NMR spectrum vizualisation software
comment: Used in NMR Assign tool for Baysil

cryoprobe
type: Class
subclass of: NMR probe

inverse detection NMR probe
type: Class
subclass of: NMR probe

5mm inverse detection cryoprobe
type: Class
subclass of: 5mm HCN probe
subclass of: cryoprobe
subclass of: inverse detection NMR probe
subclass of: solid NMR probe

NMRViewer software
type: Class
subclass of: NMR spectrum vizualisation software
source: Git: nmrML\tools\Visualizers\PMB_NMRviewer
comment: Developed by Daniel Jacob, INRA Bordeaux
example: http://services.cbib.u-bordeaux2.fr/SPECNMR/examples

material processing
type: Class
subclass of: process

AB multiplet pattern
type: Class
subclass of: multiplet feature
source: http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm

NMR solvent
type: Class
subclass of: object
comment: Use Chebi entities here.

NMR buffer
type: Class
subclass of: object
comment: Use Chebi entities here.

presat water suppression
type: Class
subclass of: pre-acquisition water suppression

Varian VNMRS 600
type: Class
subclass of: Varian VNMRS instrument

data content encoding
type: Class
subclass of: data encoding parameter

data compression scheme
type: Class
subclass of: data encoding parameter

byte format
type: Class
subclass of: data content encoding

zlib
type: Class
subclass of: binary data compression type

complex64
type: Class
subclass of: byte format
definition: This byte format uses a consecutive array of two 32bit float numbers to represent the real and imaginary part of the complex values.

complex128
type: Class
subclass of: byte format
definition: This byte format uses a consecutive array of two 64bit double precision values to represent the real and imaginary part of the complex values.

binary data compression type
type: Class
subclass of: data compression scheme

AB2 multiplet pattern
type: Class
subclass of: multiplet feature
source: http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm

data encoding parameter
type: Class
subclass of: parameter

uncompressed data
type: Class
subclass of: binary data compression type

digital signal processing firmware version
type: Class
subclass of: instrument attribute
definition: DSPFVS - DSP (Digital signal processing) firmware version corresponds to the version of the digital filter, a hardware component used by the spectrometer
has_exact_synonym: DSPFVS

decimation factor
type: Class
subclass of: NMR acquisition parameter
definition: DECIM - decimation factor is a (bruker) acquisition parameter that captures the number of raw analog points that are averaged in order to obtain a digital signal recorded in the fid.
has_exact_synonym: DECIM

group time delay
type: Class
subclass of: NMR acquisition parameter
definition: GRPDLY - is the time delay (in number of points?) between acquiring the analog signal and producing the digital signal (i.e. "The group delay is the time necessary for the digital filter function to “walk into” the raw FID and start generating significant intensity.")
has_exact_synonym: GRPDLY

NMR sampling strategy
type: Class
subclass of: NMR acquisition parameter
definition: a type of data acquisition parameter (when recording the FID) which can be continuous/uniform or sparse/non-uniform signal acquisition.

uniform sampling
type: Class
subclass of: NMR sampling strategy
has_exact_synonym: continuous sampling
definition: With uniform sampling, each sample is separated by the "dwell time".
editorial note: With uniform sampling we don't need to record the time points because we know the dwell time. We may add named strategies to the CV over time that are more specific than non-uniform

non-uniform sampling
type: Class
subclass of: NMR sampling strategy
source: http://link.springer.com/chapter/10.1007%2F1-4020-3910-7_142#page-1
has_exact_synonym: sparse sampling
definition: with non-uniform, some samples are skipped, there are different strategies for which to skip, but we can simply record the time point as well as the complex data point in order to represent this type of data.
editorial note: Non-uniform sampling is something likely to become more important in the future, because it allows you to capture higher dimension spectra much more quickly

Bruker XWIN-NMR software
type: Class
subclass of: NMR acquisition software

software attribute
type: Class
subclass of: generically dependent continuant

NMR software version
type: Class
subclass of: software attribute

ABX3 multiplet pattern
type: Class
subclass of: multiplet feature
source: http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm

AA'BB' multiplet pattern
type: Class
subclass of: multiplet feature
source: http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm

AA'XX' multiplet pattern
type: Class
subclass of: multiplet feature
source: http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm

variable size bucketing
type: Class
subclass of: bucketing

uniform bucketing
type: Class
subclass of: bucketing

intelligent bucketing
type: Class
subclass of: bucketing

bucket importing
type: Class
subclass of: bucketing

bucket resetting
type: Class
subclass of: bucketing
comment: put in as reqired by NMRProcFlow tool

global baseline correction
type: Class
subclass of: baseline correction
comment: as needed for nmrProcFlow

local baseline correction
type: Class
subclass of: baseline correction
comment: as needed for nmrProcFlow

bucket fusioning
type: Class
subclass of: bucket resetting

JNM-ECX Series FT NMR instrument
type: Class
subclass of: JEOL NMR instrument

JNM-ECZR Series FT NMR instrument
type: Class
subclass of: JEOL NMR instrument
definition: JNM-ECZR series is a new system that fully incorporates the latest digital and high frequency technologies. Improved reliability and a more compact size make possible by incorporating more advanced integrated circuits, it supports even greater expandability options than current models for multi-channel operation, high power amplifiers and other accessories. The bus line for control of attachments has been upgraded to high speed and enables highly accurate and rapid control. 400 MHz - 1 GHz

JNM-ECZS Series FT NMR instrument
type: Class
subclass of: JEOL NMR instrument
definition: The entry model ECZS spectrometer has the same basic functions, performance and capability of high-end model. The main console is amazingly small, less than 1/2 that of the current ECS series spectrometer. Coupling the use of advanced software with highly reliable automation, all routine daily measurements can be automated, while the use of the autotune Supercool probe realizes the world’s highest sensitivity in its class. Whatever your application field ECZS can demonstrate its power. 400 MHz

AVANCE III HD
type: Class
subclass of: Bruker NMR instrument

NanoBay400 MHz
type: Class
subclass of: Bruker NMR instrument

Fourier 300HD
type: Class
subclass of: Bruker NMR instrument

DNP-NMR
type: Class
subclass of: Bruker NMR instrument

LC-NMR instrument
type: Class
subclass of: Bruker NMR instrument

LC-NMR/MS instrument
type: Class
subclass of: Bruker NMR instrument

Food-Screener instrument
type: Class
subclass of: Bruker NMR instrument

AVANCE IVDr
type: Class
subclass of: Bruker NMR instrument

JEOL Resonance 400MHz YH magnet
type: Class
subclass of: JEOL magnet

JEOL Resonance 500MHz magnet
type: Class
subclass of: JEOL magnet

JEOL Resonance 600MHz magnet
type: Class
subclass of: JEOL magnet

JEOL Resonance 700MHz magnet
type: Class
subclass of: JEOL magnet

JEOL Resonance 800MHz magnet
type: Class
subclass of: JEOL magnet

single peak feature
type: Class
subclass of: peak feature

NMR instrument vendor
type: Class
subclass of: instrument attribute
definition: Any organisation ort person that sells NMR instruments to customers.

Avance I spectrometer
type: Class
subclass of: Bruker NMR instrument

Oxford Instruments
type: Class
subclass of: NMR instrument manufacturer

Spinlock SRL
type: Class
subclass of: NMR instrument manufacturer

General Electric
type: Class
subclass of: NMR instrument manufacturer

Kimble Chase
type: Class
subclass of: NMR instrument manufacturer

Phillips
type: Class
subclass of: NMR instrument manufacturer

Siemens AG
type: Class
subclass of: NMR instrument manufacturer

Varian Inova 500
type: Class
subclass of: Varian INOVA

Varian VNMRS instrument
type: Class
subclass of: Varian NMR instrument

Varian Mercury plus
type: Class
subclass of: Varian MERCURY

Varian UnityInova instrument
type: Class
subclass of: Varian NMR instrument

Varian 400-MR NMR instrument
type: Class
subclass of: Varian NMR instrument

Varian DDR2 instrument
type: Class
subclass of: Varian NMR instrument

Agilent NMR instrument
type: Class
subclass of: NMR instrument

Agilent 400-MR NMR instrument
type: Class
subclass of: Agilent NMR instrument

Varian Mercury 400
type: Class
subclass of: Varian MERCURY

Agilent Au 400 (DDR2 Console)
type: Class
subclass of: Agilent NMR instrument

Agilent DDR 2 w/ HCN cryoprobe
type: Class
subclass of: Agilent NMR instrument

BMRB identifier
type: Class
subclass of: metabolomics database identifier

left trapezoid limit
type: Class
subclass of: trapezoid window function parameter
has_exact_synonym: TM1
comment: 0<TM1<1

trapezoid window function parameter
type: Class
subclass of: window function parameter

complex64 Integer
type: Class
subclass of: byte format
definition: This byte format uses a consecutive array of two 32bit integer numbers to represent the real and imaginary part of the complex values (2x32bits=>2x4bytes=> 2 integers) for the FID datatype.

complex128 Integer
type: Class
subclass of: byte format
definition: This byte format uses a consecutive array of two 64bit long integer numbers to represent the real and imaginary part of the complex values (2x64bits => 2x8bytes => 2 longs) for the FID datatype.

right trapezoid limit
type: Class
subclass of: trapezoid window function parameter
has_exact_synonym: TM2
comment: 0<TM2<1

thirty degree pulse duration
type: Class
subclass of: pulse parameter
has_exact_synonym: 30 degree pulse duration
definition: The duration of the excitation pulse needed to rotate the magnetisation vector by 30 degrees.

InChi
type: Class
subclass of: line representation

inchikey
type: Class
subclass of: line representation

Wiswesser Line Notation
type: Class
subclass of: line representation
has_exact_synonym: WLN

ROSDAL
type: Class
subclass of: line representation

SLN-Tripos
type: Class
subclass of: line representation

smarts
type: Class
subclass of: SMILES string

line representation
type: Class
subclass of: chemical compound formula

2D topological molecule representation
type: Class
subclass of: chemical compound formula

2D bond line structure
type: Class
subclass of: 2D topological molecule representation

3D geometrical molecule representation
type: Class
subclass of: chemical compound formula

3D bond line structure
type: Class
subclass of: 3D geometrical molecule representation

CAS number
type: Class
subclass of: chemical compound attribute

fingerprint model
type: Class
subclass of: chemical compound attribute

molfile
type: Class
subclass of: chemical compound attribute

compound similarity measure
type: Class
subclass of: chemical compound attribute

Tanimoto similarity
type: Class
subclass of: compound similarity measure

Gaussian window function parameter
type: Class
subclass of: window function parameter

2,2-Dimethyl-2-silapentane-5-sulfonate
type: Class
subclass of: concentration standard
has_exact_synonym: DSS

Gaussian maximum position
type: Class
subclass of: Gaussian window function parameter

2H spectrum reference compound
type: Class
subclass of: chemical shift standard

ABX2 multiplet pattern
type: Class
subclass of: multiplet feature

DRX 600 instrument
type: Class
subclass of: Bruker NMR instrument

plot and graph generation
type: Class
subclass of: frequency domain data processing

reference deconvolution
type: Class
subclass of: deconvolution
definition: vertical alignment of on and offset of the peak of the reference compound.

spectral smoothing
type: Class
subclass of: spectral denoising
definition: the process of removing noisy jitters in a spectral curve to get clearer and more meaningful signals and peaks.

NMR database format
type: Class
subclass of: data file format

BMRB/XML file format
type: Class
subclass of: NMR database format
source: M. Yokochi, N. Kobayashi, E. L. Ulrich, A. R. Kinjo, T. Iwata, Y. E. Ioannidis, M. Livny, J. L. Markley, H. Nakamura, C. Kojima, T. Fujiwara, “Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins,” Journal of Biomedical Semantics, 5:7:16 (2016)

nD spectrum
type: Class
subclass of: NMR spectrum by dimensionality

NMR data conversion
type: Class
subclass of: file format conversion
definition: Terms used to describe types of data processing.
has_exact_synonym: data processing
has_obo_namespace: NMR
id: NMR:1000452

Axiom
annotated source: NMR data conversion
annotated property: definition
annotated target: Terms used to describe types of data processing.
database_cross_reference: MSI:NMR

sample
type: Class
subclass of: object
definition: 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
has_obo_namespace: NMR
id: NMR:1000457

Axiom
annotated source: sample
annotated property: definition
annotated target: 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
database_cross_reference: MSI:NMR

instrument
type: Class
subclass of: object
definition: Description of the instrument or the mass spectrometer.
has_exact_synonym: instrument configuration
has_obo_namespace: NMR
id: NMR:1000463

Axiom
annotated source: instrument
annotated property: definition
annotated target: Description of the instrument or the mass spectrometer.
database_cross_reference: MSI:NMR

Varian/Agilent instrument model
type: Class
subclass of: NMR instrument model
definition: Varian instrument model.
has_obo_namespace: NMR
id: NMR:1000489

Axiom
annotated source: Varian/Agilent instrument model
annotated property: definition
annotated target: Varian instrument model.
database_cross_reference: MSI:NMR

instrument attribute
type: Class
subclass of: object attribute
definition: Instrument properties that are associated with a value.
has_obo_namespace: NMR
id: NMR:1000496

Axiom
annotated source: instrument attribute
annotated property: definition
annotated target: Instrument properties that are associated with a value.
database_cross_reference: MSI:NMR

data file content
type: Class
subclass of: data file attribute
definition: Describes the data content on the file.
has_obo_namespace: NMR
id: NMR:1000524

Axiom
annotated source: data file content
annotated property: definition
annotated target: Describes the data content on the file.
database_cross_reference: MSI:NMR

instrument serial number
type: Class
subclass of: instrument attribute
definition: Serial Number of the instrument.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000529

Axiom
annotated source: instrument serial number
annotated property: definition
annotated target: Serial Number of the instrument.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: instrument serial number
annotated property: database_cross_reference
annotated target: value-type:xsd:string

file format conversion
type: Class
subclass of: data transformation
definition: Conversion of one file format to another.
has_obo_namespace: NMR
id: NMR:1000530

Axiom
annotated source: file format conversion
annotated property: definition
annotated target: Conversion of one file format to another.
database_cross_reference: MSI:NMR

software
type: Class
subclass of: realizable entity
definition: Software related to the recording or transformation of spectra.
has_obo_namespace: NMR
id: NMR:1000531

Axiom
annotated source: software
annotated property: definition
annotated target: Software related to the recording or transformation of spectra.
database_cross_reference: MSI:NMR

object attribute
type: Class
subclass of: generically dependent continuant
definition: Object Attribute.
has_obo_namespace: NMR
id: NMR:1000547

Axiom
annotated source: object attribute
annotated property: definition
annotated target: Object Attribute.
database_cross_reference: MSI:NMR

sample attribute
type: Class
subclass of: object attribute
definition: Sample properties that are associated with a value.
has_obo_namespace: NMR
id: NMR:1000548

Axiom
annotated source: sample attribute
annotated property: definition
annotated target: Sample properties that are associated with a value.
database_cross_reference: MSI:NMR

data file checksum type
type: Class
subclass of: data file attribute
definition: Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data.
has_obo_namespace: NMR
id: NMR:1000561

Axiom
annotated source: data file checksum type
annotated property: definition
annotated target: Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data.
database_cross_reference: MSI:NMR

MD5
type: Class
subclass of: data file checksum type
definition: MD5 (Message-Digest algorithm 5) is a cryptographic hash function with a 128-bit hash value used to check the integrity of files.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000568

Axiom
annotated source: MD5
annotated property: definition
annotated target: MD5 (Message-Digest algorithm 5) is a cryptographic hash function with a 128-bit hash value used to check the integrity of files.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: MD5
annotated property: database_cross_reference
annotated target: value-type:xsd:string

SHA-1
type: Class
subclass of: data file checksum type
definition: SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000569

Axiom
annotated source: SHA-1
annotated property: definition
annotated target: SHA-1 (Secure Hash Algorithm-1) is a cryptographic hash function designed by the National Security Agency (NSA) and published by the NIST as a U. S. government standard. It is also used to verify file integrity.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: SHA-1
annotated property: database_cross_reference
annotated target: value-type:xsd:string

NMR raw data file format
type: Class
subclass of: data file format
definition: Describes the type of file and its content.
has_exact_synonym: source file
has_obo_namespace: NMR
id: NMR:1000577

Axiom
annotated source: NMR raw data file format
annotated property: definition
annotated target: Describes the type of file and its content.
database_cross_reference: MSI:NMR

contact attribute
type: Class
subclass of: object attribute
definition: Details about a person or organization to contact in case of concern or discussion about the file.
has_obo_namespace: NMR
id: NMR:1000585

Axiom
annotated source: contact attribute
annotated property: definition
annotated target: Details about a person or organization to contact in case of concern or discussion about the file.
database_cross_reference: MSI:NMR

contact name
type: Class
subclass of: contact attribute
definition: Name of the contact person or organization.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000586

Axiom
annotated source: contact name
annotated property: definition
annotated target: Name of the contact person or organization.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: contact name
annotated property: database_cross_reference
annotated target: value-type:xsd:string

contact address
type: Class
subclass of: contact attribute
definition: Postal address of the contact person or organization.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000587

Axiom
annotated source: contact address
annotated property: definition
annotated target: Postal address of the contact person or organization.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: contact address
annotated property: database_cross_reference
annotated target: value-type:xsd:string

contact URL
type: Class
subclass of: contact attribute
definition: Uniform Resource Locator related to the contact person or organization.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000588

Axiom
annotated source: contact URL
annotated property: definition
annotated target: Uniform Resource Locator related to the contact person or organization.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: contact URL
annotated property: database_cross_reference
annotated target: value-type:xsd:string

contact email
type: Class
subclass of: contact attribute
definition: Email address of the contact person or organization.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000589

Axiom
annotated source: contact email
annotated property: definition
annotated target: Email address of the contact person or organization.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: contact email
annotated property: database_cross_reference
annotated target: value-type:xsd:string

contact organization
type: Class
subclass of: contact attribute
definition: Home institution of the contact person.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000590

Axiom
annotated source: contact organization
annotated property: definition
annotated target: Home institution of the contact person.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: contact organization
annotated property: database_cross_reference
annotated target: value-type:xsd:string

data processing parameter
type: Class
subclass of: parameter
definition: Data processing parameter used in the data processing performed on the data file.
has_obo_namespace: NMR
id: NMR:1000630

Axiom
annotated source: data processing parameter
annotated property: definition
annotated target: Data processing parameter used in the data processing performed on the data file.
database_cross_reference: MSI:NMR

data processing completion time
type: Class
subclass of: quality
definition: The time that a data processing action was finished.
database_cross_reference: value-type:xsd:date
has_obo_namespace: NMR
id: NMR:1000747

Axiom
annotated source: data processing completion time
annotated property: definition
annotated target: The time that a data processing action was finished.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: data processing completion time
annotated property: database_cross_reference
annotated target: value-type:xsd:date

FID format
type: Class
subclass of: NMR raw data file format
definition: Describes how the native spectrum identifiers are formated.
has_exact_synonym: nativeID format
has_obo_namespace: NMR
id: NMR:1000767

Axiom
annotated source: FID format
annotated property: definition
annotated target: Describes how the native spectrum identifiers are formated.
database_cross_reference: MSI:NMR

Bruker FID format
type: Class
subclass of: FID format
definition: file=xsd:IDREF.
has_obo_namespace: NMR
id: NMR:1000773
comment: The nativeID must be the same as the source file ID.

Axiom
annotated source: Bruker FID format
annotated property: definition
annotated target: file=xsd:IDREF.
database_cross_reference: MSI:NMR

custom unreleased software
type: Class
subclass of: software
definition: A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the MSI-NMR working group in order to have another CV term added.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000799

Axiom
annotated source: custom unreleased software
annotated property: definition
annotated target: A software tool that has not yet been released. The value should describe the software. Please do not use this term for publicly available software - contact the MSI-NMR working group in order to have another CV term added.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: custom unreleased software
annotated property: database_cross_reference
annotated target: value-type:xsd:string

sample preparation information
type: Class
subclass of: sample attribute
definition: Description of the preparation steps which took place before the measurement was performed.
has_obo_namespace: NMR
id: NMR:1000831

Axiom
annotated source: sample preparation information
annotated property: definition
annotated target: Description of the preparation steps which took place before the measurement was performed.
database_cross_reference: MSI:NMR

molecule
type: Class
subclass of: chemical compound
definition: A molecules is a fundamental component of a chemical compound that is the smallest part of the compound that can participate in a chemical reaction.
has_obo_namespace: NMR
id: NMR:1000859

Axiom
annotated source: molecule
annotated property: definition
annotated target: A molecules is a fundamental component of a chemical compound that is the smallest part of the compound that can participate in a chemical reaction.
database_cross_reference: MSI:NMR

peptide
type: Class
subclass of: chemical compound
definition: A compound of low molecular weight that is composed of two or more amino acids.
has_obo_namespace: NMR
id: NMR:1000860

Axiom
annotated source: peptide
annotated property: definition
annotated target: A compound of low molecular weight that is composed of two or more amino acids.
database_cross_reference: MSI:NMR

chemical compound attribute
type: Class
subclass of: object attribute
definition: A describable property of a chemical compound.
has_obo_namespace: NMR
id: NMR:1000861

Axiom
annotated source: chemical compound attribute
annotated property: definition
annotated target: A describable property of a chemical compound.
database_cross_reference: MSI:NMR

isoelectric point
type: Class
subclass of: chemical compound attribute
definition: The pH of a solution at which a charged molecule does not migrate in an electric field.
database_cross_reference: value-type:xsd:float
has_exact_synonym: pI
has_obo_namespace: NMR
id: NMR:1000862

Axiom
annotated source: isoelectric point
annotated property: definition
annotated target: The pH of a solution at which a charged molecule does not migrate in an electric field.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: isoelectric point
annotated property: database_cross_reference
annotated target: value-type:xsd:float

predicted isoelectric point
type: Class
subclass of: chemical compound attribute
definition: The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm.
database_cross_reference: value-type:xsd:float
has_exact_synonym: predicted pI
has_obo_namespace: NMR
id: NMR:1000863

Axiom
annotated source: predicted isoelectric point
annotated property: definition
annotated target: The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: predicted isoelectric point
annotated property: database_cross_reference
annotated target: value-type:xsd:float

chemical compound formula
type: Class
subclass of: chemical compound attribute
definition: A combination of symbols used to express the chemical composition of a compound.
has_obo_namespace: NMR
id: NMR:1000864

Axiom
annotated source: chemical compound formula
annotated property: definition
annotated target: A combination of symbols used to express the chemical composition of a compound.
database_cross_reference: MSI:NMR

empirical formula
type: Class
subclass of: chemical compound formula
definition: A chemical formula which expresses the proportions of the elements present in a substance.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000865

Axiom
annotated source: empirical formula
annotated property: definition
annotated target: A chemical formula which expresses the proportions of the elements present in a substance.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: empirical formula
annotated property: database_cross_reference
annotated target: value-type:xsd:string

molecular formula
type: Class
subclass of: line representation
definition: A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000866

Axiom
annotated source: molecular formula
annotated property: definition
annotated target: A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: molecular formula
annotated property: database_cross_reference
annotated target: value-type:xsd:string

structural formula
type: Class
subclass of: chemical compound formula
definition: A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000867

Axiom
annotated source: structural formula
annotated property: definition
annotated target: A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: structural formula
annotated property: database_cross_reference
annotated target: value-type:xsd:string

SMILES string
type: Class
subclass of: line representation
definition: The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000868

Axiom
annotated source: SMILES string
annotated property: definition
annotated target: The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: SMILES string
annotated property: database_cross_reference
annotated target: value-type:xsd:string

external reference identifier
type: Class
subclass of: reference
definition: An identifier/accession number to an external reference database.
has_obo_namespace: NMR
id: NMR:1000878

Axiom
annotated source: external reference identifier
annotated property: definition
annotated target: An identifier/accession number to an external reference database.
database_cross_reference: MSI:NMR

PubMed identifier
type: Class
subclass of: external reference identifier
definition: A unique identifier for a publication in the PubMed database (MIR:00000015).
database_cross_reference: value-type:xsd:integer
has_obo_namespace: NMR
id: NMR:1000879

Axiom
annotated source: PubMed identifier
annotated property: definition
annotated target: A unique identifier for a publication in the PubMed database (MIR:00000015).
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: PubMed identifier
annotated property: database_cross_reference
annotated target: value-type:xsd:integer

chemical compound
type: Class
subclass of: object
definition: A substance formed by chemical union of two or more elements or ingredients in definite proportion by weight.
has_obo_namespace: NMR
id: NMR:1000881
comment: Use Chebi entities here.

Axiom
annotated source: chemical compound
annotated property: definition
annotated target: A substance formed by chemical union of two or more elements or ingredients in definite proportion by weight.
database_cross_reference: MSI:NMR

protein
type: Class
subclass of: chemical compound
definition: A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA coding for the protein.
has_obo_namespace: NMR
id: NMR:1000882

Axiom
annotated source: protein
annotated property: definition
annotated target: A compound composed of one or more chains of amino acids in a specific order determined by the base sequence of nucleotides in the DNA coding for the protein.
database_cross_reference: MSI:NMR

protein short name
type: Class
subclass of: protein attribute
definition: A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN).
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000883

Axiom
annotated source: protein short name
annotated property: definition
annotated target: A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN).
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: protein short name
annotated property: database_cross_reference
annotated target: value-type:xsd:string

protein attribute
type: Class
subclass of: object attribute
definition: An nonphysical attribute describing a specific protein.
has_obo_namespace: NMR
id: NMR:1000884

Axiom
annotated source: protein attribute
annotated property: definition
annotated target: An nonphysical attribute describing a specific protein.
database_cross_reference: MSI:NMR

protein accession
type: Class
subclass of: protein attribute
definition: Accession number for a specific protein in a database.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000885

Axiom
annotated source: protein accession
annotated property: definition
annotated target: Accession number for a specific protein in a database.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: protein accession
annotated property: database_cross_reference
annotated target: value-type:xsd:string

protein name
type: Class
subclass of: protein attribute
definition: A long name describing the function of the protein.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000886

Axiom
annotated source: protein name
annotated property: definition
annotated target: A long name describing the function of the protein.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: protein name
annotated property: database_cross_reference
annotated target: value-type:xsd:string

peptide attribute
type: Class
subclass of: object attribute
definition: An nonphysical attribute that can be used to describe a peptide.
has_obo_namespace: NMR
id: NMR:1000887

Axiom
annotated source: peptide attribute
annotated property: definition
annotated target: An nonphysical attribute that can be used to describe a peptide.
database_cross_reference: MSI:NMR

unmodified peptide sequence
type: Class
subclass of: peptide attribute
definition: A sequence of letter symbols denoting the order of amino acids that compose the peptide, without encoding any amino acid mass modifications that might be present.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000888

Axiom
annotated source: unmodified peptide sequence
annotated property: definition
annotated target: A sequence of letter symbols denoting the order of amino acids that compose the peptide, without encoding any amino acid mass modifications that might be present.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: unmodified peptide sequence
annotated property: database_cross_reference
annotated target: value-type:xsd:string

modified peptide sequence
type: Class
subclass of: peptide attribute
definition: A sequence of letter symbols denoting the order of amino acids that compose the peptide plus the encoding any amino acid mass modifications that are present using the notation where the total mass of the modified amino acid is specified in square bracketed numbers following the letter (e.g. R[162.10111] indicates an arginine whose final modified mass is 162.10111 amu).
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000889

Axiom
annotated source: modified peptide sequence
annotated property: definition
annotated target: A sequence of letter symbols denoting the order of amino acids that compose the peptide plus the encoding any amino acid mass modifications that are present using the notation where the total mass of the modified amino acid is specified in square bracketed numbers following the letter (e.g. R[162.10111] indicates an arginine whose final modified mass is 162.10111 amu).
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: modified peptide sequence
annotated property: database_cross_reference
annotated target: value-type:xsd:string

peptide labeling state
type: Class
subclass of: peptide attribute
definition: A state description of how a peptide might be isotopically or isobarically labelled.
has_obo_namespace: NMR
id: NMR:1000890

Axiom
annotated source: peptide labeling state
annotated property: definition
annotated target: A state description of how a peptide might be isotopically or isobarically labelled.
database_cross_reference: MSI:NMR

heavy labeled peptide
type: Class
subclass of: peptide attribute
definition: A peptide that has been created or labeled with some heavier-than-usual isotopes.
has_obo_namespace: NMR
id: NMR:1000891

Axiom
annotated source: heavy labeled peptide
annotated property: definition
annotated target: A peptide that has been created or labeled with some heavier-than-usual isotopes.
database_cross_reference: MSI:NMR

unlabeled peptide
type: Class
subclass of: peptide attribute
definition: A peptide that has not been labeled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy".
has_exact_synonym: light labeled peptide
has_obo_namespace: NMR
id: NMR:1000892

Axiom
annotated source: unlabeled peptide
annotated property: definition
annotated target: A peptide that has not been labeled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy".
database_cross_reference: MSI:NMR

peptide group label
type: Class
subclass of: peptide attribute
definition: An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000893

Axiom
annotated source: peptide group label
annotated property: definition
annotated target: An arbitrary string label used to mark a set of peptides that belong together in a set, whereby the members are differentiated by different isotopic labels. For example, the heavy and light forms of the same peptide will both be assigned the same peptide group label.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: peptide group label
annotated property: database_cross_reference
annotated target: value-type:xsd:string

data standard
type: Class
subclass of: generically dependent continuant
definition: Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence.
has_obo_namespace: NMR
id: NMR:1000898

Axiom
annotated source: data standard
annotated property: definition
annotated target: Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence.
database_cross_reference: MSI:NMR

de facto standard
type: Class
subclass of: data standard
definition: A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard.
database_cross_reference: MS_1000899
has_obo_namespace: NMR
id: NMR:1000899

Axiom
annotated source: de facto standard
annotated property: definition
annotated target: A practice or product that has become a standard not because it has been approved by a standards organization but because it is widely used and recognized by the industry as being standard.
database_cross_reference: MSI:NMR

minimum information standard
type: Class
subclass of: data standard
definition: A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result.
database_cross_reference: MS_1000899
has_obo_namespace: NMR
id: NMR:1000900

Axiom
annotated source: minimum information standard
annotated property: definition
annotated target: A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result.
database_cross_reference: MSI:NMR

tab delimited text file
type: Class
subclass of: text file
definition: A file that has two or more columns of tabular data where each column is separated by a TAB character.
has_obo_namespace: NMR
id: NMR:1000914

Axiom
annotated source: tab delimited text file
annotated property: definition
annotated target: A file that has two or more columns of tabular data where each column is separated by a TAB character.
database_cross_reference: MSI:NMR

protein modification
type: Class
subclass of: protein attribute
definition: Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000933

Axiom
annotated source: protein modification
annotated property: definition
annotated target: Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: protein modification
annotated property: database_cross_reference
annotated target: value-type:xsd:string

gene name
type: Class
subclass of: protein attribute
definition: Name of the gene from which the protein is translated.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1000934

Axiom
annotated source: gene name
annotated property: definition
annotated target: Name of the gene from which the protein is translated.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: gene name
annotated property: database_cross_reference
annotated target: value-type:xsd:string

intermediate analysis format
type: Class
subclass of: data file format
definition: Type of the source file, the nmrIdentML was created from.
has_obo_namespace: NMR
id: NMR:1001040

Axiom
annotated source: intermediate analysis format
annotated property: definition
annotated target: Type of the source file, the nmrIdentML was created from.
database_cross_reference: MSI:MI

data stored in database
type: Class
subclass of: data file format
definition: Source file for this nmrIdentML was a data set in a database.
has_obo_namespace: NMR
id: NMR:1001107
editorial note: retire? Consider: "NMR database format" ?

Axiom
annotated source: data stored in database
annotated property: definition
annotated target: Source file for this nmrIdentML was a data set in a database.
database_cross_reference: MSI:MI

software vendor
type: Class
subclass of: vendor
has_obo_namespace: NMR
id: NMR:1001267

programmer
type: Class
subclass of: contact role
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001268

The allowed value-type for this CV term.
type: Axiom
annotated source: programmer
annotated property: database_cross_reference
annotated target: value-type:xsd:string

instrument vendor
type: Class
subclass of: vendor
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001269

The allowed value-type for this CV term.
type: Axiom
annotated source: instrument vendor
annotated property: database_cross_reference
annotated target: value-type:xsd:string

lab personnel
type: Class
subclass of: contact role
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001270

The allowed value-type for this CV term.
type: Axiom
annotated source: lab personnel
annotated property: database_cross_reference
annotated target: value-type:xsd:string

researcher
type: Class
subclass of: contact role
has_obo_namespace: NMR
id: NMR:1001271

analysis software
type: Class
subclass of: software
definition: Analysis software.
has_obo_namespace: NMR
id: NMR:1001456

Axiom
annotated source: analysis software
annotated property: definition
annotated target: Analysis software.
database_cross_reference: MSI:NMR

data processing software
type: Class
subclass of: software
definition: Conversion software.
has_obo_namespace: NMR
id: NMR:1001457

Axiom
annotated source: data processing software
annotated property: definition
annotated target: Conversion software.
database_cross_reference: MSI:NMR

data file format
type: Class
subclass of: data file attribute
definition: Format of data files.
has_obo_namespace: NMR
id: NMR:1001459

Axiom
annotated source: data file format
annotated property: definition
annotated target: Format of data files.
database_cross_reference: MSI:NMR

contact phone number
type: Class
subclass of: contact attribute
definition: Phone number of the contact person or organization.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001755

Axiom
annotated source: contact phone number
annotated property: definition
annotated target: Phone number of the contact person or organization.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: contact phone number
annotated property: database_cross_reference
annotated target: value-type:xsd:string

contact fax number
type: Class
subclass of: contact attribute
definition: Fax number for the contact person or organization.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001756

Axiom
annotated source: contact fax number
annotated property: definition
annotated target: Fax number for the contact person or organization.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: contact fax number
annotated property: database_cross_reference
annotated target: value-type:xsd:string

contact toll-free phone number
type: Class
subclass of: contact attribute
definition: Toll-free phone number of the contact person or organization.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001757

Axiom
annotated source: contact toll-free phone number
annotated property: definition
annotated target: Toll-free phone number of the contact person or organization.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: contact toll-free phone number
annotated property: database_cross_reference
annotated target: value-type:xsd:string

Digital Object Identifier (DOI)
type: Class
subclass of: external reference identifier
definition: DOI unique identifier.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001922

Axiom
annotated source: Digital Object Identifier (DOI)
annotated property: definition
annotated target: DOI unique identifier.
database_cross_reference: MSI:MI

The allowed value-type for this CV term.
type: Axiom
annotated source: Digital Object Identifier (DOI)
annotated property: database_cross_reference
annotated target: value-type:xsd:string

external reference keyword
type: Class
subclass of: keyword
definition: Free text attribute that can enrich the information about an entity.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001923

Axiom
annotated source: external reference keyword
annotated property: definition
annotated target: Free text attribute that can enrich the information about an entity.
database_cross_reference: MSI:MI

The allowed value-type for this CV term.
type: Axiom
annotated source: external reference keyword
annotated property: database_cross_reference
annotated target: value-type:xsd:string

journal article keyword
type: Class
subclass of: keyword
definition: Keyword present in a scientific publication.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001924

Axiom
annotated source: journal article keyword
annotated property: definition
annotated target: Keyword present in a scientific publication.
database_cross_reference: MSI:MI

The allowed value-type for this CV term.
type: Axiom
annotated source: journal article keyword
annotated property: database_cross_reference
annotated target: value-type:xsd:string

submitter keyword
type: Class
subclass of: keyword
definition: Keyword assigned by the data submitter.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001925

Axiom
annotated source: submitter keyword
annotated property: definition
annotated target: Keyword assigned by the data submitter.
database_cross_reference: MSI:MI

The allowed value-type for this CV term.
type: Axiom
annotated source: submitter keyword
annotated property: database_cross_reference
annotated target: value-type:xsd:string

curator keyword
type: Class
subclass of: keyword
definition: Keyword assigned by a data curator.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001926

Axiom
annotated source: curator keyword
annotated property: definition
annotated target: Keyword assigned by a data curator.
database_cross_reference: MSI:MI

The allowed value-type for this CV term.
type: Axiom
annotated source: curator keyword
annotated property: database_cross_reference
annotated target: value-type:xsd:string

NMR acquisition parameter
type: Class
subclass of: parameter
definition: Parameters used in the NMR spectrometry acquisition.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1001954

Axiom
annotated source: NMR acquisition parameter
annotated property: definition
annotated target: Parameters used in the NMR spectrometry acquisition.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: NMR acquisition parameter
annotated property: database_cross_reference
annotated target: value-type:xsd:string

HMDB identifier
type: Class
subclass of: metabolomics database identifier
definition: A unique identifier for a metabolite in the HMDB database (HMDB00001).
database_cross_reference: value-type:xsd:integer
has_obo_namespace: NMR
id: NMR:1002000

Axiom
annotated source: HMDB identifier
annotated property: definition
annotated target: A unique identifier for a metabolite in the HMDB database (HMDB00001).
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: HMDB identifier
annotated property: database_cross_reference
annotated target: value-type:xsd:integer

Chenomx software
type: Class
subclass of: commercial NMR software
definition: Chenomx software for data acquisition and analysis.
has_obo_namespace: NMR
id: NMR:1002001

Axiom
annotated source: Chenomx software
annotated property: definition
annotated target: Chenomx software for data acquisition and analysis.
database_cross_reference: MSI:NMR

Chenomx NMR Suite software
type: Class
subclass of: Chenomx software
definition: Chenomx software for data analysis.
source: http://www.chenomx.com/software/
has_obo_namespace: NMR
id: NMR:1002002

Axiom
annotated source: Chenomx NMR Suite software
annotated property: definition
annotated target: Chenomx software for data analysis.
database_cross_reference: MSI:NMR

Varian FID format
type: Class
subclass of: FID format
definition: file=xsd:IDREF.
has_obo_namespace: NMR
id: NMR:1002003
comment: The nativeID must be the same as the source file ID.

Axiom
annotated source: Varian FID format
annotated property: definition
annotated target: file=xsd:IDREF.
database_cross_reference: MSI:NMR

NMR spectrometer file format
type: Class
subclass of: NMR software data format
definition: The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format.
has_obo_namespace: NMR
id: NMR:1002004

Axiom
annotated source: NMR spectrometer file format
annotated property: definition
annotated target: The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format.
database_cross_reference: MSI:NMR

text file
type: Class
subclass of: data file format
definition: Simple text file of peaks.
has_obo_namespace: NMR
id: NMR:1002005

Axiom
annotated source: text file
annotated property: definition
annotated target: Simple text file of peaks.
database_cross_reference: MSI:PI

acquisition parameter file
type: Class
subclass of: data file
definition: Parameter file used to configure the acquisition of raw data on the instrument.
has_obo_namespace: NMR
id: NMR:1002006

Axiom
annotated source: acquisition parameter file
annotated property: definition
annotated target: Parameter file used to configure the acquisition of raw data on the instrument.
database_cross_reference: MSI:NMR

NMR spectrum
type: Class
subclass of: data file content
definition: 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'. def: A NMR spectrum is a set of chemical shifts representing a chemical analysis. synonym: NMR spectrum
source: as designated Experiment type on http://www.bmrb.wisc.edu/tools/choose_pulse_info.php
has_obo_namespace: NMR
id: NMR:1002007

conversion to nmrML
type: Class
subclass of: NMR data conversion
definition: Conversion of a file format to Metabolomics Standards Initiative nmrData file format.
has_obo_namespace: NMR
id: NMR:1002008

Axiom
annotated source: conversion to nmrML
annotated property: definition
annotated target: Conversion of a file format to Metabolomics Standards Initiative nmrData file format.
database_cross_reference: MSI:NMR

conversion to JCAMP-DX
type: Class
subclass of: NMR data conversion
definition: Conversion of a file format to JCAMP-DX file format.
has_obo_namespace: NMR
id: NMR:1002009

Axiom
annotated source: conversion to JCAMP-DX
annotated property: definition
annotated target: Conversion of a file format to JCAMP-DX file format.
database_cross_reference: MSI:NMR

NMR solvent information
type: Class
subclass of: sample attribute
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1002010

The allowed value-type for this CV term.
type: Axiom
annotated source: NMR solvent information
annotated property: database_cross_reference
annotated target: value-type:xsd:string

pH
type: Class
subclass of: sample attribute
definition: pH.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1002011

Axiom
annotated source: pH
annotated property: definition
annotated target: pH.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: pH
annotated property: database_cross_reference
annotated target: value-type:xsd:string

chemical shift reference
type: Class
subclass of: quality check compound signal
definition: Chemical shift reference is a run attribute to designate the parts-per-million value of the peak used to reference a spectrum. It points to a fix chemical shift number, for examples 0 ppm for DSS or TSP. It can also have a calculated concentration, for examples 0.1 mM.
bug-database: https://github.com/nmrML/nmrML/issues/29#issue
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1002013

Axiom
annotated source: chemical shift reference
annotated property: definition
annotated target: Chemical shift reference is a run attribute to designate the parts-per-million value of the peak used to reference a spectrum. It points to a fix chemical shift number, for examples 0 ppm for DSS or TSP. It can also have a calculated concentration, for examples 0.1 mM.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: chemical shift reference
annotated property: database_cross_reference
annotated target: value-type:xsd:string

binned spectrum descriptor
type: Class
subclass of: NMR spectrum descriptor
definition: A bin for a spectrum.
database_cross_reference: value-type:xsd:string
has_exact_synonym: bucketed spectrum descriptor
has_obo_namespace: NMR
id: NMR:1002014

Axiom
annotated source: binned spectrum descriptor
annotated property: definition
annotated target: A bin for a spectrum.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: binned spectrum descriptor
annotated property: database_cross_reference
annotated target: value-type:xsd:string

bin label
type: Class
subclass of: binned spectrum descriptor
definition: Bin label.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1002015

Axiom
annotated source: bin label
annotated property: definition
annotated target: Bin label.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: bin label
annotated property: database_cross_reference
annotated target: value-type:xsd:string

bin start
type: Class
subclass of: binned spectrum descriptor
definition: Bin start.
database_cross_reference: value-type:xsd:decimal
has_obo_namespace: NMR
id: NMR:1002016

Axiom
annotated source: bin start
annotated property: definition
annotated target: Bin start.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: bin start
annotated property: database_cross_reference
annotated target: value-type:xsd:decimal

bin end
type: Class
subclass of: binned spectrum descriptor
definition: Bin end.
database_cross_reference: value-type:xsd:decimal
has_obo_namespace: NMR
id: NMR:1002017

Axiom
annotated source: bin end
annotated property: definition
annotated target: Bin end.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: bin end
annotated property: database_cross_reference
annotated target: value-type:xsd:decimal

bin area
type: Class
subclass of: binned spectrum descriptor
definition: Bin area.
database_cross_reference: value-type:xsd:decimal
has_obo_namespace: NMR
id: NMR:1002018

Axiom
annotated source: bin area
annotated property: definition
annotated target: Bin area.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: bin area
annotated property: database_cross_reference
annotated target: value-type:xsd:decimal

assigned chemical compound name
type: Class
subclass of: binned spectrum descriptor
definition: Name of metabolite.
database_cross_reference: value-type:xsd:string
has_obo_namespace: NMR
id: NMR:1002020

Axiom
annotated source: assigned chemical compound name
annotated property: definition
annotated target: Name of metabolite.
database_cross_reference: MSI:NMR

The allowed value-type for this CV term.
type: Axiom
annotated source: assigned chemical compound name
annotated property: database_cross_reference
annotated target: value-type:xsd:string

assigned chemical compound concentration
type: Class
subclass of: binned spectrum descriptor
database_cross_reference: value-type:xsd:decimal
has_obo_namespace: NMR
id: NMR:1002021

The allowed value-type for this CV term.
type: Axiom
annotated source: assigned chemical compound concentration
annotated property: database_cross_reference
annotated target: value-type:xsd:decimal

Hilbert transformation based scaling
type: Class
subclass of: scaling

optional part of NMR instrument
type: Class
subclass of: instrument
comment: 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...
version info: TODO: Discuss "obligatory_part_of".

autosampler
type: Class
subclass of: optional part of NMR instrument
comment: 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.

multiplicity feature
type: Class
subclass of: peak feature
IAO_0000119: http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm
has_exact_synonym: multiplicity

projected spectrum
type: Class
subclass of: NMR spectrum by processing step
comment: 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

bucketed spectrum
type: Class
subclass of: NMR spectrum by processing step
has_exact_synonym: binned spectrum
comment: 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.
version info: TODO: has spectral post processing parameter

peak-picked spectrum
type: Class
subclass of: NMR spectrum by processing step
comment: defneed
version info: TODO: has spectral post processing parameter.

cardinal part of NMR instrument
type: Class
subclass of: instrument
comment: 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

acquisition computer
type: Class
subclass of: cardinal part of NMR instrument
comment: 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.

NMR probe
type: Class
subclass of: cardinal part of NMR instrument
comment: 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.

console
type: Class
subclass of: cardinal part of NMR instrument
comment: def: A component of an NMR instrument that controls the activities of the other components.
version info: TODO: same as or part of acquisition computer?

number of acquisition data points
type: Class
subclass of: NMR acquisition parameter
comment: tempdef: The number of data points in a data set.

hadamard frequency
type: Class
subclass of: NMR acquisition parameter
comment: def: A frequency used during Hadamard encoding.

projection axis
type: Class
subclass of: NMR acquisition parameter
comment: def: The axis onto which the spectrum was projected.

ninety degree pulse duration
type: Class
subclass of: pulse parameter
has_exact_synonym: 90 degree pulse duration
definition: The duration of the excitation pulse needed to rotate the magnetisation vector by 90 degrees.

dwell time
type: Class
subclass of: NMR acquisition parameter
comment: def: A digital sampling interval. alsprcls: time interval

sample temperature in autosampler
type: Class
subclass of: sample temperature information
comment: def: The temperature of an item of analysis material whilst in an autosampler.

sample temperature in magnet
type: Class
subclass of: sample temperature information
comment: def: The temperature of an NMR sample whilst in the magnet of an NMR instrument.

irradiation frequency
type: Class
subclass of: NMR acquisition parameter
comment: def: The frequency of the RF radiation used to irradiate an NMR sample.

field strength
type: Class
subclass of: NMR acquisition parameter
comment: def: The intensity of an electric, magnetic, or other field.

spinning rate
type: Class
subclass of: NMR acquisition parameter
comment: def: The rate at which an item of analysis material is spun.

decoupled nucleus flag
type: Class
subclass of: NMR acquisition parameter
comment: def: An indication of whether the nucleus being studied is the acquitsition nucleus.

buffer information
type: Class
subclass of: sample attribute
comment: def: A compound added to a sample to alter its pH value.

calibration compound
type: Class
subclass of: chemical compound
has_exact_synonym: reference compound
has_exact_synonym: reference standard
comment: def: The compound that produced the peak used to reference a spectrum during data pre-processing.

chemical shift standard
type: Class
subclass of: calibration compound
source: http://www.nmrnotes.org/NMRPages/refcomps.html
bug-database: https://github.com/nmrML/nmrML/issues/31
bug-database: https://github.com/nmrML/nmrML/issues/33
has_exact_synonym: chemical shift reference compound
comment: 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 check compound signal
type: Class
subclass of: NMR quality check parameter set
comment: def: The compound that produced a peak that is measured to assess the quality of a data set.

NMR pulse sequence
type: Class
subclass of: pulse parameter
source: http://www.bmrb.wisc.edu/tools/choose_pulse_info.php
bug-database: https://github.com/nmrML/nmrML/issues/40
comment: def: A sequence of excitation pulses.
editorial note: May later import from http://purl.obolibrary.org/obo/CHMO_0001841
editorial note: See also http://www.jcamp-dx.org/protocols/NMR%20Pulse%20Sequences%20PAC%2079(11)%20pp1748-1764%202001.pdf

frequency domain data processing
type: Class
subclass of: NMR data processing
has_exact_synonym: nmr-spectrum data processing
has_exact_synonym: post-FT data processing
comment: def: Automatic or manual procedures performed upon pre-processed NMR data sets that aim to summarise them or annotate them with speculative values.

time domain data processing
type: Class
subclass of: NMR data processing
has_exact_synonym: pre-FT data processing
comment: def: The post acquisition process of producing or refining a spectrum from raw data. defprov: Daniel Schober

NMR data processing
type: Class
subclass of: data transformation
comment: def: A data transformation that converts an NMR input data set into an output data set in a tracable and useful manner.

non-fourier FID transformation
type: Class
subclass of: time domain data processing
comment: tempdef: A non FT based method for converting from the time to the frequency domain.
version info: TODO:Exclusion guided definition.

data encoding
type: Class
subclass of: NMR data processing
bug-database: https://github.com/nmrML/nmrML/issues/37
comment: tempdef: A data processing which alteres a data file for a specific purpose. defprov: Daniel Schober

G matrix fourier transform projection
type: Class
subclass of: spectral projection
comment: 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

time proportional phase incrementation
type: Class
subclass of: data encoding
comment: defneed synonym: TPPI

states-time proportional phase incrementation
type: Class
subclass of: data encoding
comment: def: A method for quadrature detection. synonym: S-TPPI

Hadamard encoding
type: Class
subclass of: data encoding
comment: defneed

Frydman encoding
type: Class
subclass of: data encoding
source: http://www.magnet.fsu.edu/library/publications/NHMFL_Publication-6859.pdf
comment: defneed

echo anti-echo coherence selection
type: Class
subclass of: quadrature detection
comment: defneed

NMR instrument
type: Class
subclass of: instrument
comment: def: An Instrument which is used to carry out a NMR analysis of some sample. synonym: NMR instrument

NMR instrument acquisition parameter set
type: Class
subclass of: NMR instrument parameter set
comment: 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

data transformation
type: Class
subclass of: process
has broad synonym: method
comment: defneed
version info: altspcls: process ???

normalisation
type: Class
subclass of: scaling
IAO_0000117: Philippe Rocca Serra
IAO_0000119: http://pubs.acs.org/doi/pdf/10.1021/ac0519312 10.1021/ac0519312 Scaling and Normalization Effects in NMR Spectroscopic Metabonomic Data Sets Andrew Craig , Olivier Cloarec , Elaine Holmes , Jeremy K. Nicholson , and John C. Lindon * Biological Chemistry, Faculty of Natural Sciences, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ U.K.
IAO_0000119: http://stats.stackexchange.com/questions/35591/normalization-vs-scaling
definition: normalization is a data transformation process which aims at making data seem roughly normally distributied by applying a mathematical function, which is most of time a continuous function. This is a row operation that is applied to the data from each sample and comprises methods to make the data from all samples directly comparable with each other. A common use is to remove or minimize the effects of variable dilution of the samples.

pre-acquisition water suppression
type: Class
subclass of: pre-acquisition solvent suppression
comment: tempdef: A technique used to suppress the water resonance 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

window function for apodization
type: Class
subclass of: parameter
definition: A function applied to a FID to increase the signal-to-noise ratio or the resolution.
source: http://www.uwyo.edu/wheelernmr/nmr/window_functions.pdf
bug-database: https://github.com/nmrML/nmrML/issues/39
bug-database: https://github.com/nmrML/nmrML/issues/67
has_exact_synonym: apodization function

exponential multiplication window function
type: Class
subclass of: window function for apodization
definition: The exponential function used to multiply a FID by to produce a desitred amount of line broadening.
has_exact_synonym: exponential apodization
comment: Functional form: em(x_i) = exp(-pi*i*lb) Parameters: * data Array of spectral data. * lp Exponential line broadening. * inv Set True for inverse apodization.

Gaussian window function
type: Class
subclass of: window function for apodization
has_exact_synonym: gaussian broadening
comment: defneed

sine window function
type: Class
subclass of: window function for apodization
has_exact_synonym: sine
has_exact_synonym: sine bell window function
comment: defneed

sine squared window
type: Class
subclass of: sine window function
has_exact_synonym: QSINE
comment: defneed

spectral denoising
type: Class
subclass of: frequency domain data processing
comment: def: A method for eliminating or reducing the noise in a spectrum.

baseline correction
type: Class
subclass of: frequency domain data processing
comment: def: A method of flattening the baseline of a spectrum.

spectral projection
type: Class
subclass of: data encoding
comment: A method of spectral projection.

maximum intensity projection
type: Class
subclass of: spectral projection
comment: defneed

summation projection
type: Class
subclass of: spectral projection
comment: 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.

zero order phase correction
type: Class
subclass of: phase correction
comment: 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.

first order phase correction
type: Class
subclass of: phase correction
comment: defneed

symmetrisation
type: Class
subclass of: frequency domain data processing
comment: defneed

acquisition nucleus
type: Class
subclass of: object
comment: 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.

quality check peak feature
type: Class
subclass of: NMR quality check parameter set
comment: def: A feature of a peak that is measured to assess the quality of a data set.

number of scans
type: Class
subclass of: NMR acquisition parameter
comment: def: The number of repeat scans performed and summed to create the data set for an NMR sample.

number of steady state scans
type: Class
subclass of: number of scans
comment: 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.

atom environment encoding
type: Class
subclass of: NMR acquisition parameter
comment: def: A scheme for producing a numerical representation of the environment of an atom.

relaxation delay
type: Class
subclass of: NMR acquisition parameter
comment: def: The delay between repeat scans to allow nuclei to relax back to their steady state.

x-axis unit
type: Class
subclass of: 1D spectrum coordinate system descriptor
comment: 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).

y-axis unit
type: Class
subclass of: 1D spectrum coordinate system descriptor
comment: defneed

additional axis unit
type: Class
subclass of: parameter
comment: def: The unit of measurement of the second dimension of a 2D NMR dataset.

x start value
type: Class
subclass of: 1D spectrum coordinate system descriptor
comment: 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.

x end value
type: Class
subclass of: NMR data pre-processing parameter set
comment: 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.

window function parameter
type: Class
subclass of: parameter
comment: def: A parameter to a window function.

line broadening
type: Class
subclass of: apodization
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: http://www.chem.wisc.edu/areas/reich/nmr/08-tech-01-relax.htm. Hans J. Reich 2015, University of Wisconsin
comment: defneed
definition: line broadening is a process resulting in spectral peak signal becoming hard to interpret and analysed. Line broadening is affected by spin-spin relaxation and/or spin-lattice relaxation processes. When relaxation is very fast, NMR lines are broad, J-coupling may not be resolved or the signal may even be difficult or impossible to detect. The maximum repetition rate during acquisition of an NMR signal is governed by T1 - short T1 means the magnetization recovers more rapidly, and a spectrum can be acquired in less time. Line broadening may be caused by: Sample inhomogeneity (poor mixing. solid particles), Temperature gradients across sample, Paramagnetic impurities.

line sharpening
type: Class
subclass of: apodization
IAO_0000117: Philippe Rocca-Serra
IAO_0000119: http://www.chem.wisc.edu/areas/reich/nmr/08-tech-01-relax.htm. Hans J. Reich 2015, University of Wisconsin
comment: defneed
definition: line sharpening is a data transformation process inverse to that of line broadening, which aims to improve the quality of the signal being acquired and being analyzed in order to obtain clear, sharp peaks, in turn making interpretation easier. Line sharpening can be optimized during data acquisition or performed during data analysis by applied digital processing and filtering.

parameter
type: Class
subclass of: generically dependent continuant
comment: defneed

NMR spectral projection parameter set
type: Class
subclass of: NMR data post-processing parameter set
comment: 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

NMR data post-processing parameter set
type: Class
subclass of: data processing parameter
comment: 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
version info: TODO: altsprcls: process, not clear wether set is plural (list) or process.

NMR quality check parameter set
type: Class
subclass of: NMR data post-processing parameter set
comment: 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

post-acquisition water suppression
type: Class
subclass of: post-acquisition solvent suppression
has_exact_synonym: excitation sculpting
comment: tempdef: A data processing technique used to suppress the water peak in a spectrum in order to get clearer results. defprov: Daniel Schober

hankel singular value decomposition
type: Class
subclass of: post-acquisition water suppression
comment: 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

convolution
type: Class
subclass of: post-acquisition water suppression
comment: defneed

polynomial fitting
type: Class
subclass of: post-acquisition water suppression
comment: defneed

WaveWat
type: Class
subclass of: post-acquisition water suppression
comment: def: A computational method that archieves water suppression via wavlet multi resolution analysis.

NMR data pre-processing parameter set
type: Class
subclass of: data processing parameter
comment: defneed synonym: NMR data pre-processing parameter set

NMR quality check
type: Class
subclass of: data transformation
comment: def: The process of ensuring the quality of the raw data that results from an NMR analysis. synonym: NMR quality check

reference
type: Class
subclass of: generically dependent continuant
comment: 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.

FID file
type: Class
subclass of: data file
has_exact_synonym: FID file reference
comment: def: A reference to a file containing the raw FID. synonym: FID file reference

pulse sequence literature reference
type: Class
subclass of: external reference identifier
comment: def: A reference to a description of a pulse sequence in the literature.

shaped pulse file
type: Class
subclass of: pulse sequence file
comment: def: A reference to a file containing a specfication of the shape of an excitation pulse.

pulse sequence file
type: Class
subclass of: data file
comment: def: A reference to a file containing a specification of a pulse sequence.

processing parameter file
type: Class
subclass of: data file
comment: def: A reference to a file of data pre-processing parameters produced by the machine.

NMR sample identifier
type: Class
subclass of: external reference identifier
comment: PRS: rename 'reference' to 'identifier'
comment: def: A reference to information on the provenance of the NMR sample. synonym: NMR sample reference

NMR quality check descriptor
type: Class
subclass of: NMR spectrum descriptor
comment: def: A result of an NMR quality check. synonym: NMR quality check result

NMR sample
type: Class
subclass of: sample
comment: 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

sample introduction parameter
type: Class
subclass of: sample attribute
comment: tempdef: A sample introduction parameter is a parameter that describes the particular method of introducing the sample under investigation into the NMR instrument.

magic angle spinning rotor
type: Class
subclass of: sample introduction parameter
comment: defneed synonym: MAS rotor

flow probe
type: Class
subclass of: sample introduction parameter
comment: defneed

NMR sample tube
type: Class
subclass of: cardinal part of NMR instrument
definition: The sample-tube holds the NMR sample and sits in the NMR probe. It is usually a glass tube of 5-20mm diameter.
source: http://en.wikipedia.org/wiki/NMR_tube
bug-database: https://github.com/nmrML/nmrML/issues/54
has_exact_synonym: sample tube
comment: sortal dimensions are Vendor, Size (Diameter, length), Material (glass, quarz, pyrex ...), Frequency, Concentricity, OD and ID

spectrum pre-processing software
type: Class
subclass of: NMR software
comment: def: A software artifact used during data pre-processing.

spectrum post-processing software
type: Class
subclass of: NMR software
comment: def: A software artifact used during spectral post-processing.

peak picking
type: Class
subclass of: peak processing
comment: defneed

bucketing
type: Class
subclass of: peak processing
has_exact_synonym: binning
comment: 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.
comment: for bucket parameters see 'binned spectrum descriptor'

presat pulse sequence
type: Class
subclass of: NMR pulse sequence
has_exact_synonym: presaturation of the solvent resonance
comment: defneed synonym: presaturation

water suppression enhanced through T1 effects
type: Class
subclass of: NMR pulse sequence
comment: 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
alternative label: WET

nuclear overhauser and exchange spectroscopy-presat
type: Class
subclass of: presat pulse sequence
has_exact_synonym: NOESY presat
comment: 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

watergate
type: Class
subclass of: NMR pulse sequence
comment: defneed

coherence pathway rejection
type: Class
subclass of: pre-acquisition water suppression
comment: 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

flip-back watergate
type: Class
subclass of: watergate
comment: defneed

jump and return pulse sequence
type: Class
subclass of: NMR pulse sequence
comment: tempdef: A jump and return pulse sequence method is a water suppression method that uses a defined pulse sequence to make fast exchanging protons visible.

jump and return 1-1
type: Class
subclass of: jump and return pulse sequence
comment: 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 1-3-3-1
type: Class
subclass of: jump and return pulse sequence
comment: 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).

1D spectrum
type: Class
subclass of: NMR spectrum by dimensionality
comment: defneed synonym: 1D spectrum

2D spectrum
type: Class
subclass of: NMR spectrum by dimensionality
comment: defneed synonym: 2D spectrum

1D NMR acquisition parameter set
type: Class
subclass of: NMR instrument acquisition parameter set
comment: defneed synonym: 1D NMR acquisition parameter set

2D NMR acquisition parameter set
type: Class
subclass of: NMR instrument acquisition parameter set
comment: defneed synonym: 2D NMR acquisition parameter set

carr purcell meiboom gill pulse sequence
type: Class
subclass of: 1D pulse sequence
comment: 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
alternative label: CPMG

total correlation spectroscopy pulse sequence
type: Class
subclass of: 2D pulse sequence
has_exact_synonym: TCOSY pulse sequence
comment: 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 pulse sequence

1D pulse sequence
type: Class
subclass of: NMR pulse sequence
comment: def: One dimensional (referring to a FID, pre-processed spectrum, or post-processed spectrum). synonym: 1D

J-resolved pulse sequence
type: Class
subclass of: 2D pulse sequence
comment: tempdef: In 1D 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

hadamard total correlation spectroscopy pulse sequence
type: Class
subclass of: 2D pulse sequence
comment: defneed synonym: 2D hadamard TOCSY

diffusion edited pulse sequence
type: Class
subclass of: 1D pulse sequence
comment: defneed synonym: 1D diffusion edited

NMR magnet
type: Class
subclass of: cardinal part of NMR instrument
comment: 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.

Bruker NMR magnet
type: Class
subclass of: NMR magnet
comment: defneed

UltraShield
type: Class
subclass of: Bruker NMR magnet
comment: defneed

Ultrastabilized
type: Class
subclass of: Bruker NMR magnet

US 2
type: Class
subclass of: Bruker NMR magnet
version info: ??? How to model "hoch 2"?

UltraShield Plus
type: Class
subclass of: Bruker NMR magnet

Bruker CryoProbe
type: Class
subclass of: cryoprobe
subclass of: Bruker NMR probe
comment: 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

high resolution magic angle spin probe
type: Class
subclass of: high resolution probe
comment: 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

solid magic angle spinning probe
type: Class
subclass of: Bruker NMR probe
comment: 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

1mm MicroProbe
type: Class
subclass of: Bruker NMR probe
comment: 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

flow high resolution probe
type: Class
subclass of: high resolution probe
comment: 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

NMR instrument parameter set
type: Class
subclass of: parameter
comment: defneed

AVANCE II spectrometer
type: Class
subclass of: Bruker NMR instrument
comment: defneed
version info: TODO: May need no definition

Bruker NMR instrument
type: Class
subclass of: NMR instrument
comment: defneed

Metabolic Profiler instrument
type: Class
subclass of: Bruker NMR instrument
comment: For metabolism studies, and analysis of complex mixtures.

Hyphenated NMR instrument
type: Class
subclass of: NMR instrument type
comment: NMR Instruments using hyphenated analytical techniques combining mass spectrometry and chromatograph.

Capillary LC-NMR
type: Class
subclass of: Bruker NMR instrument

NMR Case
type: Class
subclass of: Bruker autosampler
comment: 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 tube washing system
type: Class
subclass of: optional part of NMR instrument
comment: defneed

Bruker AutoClean
type: Class
subclass of: NMR tube washing system
comment: 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 BEST NMR
type: Class
subclass of: Bruker autosampler
comment: 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

SampleRail
type: Class
subclass of: autosampler
comment: 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

SampleJet
type: Class
subclass of: Bruker autosampler
comment: 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

Bruker autosampler
type: Class
subclass of: autosampler
comment: defneed

B-ACS
type: Class
subclass of: Bruker autosampler
comment: 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

Bruker MATCH
type: Class
subclass of: NMR sample holder
comment: 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

NMR sample holder
type: Class
subclass of: cardinal part of NMR instrument
comment: def: A NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the NMR sample.

NMR software
type: Class
subclass of: software
comment: defneed

Bruker NMR software
type: Class
subclass of: commercial NMR software
comment: defneed
version info: TODO: May need no definition.

Bruker TopSpin software
type: Class
subclass of: Bruker NMR software

SampleTrack software
type: Class
subclass of: Bruker NMR software

Paravision software
type: Class
subclass of: Bruker NMR software

AURELIA software
type: Class
subclass of: Bruker NMR software

AUREMOL software
type: Class
subclass of: Bruker NMR software

AMIX VIEWER & AMIX-TOOLS
type: Class
subclass of: Bruker NMR software

high resolution probe
type: Class
subclass of: Bruker NMR probe
comment: 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

high resolution probe with ATM
type: Class
subclass of: high resolution probe
comment: 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 probe with ATM

micro imaging probe
type: Class
subclass of: Bruker NMR probe
comment: defneed

JEOL NMR instrument
type: Class
subclass of: NMR instrument

JNM-ECX Series FT NMR instrument
type: Class
subclass of: JEOL NMR instrument
definition: The JNM-ECX series is an FT NMR spectrometer developed making full use of the latest digital and high frequency technology. This high performance, sophisticated spectrometer designed to take advantage of high field magnet development to include 1GHz. Innovative features to support not only the conventional NMR applications such as structural analysis of molecules and evaluation of materials but also future progress of science and technologies including research for development of new drugs, postgenome research and development of new materials.

JNM-ECA Series FT NMR instrument
type: Class
subclass of: JEOL NMR instrument
definition: The JNM-ECA series is an FT NMR spectrometer developed making full use of the latest digital and high frequency technology. This high performance, sophisticated spectrometer designed to take advantage of high field magnet development to include 1GHz. Innovative features to support not only the conventional NMR applications such as structural analysis of molecules and evaluation of materials but also future progress of science and technologies including research for development of new drugs, postgenome research and development of new materials.

JEOL NMR software
type: Class
subclass of: commercial NMR software

Delta NMR software
type: Class
subclass of: JEOL NMR software

Bruker NMR probe
type: Class
subclass of: NMR probe
comment: https://www.bruker.com/products/mr/nmr/probes/probes.html

JEOL NMR probe
type: Class
subclass of: NMR probe
comment: defneed

CapNMR probe
type: Class
subclass of: JEOL NMR probe

Varian NMR instrument
type: Class
subclass of: NMR instrument

Varian MERCURY
type: Class
subclass of: Varian NMR instrument

Varian INOVA
type: Class
subclass of: Varian NMR instrument

Varian UNITY
type: Class
subclass of: Varian NMR instrument

Varian VXR
type: Class
subclass of: Varian NMR instrument

Varian GEMINI
type: Class
subclass of: Varian NMR instrument

AMX instrument
type: Class
subclass of: Bruker NMR instrument

AC instrument
type: Class
subclass of: Bruker NMR instrument

liquid NMR probe
type: Class
subclass of: NMR probe

solid NMR probe
type: Class
subclass of: NMR probe
comment: defneed

NMR imaging probe
type: Class
subclass of: NMR probe
comment: defneed

tecmag console
type: Class
subclass of: console

DISCOVERY console
type: Class
subclass of: tecmag console
comment: 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

tecmag EAGLE probe
type: Class
subclass of: solid NMR probe
comment: 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

APOLLO console
type: Class
subclass of: tecmag console
comment: defneed

tecmag NMR instrument
type: Class
subclass of: NMR instrument

CAT
type: Class
subclass of: tecmag NMR instrument

magnetic field strength
type: Class
subclass of: field strength
comment: defneed

vendor
type: Class
subclass of: contact role
comment: defneed
version info: TODO: Belongs in Ref Ontol.

NMR instrument manufacturer
type: Class
subclass of: instrument attribute
comment: A manufacturer that produces (and eventually sells) NMR instruments.

Bruker
type: Class
subclass of: NMR instrument manufacturer
comment: defneed
version info: TODO: May not need definition due to its instance character.

Varian
type: Class
subclass of: NMR instrument manufacturer

JEOL
type: Class
subclass of: NMR instrument manufacturer

MR Resources
type: Class
subclass of: NMR instrument manufacturer

tecmag
type: Class
subclass of: NMR instrument manufacturer

sample temperature information
type: Class
subclass of: sample attribute
comment: 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.

Doty Scientific
type: Class
subclass of: NMR instrument manufacturer

Wilmad
type: Class
subclass of: NMR instrument manufacturer

JS Research
type: Class
subclass of: NMR instrument manufacturer

data file
type: Class
subclass of: generically dependent continuant
alternative label: file
definition: Any data file as generated by some acquisition computer or console.
editorial note: This is a class annotation exemplifying skos usage. We assume the rdfs:label to capture the skos:preferedLabel.
example: an FID raw data file
scope note: In the NMR case a file generated by an NMR acquisition computer, console or NMR processing software.

Acorn NMR Inc
type: Class
subclass of: NMR instrument manufacturer

liquid chromatography NMR
type: Class
subclass of: Hyphenated NMR instrument
has_exact_synonym: LC NMR

LC MS NMR
type: Class
subclass of: liquid chromatography NMR
comment: Includes the connection to a high-resolution TOF-LC-MS system.

solid phase extraction NMR
type: Class
subclass of: NMR instrument type
has_exact_synonym: SPE NMR
comment: A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE™ NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra.

Capillary LC-NMR
type: Class
subclass of: liquid chromatography NMR
comment: Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume.

direct detection probe
type: Class
subclass of: NMR probe

indirect detection probe
type: Class
subclass of: NMR probe

continuous wave NMR
type: Class
subclass of: NMR instrument type
comment: Continuous wave NMR spectrometers are similar in principle to optical spectrometers. The sample is held in a strong magnetic field, and the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned). Defprov: http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm

fourier transformation NMR instrument
type: Class
subclass of: NMR instrument type
comment: In FT-NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation. Defprov: http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm

NMR software data format
type: Class
subclass of: data file format

ChemMagnetics format
type: Class
subclass of: NMR software data format

GE Omega format
type: Class
subclass of: NMR software data format

JEOL Lambda format
type: Class
subclass of: NMR software data format

JEOL Alpha format
type: Class
subclass of: NMR software data format

Jeol Delta format
type: Class
subclass of: NMR software data format

JEOL generic format
type: Class
subclass of: NMR software data format

JEOL AL95 format
type: Class
subclass of: NMR software data format

JEOL EX format
type: Class
subclass of: NMR software data format

TecMag format
type: Class
subclass of: NMR software data format

Varian VNMR format
type: Class
subclass of: NMR software data format

Galactic format
type: Class
subclass of: NMR software data format

Felix format
type: Class
subclass of: NMR software data format

JCAMP DX format
type: Class
subclass of: NMR software data format

Lybrics format
type: Class
subclass of: NMR software data format

Nuts format
type: Class
subclass of: NMR software data format

MACNMR format
type: Class
subclass of: NMR software data format

Nicolet GE/QE-300 format
type: Class
subclass of: NMR software data format

multiplet feature
type: Class
subclass of: multiplicity feature
has_exact_synonym: m
comment: J-coupler

ThermoMattson
type: Class
subclass of: NMR instrument manufacturer

FOSS
type: Class
subclass of: NMR instrument manufacturer

Jasco
type: Class
subclass of: NMR instrument manufacturer

Agilent Technologies
type: Class
subclass of: NMR instrument manufacturer

micromass
type: Class
subclass of: NMR instrument manufacturer

Waters
type: Class
subclass of: NMR instrument manufacturer

ThermoNicolet
type: Class
subclass of: NMR instrument manufacturer

Perkin Elmer
type: Class
subclass of: NMR instrument manufacturer

OceanOptics
type: Class
subclass of: NMR instrument manufacturer

ThermoFinnigan
type: Class
subclass of: NMR instrument manufacturer

Applied Biosystems
type: Class
subclass of: NMR instrument manufacturer

TX
type: Class
subclass of: NMR instrument manufacturer

Net CDF format
type: Class
subclass of: NMR software data format

Bruker DISNMR format
type: Class
subclass of: NMR software data format

Bruker UXNMR/XWIN-NMR format
type: Class
subclass of: NMR software data format

Bruker WIN NMR format
type: Class
subclass of: NMR software data format

acdlabs
type: Class
subclass of: NMR instrument manufacturer