en
http://nmrml.org/examples/
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.
BFO 2 Reference: BFO does not claim to provide complete coverage of entities of all types. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning - coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation.
BFO 2 Reference: BFO's treatment of continuants and occurrents - as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality - earlier called the 'SNAP' and 'SPAN' perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science.
BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. 'Entity' is an example of a primitive term. Primitive terms in a highest-level ontology such as BFO are terms that are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms.
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
solvent suppression method-->solvent suppression method
encoding scheme (Quadrature detection method)-->encoding method
window function parameter-->window function parameter
CVParamWithUnitType occurrences:
CVParamWithUnitType is currently not used in the xsd and dangling ! I assume ValueWithUnitType substitutes it ?
UserParamType occurrences:
No CV terms needed
ValueWithUnitType occurrences:
These will have to be used from the Unit ontology.
Alan Ruttenberg
Albert Goldfain
Annick Moing
Barry Smith
Bill Duncan
Bjoern Peters
Catherine Deborde
Chris Mungall
Daniel Jacob
Daniel Schober
David Osumi-Sutherland
Fabian Neuhaus
Holger Stenzhorn
James A. Overton
Janna Hastings
Jie Zheng
Jonathan Bona
Joseph Cruz
Larry Hunter
Leonard Jacuzzo
Ludger Jansen
Mark Ressler
Mathias Brochhausen
Mauricio Almeida
Melanie Courtot
Michael Wilson
Philippe Rocca-Serra
Pierre Grenon
Randall Dipert
Reza Salek
Ron Rudnicki
Selja Seppälä
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, Antonio; Klein, Matthias; Lewis, Ian; Luchinat, Claudio; Jones, Andrew; Grauslys, Arturas; Larralde, Martin; Yokochi, Masashi; Kobayashi, Naohiro; Porzel, Andrea; Griffin, Julian; Viant, Mark; Wishart, David; Steinbeck, Christoph; Salek, Reza; Neumann, Steffen
Stefan Schulz
Steffen Neumann
Thomas Bittner
Werner Ceusters
Yongqun "Oliver" He
Nuclear magnetic resonance (NMR) data annotation as required by the msi sanctioned open access nmrML XML format developed by the COSMOS EU project.
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).)
Creative Commons Public Domain Mark 1.0
nuclear magnetic resonance CV
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.
https://github.com/nmrML/nmrML/issues
Daniel Schober
https://github.com/nmrML/nmrML
https://github.com/nmrML/nmrML/tree/master/ontologies
https://groups.google.com/forum/?hl=en#!forum/nmrml/join
http://www.metabolomics-msi.org/
http://phenomenal-h2020.eu/home/
http://www.cosmos-fp7.eu/WP2
OBO-Edit 2.2
Daniel Schober
2017-10-19T10:11:26Z
1.2
dschober
Please see the project site https://github.com/BFO-ontology/BFO, the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel, the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx. This ontology is generated from a specification at https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/ and with the code that generates the OWL version in https://github.com/BFO-ontology/BFO/tree/master/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif.
The BSD license on the BFO project site refers to code used to build BFO.
This BFO 2.0 version represents a major update to BFO and is not strictly backwards compatible with BFO 1.1. The previous OWL version of BFO, version 1.1.1 will remain available at http://ifomis.org/bfo/1.1 and will no longer be updated. The BFO 2.0 OWL is a classes-only specification. The incorporation of core relations has been held over for a later version.
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.
http://www.metabolomicscentre.ca/nmrML/msi-nmr.obo
1.1.0
http://nmrml.org/cv/
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
Person:Alan Ruttenberg
Really of interest to developers only
BFO CLIF specification label
editor preferred term
example of usage
definition
definition
editor note
term editor
alternative term
definition source
curator note
imported from
elucidation
has associated axiom(nl)
has associated axiom(fol)
has axiom label
database_cross_reference
has_exact_synonym
has_obo_format_version
has_obo_namespace
BFO_0000001
entity
For 1r/1i spectra and for Bruker, this term describe an array of integers (32bits).
integer32
A reference number relevant to the sample under study.
value-type:xsd:string
NMR
NMR:1000001
sample number
NMR:1000001
A reference number relevant to the sample under study.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
For 1r/1i spectra and for Bruker, this term describe an array of longs (64bits).
long64
The chemical phase of a pure sample, or the state of a mixed sample.
NMR
NMR:1000003
sample state information
NMR:1000003
The chemical phase of a pure sample, or the state of a mixed sample.
MSI:NMR
Total mass of sample used.
value-type:xsd:float
NMR
NMR:1000004
sample mass information
NMR:1000004
Total mass of sample used.
MSI:NMR
value-type:xsd:float
The allowed value-type for this CV term.
Total volume of solution used.
value-type:xsd:float
NMR
NMR:1000005
sample volume
NMR:1000005
Total volume of solution used.
MSI:NMR
value-type:xsd:float
The allowed value-type for this CV term.
Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used.
value-type:xsd:float
NMR
NMR:1000006
sample concentration
NMR:1000006
Concentration of sample in picomol/ul, femtomol/ul or attomol/ul solution used.
MSI:NMR
value-type:xsd:float
The allowed value-type for this CV term.
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.
quadrature detection
contact role
data file attribute
NMR instrument type
1D spectrum coordinate system descriptor
pre-acquisition solvent suppression
peak processing
Hexafluorobenzene
CDCl3
Chloroform-d
CHEBI:41981
D2O
heavy water
sample pH
post buffer pH
Philippe Rocca-Serra
http://www.scs.illinois.edu/nmr/handouts/general_pdf/ugi034.pdf
apodization
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
http://www.metabolomicssociety.org/databases
PRS: rename 'reference' to 'identifier'
metabolomics database identifier
Metabolights identifier
acetonitrile
1,4-Dioxane
1H spectrum reference compound
DSS
2,2-Dimethyl-2-silapentane-5-sulfonate
sodium acetate
TMS
tetramethylsilane
13C spectrum reference compound
Instrument model name not including the vendor's name.
NMR
NMR:1000031
NMR instrument model
NMR:1000031
Instrument model name not including the vendor's name.
MSI:NMR
Free text description of a single customization made to the instrument; for several modifications, use several entries.
value-type:xsd:string
NMR
NMR:1000032
instrument customization
NMR:1000032
Free text description of a single customization made to the instrument; for several modifications, use several entries.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
Chloroform-d1
keyword
tetramethylammonium bromide
15N spectrum reference compound
ammonia (liquid)
ammonium bromide
1,4-morpholine
nitromethane
pyridine
sodium nitrate
solvent filtering
post-acquisition solvent suppression
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.
http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_decoupling
decoupling method
homonuclear decoupling
heteronuclear decoupling
State if the sample is in emulsion form.
NMR
NMR:1000047
emulsion
NMR:1000047
State if the sample is in emulsion form.
MSI:NMR
State if the sample is in gaseous form.
NMR
NMR:1000048
gas
NMR:1000048
State if the sample is in gaseous form.
MSI:NMR
State if the sample is in liquid form.
NMR
NMR:1000049
liquid
NMR:1000049
State if the sample is in liquid form.
MSI:NMR
State if the sample is in solid form.
NMR
NMR:1000050
solid
NMR:1000050
State if the sample is in solid form.
MSI:NMR
State if the sample is in solution form.
NMR
NMR:1000051
solution
NMR:1000051
State if the sample is in solution form.
MSI:NMR
State if the sample is in suspension form.
NMR
NMR:1000052
suspension
NMR:1000052
State if the sample is in suspension form.
MSI:NMR
Sample batch lot identifier.
value-type:xsd:string
NMR
NMR:1000053
sample batch information
NMR:1000053
Sample batch lot identifier.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
broad band decoupling
off resonance decoupling
band-selective decoupling
narowband decoupling
specific decoupling
angle of sinusoid
31P spectrum reference compound
H3PO4
phosphoric acid
P4
phosphorus
(CH3O)3PO
trimethyl phosphate
P(C6H5)3
triphenylphosphine
O=P(C6H5)3
triphenylphosphine oxide
co-dissolved internal reference
synthetic reference signal
residual solvent signal
FID zero filling
data extrapolation using linear prediction
multiplying FID by window function
FID fourier transformation
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.
phasing
spectral phasing
phase correction
peak integration
peak alignment
peak shape fitting
spectral referencing
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
TMSP
trimethylsilyl propanoic acid
sodium trimethylsilyl-propionate
used to be 'linear scaling algorithm'
linear scaling
used to be called 'scaling algorithm'
scaling
used to be postfixed with algorithm
non-linear scaling
total spectral area scaling
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.
probabilistic quotient normalization
glog scaling
scaling by generalized logarithmic transformation
pareto scaling
autoscaling
JRES spectrum
2D J-resolved spectrum
http://www.biomedcentral.com/1471-2105/12/366#B2
MetaboLab software
Metaboquant software
rNMR software
open source NMR software
commercial NMR software
Günther U, Ludwig C, Rüterjans H: NMRLAB - advanced NMR data processing in Matlab., J Magn Reson 2000, 145(2):201-208.
NMRLab software
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.
NMRPipe software
van Beek JD: matNMR: a flexible toolbox for processing, analyzing and visualizing magnetic resonance data in Matlab. J Magn Reson 2007, 187:19-26.
matNMR software
concentration of chemical compound
manual phase correction
automatic phase correction
DC offset correction
http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-366
Gibbs multiplication
skyline projection
shifted sine apodization
shifted sine window function
SINC
Sinc window multiplication
sinc window multiplication of FID (1D)
http://www.sciencedirect.com/science/article/pii/S0003267008000950
https://github.com/nmrML/nmrML/issues/36
combined sine-bell–exponential window function
SEM window function
TRAP
trapezoid apodization
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.
trapezoid window function
shifted gaussian window function
baseline correction using spline function
HSQC NMR spectrum
heteronuclear single quantum coherence spectrum
Zangger-Sterk pulse sequence
http://nmr.chemistry.manchester.ac.uk/?q=node/256
pure shift 1D Zangger-Sterk pulse sequence
http://nmr.chemistry.manchester.ac.uk/?q=node/264
oneshot pulse sequence
http://nmr.chemistry.manchester.ac.uk/?q=node/265
pure shift oneshot pulse sequence
http://nmr.chemistry.manchester.ac.uk/?q=node/285
PE Watergate pulse sequence
perfect echo watergate pulse sequence
NMR Star 3.1 file format
NMR Star 2.1 file format
three dimensional spectrum
3D spectrum
four dimensional spectrum
4D spectrum
NMR spectrum by dimensionality
homonuclear chemical shift spectrum
heteronuclear chemical shift spectrum
Bruker instrument model.
NMR
NMR:1000122
Bruker instrument model
NMR:1000122
Bruker instrument model.
MSI:NMR
homonuclear exchange spectroscopy spectrum
heteronuclear exchange spectroscopy spectrum
homonuclear J-resolved spectrum
heteronuclear J-resolved spectrum
calibration test spectrum
NMR star software
http://www.felixnmr.com/
Felix software
PIPP software
TALOS+ software
http://www.cyana.org/wiki/index.php/Main_Page
CYANA software
http://nmr.cit.nih.gov/xplor-nih/
XPLOR-NIH software
computed concentration
request these in UO ?
http://www.bpc.uni-frankfurt.de/guentert/wiki/index.php/XEASY
XEASY software
sparky software
http://nmr-software.blogspot.de/2007/04/cara.html
CARA software
Wattos software
MADNMR software
Pronto software
TRIAD NMR software
library based computed concentration
Lorenzian (-Integration) (Modeled Area) Estimated Concentration
https://docs.google.com/spreadsheets/d/1egsLQWoQuCxAYPr9MIo-F0A5K9RCbJSC8yWZyYq_fiQ/edit?usp=sharing
Lorenzian estimated concentration
Measured Area (Integration) based Concentration
measured area based concentration
time-domain amplitude computed concentration
group time delay compensation
http://nmr-analysis.blogspot.fr/2008/02/why-arent-bruker-fids-time-corrected.html
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
back calculation of first points by linear-prediction
scaling by mirror image linear prediction
digital filtering
Daniel Schober
http://jjhelmus.github.io/nmrglue/current/jbnmr_examples/s11_strip_plots.html
3D strip plot generation
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
JEOL instrument model
tecmag instrument model
Bao et al. (2013) A new automatic baseline correction method based on iterative method, J. Magn. Res. 218:35-43
Golotvin & Williams (2000), Improved baseline recognition and modeling of FT NMR spectra, J. Magn. Res. 146:122-125
automatic baseline recognition
TSP
Trimethylsilyl propionate
pulse sequence from Wishart lab library
TMIC lab pulse sequence
probe gradient strength
e.g. Linux or Windows, ...
NMR acquisition computer operating system
e.g. Bruker Biospin ICON-NMR
NMR autosampler software
Bruker Biospin ICON-NMR software
http://www.bruker.com/products/mr/nmr/nmr-software/software/iconnmr/overview.html
buffer pH
e.g. heavy water (D2O)
lock frequency
field frequency lock
quantitation standard
concentration standard
NMR acquisition software
CIMR MI standard
signal line width check
signal line width at five percent intensity check
NMR spectrum descriptor
pulse width
hard pulse width
spectrum width
sweep width
number of data points in spectrum
number of first dimension data points
number of data points
tempdef: The end value for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum.
x end value
y-axis type
bucket x center
center of bin on x-axis
NMR spectrum quantification method
spectral quantitation algorithm
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.
NMRProcFlow software
http://www.nmrprocflow.org/
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.
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.
Bayesil software
http://bayesil.ca/
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.
Uses JspectraView Software
nmrML Assign
http://nmrml.bayesil.ca/
d
doublet feature
t
triplet feature
q
quatruplet feature
a set of peaks that are highly correlated in a series of samples
a feature request by Daniel Jacob inserted at IBP hackathon
cluster of peaks across samples
simulated spectrum
pulse parameter
JEOL FID format
dd
doublet of doublets feature
ABX multiplet pattern
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.
http://www.chem.wisc.edu/areas/reich/nmr/05-hmr-12-abx.htm
s
singlet feature
qi
quintet feature
dt
doublet of triplets
td
triplet of douplets
tt
triplet of triplets
NMR spectrum by pulse sequence
NMR spectrum by processing step
2D spectrum coordinate system descriptor
y-axis value type
the subclasses come from the Rubtsov specification
power value type
magnitude value type
real value type
imaginary value type
complex value types
spectral projection axis
f1 axis
f2 axis
NMR Format converter
BML-NMR identifier
will be further specified via a concentration value
creatinine
2D pulse sequence
used to be labeled 'NMR spectrum simulation'
data simulation
DNP NMR
dynamic nuclear polarization enhanced NMR system
dynamic nuclear polarization NMR
Chemical shift is the resonance frequency of a nucleus related to a chemical shift standard. in ppm along x-axis
http://en.wikipedia.org/wiki/Chemical_shift
chemical shift
an information object that describes the strength of the NMR signal
nmr signal intensity
baseline correction using polynomial function
first transient of the tnnoesy-presaturation pulse sequence
Varian acquisition parameter file
procpar
acqus
Bruker acquisition parameter file
NMR
NMR:1000231
peak feature
NMR:1000231
global
Varian autosampler
Varian SMS 50
Varian probe
5mm HCN probe
Varian liquid cold probe
e.g as in HMDB
reference compound NMR spectrum
Mestrelab software
ACD spectrus software
Mat NMR 3 software
NMRLab software
Spinworks NMR software
NMR software vendor
Spinworks
iNMR software
NMR pipe
cule NMR software
Git: nmrML\tools\Parser_and_Converters\Matlab
By Batman/ Tim Ebbels Group
Matlab to nmrML converter
Bruker processing parameter file
procs
Varian processing parameter file
http://mmcd.nmrfam.wisc.edu/
PRS: rename 'identifyer' to 'identifier'
Madison Metabolomics Consortium Database MMCD identifier
http://bigg.ucsd.edu/
Bigg metabolomics database identifier
Lorentz-to-Gauss apodization
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.
Lorentz Gaussian window function
TRAF
Transform of Reverse Added FIDs
traf window function
A Window function described by Daniel Traficante in their original paper.
TRAFS
trafs window function
peak fitting
peak assignment
deconvolution
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.
chemical shift sorting
fid file
Varian FID file
Bruker FID file
Jacob D. et al (2013) Analytical and Bioanalytical Chemistry, 405, 5049-5061
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
ERVA-based bucketing
cluster of peaks
Match NMR tube
shaped tube
Shigemi tube
standard tube
Bruker tube
JEOL magnet
http://www.jeolusa.com/PRODUCTS/Nuclear-Magnetic-Resonance/Magnets
JEOL ECS magnet
JEOL ECA magnet
JEOL ECX magnet
Varian NMR software
VnmrJ software
Wilmad tube
4mm Match tube
2.5mm Match tube
3mm Match tube
5mm Match tube
1mm Match tube
1.7mm Match tube
2mm Match tube
4.25mm Match tube
3mm standard tube
5mm standard tube
1mm standard tube
1.7mm standard tube
Wilmad economy tube
Wilmad precision tube
Norell tube
JEOL FID file
Git: nmrML\tools\Parser_and_Converters\R
R statistics to nmrML. Developed by Steffen Neumann, IPB-Halle.de
nmRIO
Git: nmrML\tools\Parser_and_Converters\R\rNMR-IO
rNMR-IO
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.
Git: nmrML\tools\Parser_and_Converters\Java\converter
Developed by Daniel Jacob at INRA Bordeaux. The recommended converter for Bruker and Varian/Agilent vendor format conversion.
Vendor2nmrML_Java
Agilent magnet
Varian magnet
premium compact narrow bore magnet
premium shielded narrow bore magnet
premium shielded wide bore magnet
modified gaussian apodization
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.
modified Gaussian window function
exponentially damped J-modulation apodization
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
exponentially damped J-modulation window function
shifted sine-bell apodization
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.
shifted sine bell window function
triangle apodization
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.
triangle window function
The acquisition log file is a created during an acquisition and could useful for debugging an acquisition that has gone awry.
acquisition log file
Git: nmrML\tools\Parser_and_Converters\python
A Python based vendor to nmrML converter developed by MIchael Wilson at TMIC Edmonton.
PynmrML
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.
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
MetaboAnalyst software
www.metaboanalyst.ca
acqu2s
acqu3s
proc2s
proc3s
NMR spectrum file
Bruker NMR spectrum file
1R file
title file
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.
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
XEASY software
NMR spectrum vizualisation software
Used in NMR Assign tool for Baysil
JspectraView software
cryoprobe
inverse detection NMR probe
5mm inverse detection cryoprobe
Git: nmrML\tools\Visualizers\PMB_NMRviewer
Developed by Daniel Jacob, INRA Bordeaux
NMRViewer software
http://services.cbib.u-bordeaux2.fr/SPECNMR/examples
material processing
http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm
AB multiplet pattern
Use Chebi entities here.
NMR solvent
Use Chebi entities here.
NMR buffer
presat water suppression
Varian VNMRS 600
data content encoding
data compression scheme
byte format
zlib
complex64
This byte format uses a consecutive array of two 32bit float numbers to represent the real and imaginary part of the complex values.
complex128
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
http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm
AB2 multiplet pattern
data encoding parameter
uncompressed data
DSPFVS - DSP (Digital signal processing) firmware version corresponds to the version of the digital filter, a hardware component used by the spectrometer
DSPFVS
digital signal processing firmware version
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.
DECIM
decimation factor
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.")
GRPDLY
group time delay
NMR sampling strategy
a type of data acquisition parameter (when recording the FID) which can be continuous/uniform or sparse/non-uniform signal acquisition.
continuous sampling
uniform sampling
With uniform sampling, each sample is separated by the "dwell time".
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
http://link.springer.com/chapter/10.1007%2F1-4020-3910-7_142#page-1
sparse sampling
non-uniform sampling
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.
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
software attribute
NMR software version
http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm
ABX3 multiplet pattern
http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm
AA'BB' multiplet pattern
http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm
AA'XX' multiplet pattern
variable size bucketing
uniform bucketing
intelligent bucketing
bucket importing
put in as reqired by NMRProcFlow tool
bucket resetting
as needed for nmrProcFlow
global baseline correction
as needed for nmrProcFlow
local baseline correction
bucket fusioning
JNM-ECX Series FT NMR instrument
JNM-ECZR Series FT NMR instrument
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
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
NanoBay400 MHz
Fourier 300HD
DNP-NMR
LC-NMR instrument
LC-NMR/MS instrument
Food-Screener instrument
AVANCE IVDr
JEOL Resonance 400MHz YH magnet
JEOL Resonance 500MHz magnet
JEOL Resonance 600MHz magnet
JEOL Resonance 700MHz magnet
JEOL Resonance 800MHz magnet
single peak feature
NMR instrument vendor
Any organisation ort person that sells NMR instruments to customers.
Avance I spectrometer
Oxford Instruments
Spinlock SRL
General Electric
Kimble Chase
Phillips
Siemens AG
Varian Inova 500
Varian VNMRS instrument
Varian Mercury plus
Varian UnityInova instrument
Varian 400-MR NMR instrument
Varian DDR2 instrument
Agilent NMR instrument
Agilent 400-MR NMR instrument
Varian Mercury 400
Agilent Au 400 (DDR2 Console)
Agilent DDR 2 w/ HCN cryoprobe
BMRB identifier
TM1
0<TM1<1
left trapezoid limit
trapezoid window function parameter
complex64 Integer
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
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.
TM2
0<TM2<1
right trapezoid limit
30 degree pulse duration
thirty degree pulse duration
The duration of the excitation pulse needed to rotate the magnetisation vector by 30 degrees.
InChi
inchikey
WLN
Wiswesser Line Notation
ROSDAL
SLN-Tripos
smarts
line representation
2D topological molecule representation
2D bond line structure
3D geometrical molecule representation
3D bond line structure
CAS number
fingerprint model
molfile
compound similarity measure
Tanimoto similarity
Gaussian window function parameter
DSS
2,2-Dimethyl-2-silapentane-5-sulfonate
Gaussian maximum position
2H spectrum reference compound
ABX2 multiplet pattern
DRX 600 instrument
plot and graph generation
reference deconvolution
vertical alignment of on and offset of the peak of the reference compound.
spectral smoothing
the process of removing noisy jitters in a spectral curve to get clearer and more meaningful signals and peaks.
NMR database format
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)
BMRB/XML file format
nD spectrum
Terms used to describe types of data processing.
data processing
NMR
NMR:1000452
NMR data conversion
NMR:1000452
Terms used to describe types of data processing.
MSI:NMR
tempdef: A sample is a role that is played by an object of interest in an investigation used to obtain generalizable information about the sample source.
defprov: Daniel Schober
NMR
NMR:1000457
sample
NMR:1000457
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
MSI:NMR
Description of the instrument or the mass spectrometer.
instrument configuration
NMR
NMR:1000463
instrument
NMR:1000463
Description of the instrument or the mass spectrometer.
MSI:NMR
Varian instrument model.
NMR
NMR:1000489
Varian/Agilent instrument model
NMR:1000489
Varian instrument model.
MSI:NMR
Instrument properties that are associated with a value.
NMR
NMR:1000496
instrument attribute
NMR:1000496
Instrument properties that are associated with a value.
MSI:NMR
Describes the data content on the file.
NMR
NMR:1000524
data file content
NMR:1000524
Describes the data content on the file.
MSI:NMR
Serial Number of the instrument.
value-type:xsd:string
NMR
NMR:1000529
instrument serial number
NMR:1000529
Serial Number of the instrument.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
Conversion of one file format to another.
NMR
NMR:1000530
file format conversion
NMR:1000530
Conversion of one file format to another.
MSI:NMR
Software related to the recording or transformation of spectra.
NMR
NMR:1000531
software
NMR:1000531
Software related to the recording or transformation of spectra.
MSI:NMR
Object Attribute.
NMR
NMR:1000547
object attribute
NMR:1000547
Object Attribute.
MSI:NMR
Sample properties that are associated with a value.
NMR
NMR:1000548
sample attribute
NMR:1000548
Sample properties that are associated with a value.
MSI:NMR
Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data.
NMR
NMR:1000561
data file checksum type
NMR:1000561
Checksum is a form of redundancy check, a simple way to protect the integrity of data by detecting errors in data.
MSI:NMR
MD5 (Message-Digest algorithm 5) is a cryptographic hash function with a 128-bit hash value used to check the integrity of files.
value-type:xsd:string
NMR
NMR:1000568
MD5
NMR:1000568
MD5 (Message-Digest algorithm 5) is a cryptographic hash function with a 128-bit hash value used to check the integrity of files.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
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.
value-type:xsd:string
NMR
NMR:1000569
SHA-1
NMR:1000569
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.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
Describes the type of file and its content.
source file
NMR
NMR:1000577
NMR raw data file format
NMR:1000577
Describes the type of file and its content.
MSI:NMR
Details about a person or organization to contact in case of concern or discussion about the file.
NMR
NMR:1000585
contact attribute
NMR:1000585
Details about a person or organization to contact in case of concern or discussion about the file.
MSI:NMR
Name of the contact person or organization.
value-type:xsd:string
NMR
NMR:1000586
contact name
NMR:1000586
Name of the contact person or organization.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
Postal address of the contact person or organization.
value-type:xsd:string
NMR
NMR:1000587
contact address
NMR:1000587
Postal address of the contact person or organization.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
Uniform Resource Locator related to the contact person or organization.
value-type:xsd:string
NMR
NMR:1000588
contact URL
NMR:1000588
Uniform Resource Locator related to the contact person or organization.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
Email address of the contact person or organization.
value-type:xsd:string
NMR
NMR:1000589
contact email
NMR:1000589
Email address of the contact person or organization.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
Home institution of the contact person.
value-type:xsd:string
NMR
NMR:1000590
contact organization
NMR:1000590
Home institution of the contact person.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
Data processing parameter used in the data processing performed on the data file.
NMR
NMR:1000630
data processing parameter
NMR:1000630
Data processing parameter used in the data processing performed on the data file.
MSI:NMR
The time that a data processing action was finished.
value-type:xsd:date
NMR
NMR:1000747
data processing completion time
NMR:1000747
The time that a data processing action was finished.
MSI:NMR
value-type:xsd:date
The allowed value-type for this CV term.
Describes how the native spectrum identifiers are formated.
nativeID format
NMR
NMR:1000767
FID format
NMR:1000767
Describes how the native spectrum identifiers are formated.
MSI:NMR
file=xsd:IDREF.
NMR
NMR:1000773
The nativeID must be the same as the source file ID.
Bruker FID format
NMR:1000773
file=xsd:IDREF.
MSI:NMR
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.
value-type:xsd:string
NMR
NMR:1000799
custom unreleased software
NMR:1000799
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.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
Description of the preparation steps which took place before the measurement was performed.
NMR
NMR:1000831
sample preparation information
NMR:1000831
Description of the preparation steps which took place before the measurement was performed.
MSI:NMR
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.
NMR
NMR:1000859
molecule
NMR:1000859
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.
MSI:NMR
A compound of low molecular weight that is composed of two or more amino acids.
NMR
NMR:1000860
peptide
NMR:1000860
A compound of low molecular weight that is composed of two or more amino acids.
MSI:NMR
A describable property of a chemical compound.
NMR
NMR:1000861
chemical compound attribute
NMR:1000861
A describable property of a chemical compound.
MSI:NMR
The pH of a solution at which a charged molecule does not migrate in an electric field.
value-type:xsd:float
pI
NMR
NMR:1000862
isoelectric point
NMR:1000862
The pH of a solution at which a charged molecule does not migrate in an electric field.
MSI:NMR
value-type:xsd:float
The allowed value-type for this CV term.
The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm.
value-type:xsd:float
predicted pI
NMR
NMR:1000863
predicted isoelectric point
NMR:1000863
The pH of a solution at which a charged molecule would not migrate in an electric field, as predicted by a software algorithm.
MSI:NMR
value-type:xsd:float
The allowed value-type for this CV term.
A combination of symbols used to express the chemical composition of a compound.
NMR
NMR:1000864
chemical compound formula
NMR:1000864
A combination of symbols used to express the chemical composition of a compound.
MSI:NMR
A chemical formula which expresses the proportions of the elements present in a substance.
value-type:xsd:string
NMR
NMR:1000865
empirical formula
NMR:1000865
A chemical formula which expresses the proportions of the elements present in a substance.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked.
value-type:xsd:string
NMR
NMR:1000866
molecular formula
NMR:1000866
A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other.
value-type:xsd:string
NMR
NMR:1000867
structural formula
NMR:1000867
A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
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.
value-type:xsd:string
NMR
NMR:1000868
SMILES string
NMR:1000868
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.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
An identifier/accession number to an external reference database.
NMR
NMR:1000878
external reference identifier
NMR:1000878
An identifier/accession number to an external reference database.
MSI:NMR
A unique identifier for a publication in the PubMed database (MIR:00000015).
value-type:xsd:integer
NMR
NMR:1000879
PubMed identifier
NMR:1000879
A unique identifier for a publication in the PubMed database (MIR:00000015).
MSI:NMR
value-type:xsd:integer
The allowed value-type for this CV term.
A substance formed by chemical union of two or more elements or ingredients in definite proportion by weight.
NMR
NMR:1000881
Use Chebi entities here.
chemical compound
NMR:1000881
A substance formed by chemical union of two or more elements or ingredients in definite proportion by weight.
MSI:NMR
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.
NMR
NMR:1000882
protein
NMR:1000882
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.
MSI:NMR
A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN).
value-type:xsd:string
NMR
NMR:1000883
protein short name
NMR:1000883
A short name or symbol of a protein (e.g., HSF 1 or HSF1_HUMAN).
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
An nonphysical attribute describing a specific protein.
NMR
NMR:1000884
protein attribute
NMR:1000884
An nonphysical attribute describing a specific protein.
MSI:NMR
Accession number for a specific protein in a database.
value-type:xsd:string
NMR
NMR:1000885
protein accession
NMR:1000885
Accession number for a specific protein in a database.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
A long name describing the function of the protein.
value-type:xsd:string
NMR
NMR:1000886
protein name
NMR:1000886
A long name describing the function of the protein.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
An nonphysical attribute that can be used to describe a peptide.
NMR
NMR:1000887
peptide attribute
NMR:1000887
An nonphysical attribute that can be used to describe a peptide.
MSI:NMR
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.
value-type:xsd:string
NMR
NMR:1000888
unmodified peptide sequence
NMR:1000888
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.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
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).
value-type:xsd:string
NMR
NMR:1000889
modified peptide sequence
NMR:1000889
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).
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
A state description of how a peptide might be isotopically or isobarically labelled.
NMR
NMR:1000890
peptide labeling state
NMR:1000890
A state description of how a peptide might be isotopically or isobarically labelled.
MSI:NMR
A peptide that has been created or labeled with some heavier-than-usual isotopes.
NMR
NMR:1000891
heavy labeled peptide
NMR:1000891
A peptide that has been created or labeled with some heavier-than-usual isotopes.
MSI:NMR
A peptide that has not been labeled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy".
light labeled peptide
NMR
NMR:1000892
unlabeled peptide
NMR:1000892
A peptide that has not been labeled with heavier-than-usual isotopes. This is often referred to as "light" to distinguish from "heavy".
MSI:NMR
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.
value-type:xsd:string
NMR
NMR:1000893
peptide group label
NMR:1000893
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.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence.
NMR
NMR:1000898
data standard
NMR:1000898
Something, such as a practice or a product, that is widely recognized or employed, especially because of its excellence.
MSI:NMR
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.
MS_1000899
NMR
NMR:1000899
de facto standard
NMR:1000899
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.
MSI:NMR
A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result.
MS_1000899
NMR
NMR:1000900
minimum information standard
NMR:1000900
A specification of a minimum amount of information needed to reproduce or fully interpret a scientific result.
MSI:NMR
A file that has two or more columns of tabular data where each column is separated by a TAB character.
NMR
NMR:1000914
tab delimited text file
NMR:1000914
A file that has two or more columns of tabular data where each column is separated by a TAB character.
MSI:NMR
Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation.
value-type:xsd:string
NMR
NMR:1000933
protein modification
NMR:1000933
Encoding of modifications of the protein sequence from the specified accession, written in PEFF notation.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
Name of the gene from which the protein is translated.
value-type:xsd:string
NMR
NMR:1000934
gene name
NMR:1000934
Name of the gene from which the protein is translated.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
Type of the source file, the nmrIdentML was created from.
NMR
NMR:1001040
intermediate analysis format
NMR:1001040
Type of the source file, the nmrIdentML was created from.
MSI:MI
Source file for this nmrIdentML was a data set in a database.
NMR
NMR:1001107
data stored in database
retire? Consider: "NMR database format" ?
NMR:1001107
Source file for this nmrIdentML was a data set in a database.
MSI:MI
NMR
NMR:1001267
software vendor
NMR:1001267
value-type:xsd:string
NMR
NMR:1001268
programmer
NMR:1001268
value-type:xsd:string
The allowed value-type for this CV term.
value-type:xsd:string
NMR
NMR:1001269
instrument vendor
NMR:1001269
value-type:xsd:string
The allowed value-type for this CV term.
value-type:xsd:string
NMR
NMR:1001270
lab personnel
NMR:1001270
value-type:xsd:string
The allowed value-type for this CV term.
NMR
NMR:1001271
researcher
NMR:1001271
Analysis software.
NMR
NMR:1001456
analysis software
NMR:1001456
Analysis software.
MSI:NMR
Conversion software.
NMR
NMR:1001457
data processing software
NMR:1001457
Conversion software.
MSI:NMR
Format of data files.
NMR
NMR:1001459
data file format
NMR:1001459
Format of data files.
MSI:NMR
Phone number of the contact person or organization.
value-type:xsd:string
NMR
NMR:1001755
contact phone number
NMR:1001755
Phone number of the contact person or organization.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
Fax number for the contact person or organization.
value-type:xsd:string
NMR
NMR:1001756
contact fax number
NMR:1001756
Fax number for the contact person or organization.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
Toll-free phone number of the contact person or organization.
value-type:xsd:string
NMR
NMR:1001757
contact toll-free phone number
NMR:1001757
Toll-free phone number of the contact person or organization.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
DOI unique identifier.
value-type:xsd:string
NMR
NMR:1001922
Digital Object Identifier (DOI)
NMR:1001922
DOI unique identifier.
MSI:MI
value-type:xsd:string
The allowed value-type for this CV term.
Free text attribute that can enrich the information about an entity.
value-type:xsd:string
NMR
NMR:1001923
external reference keyword
NMR:1001923
Free text attribute that can enrich the information about an entity.
MSI:MI
value-type:xsd:string
The allowed value-type for this CV term.
Keyword present in a scientific publication.
value-type:xsd:string
NMR
NMR:1001924
journal article keyword
NMR:1001924
Keyword present in a scientific publication.
MSI:MI
value-type:xsd:string
The allowed value-type for this CV term.
Keyword assigned by the data submitter.
value-type:xsd:string
NMR
NMR:1001925
submitter keyword
NMR:1001925
Keyword assigned by the data submitter.
MSI:MI
value-type:xsd:string
The allowed value-type for this CV term.
Keyword assigned by a data curator.
value-type:xsd:string
NMR
NMR:1001926
curator keyword
NMR:1001926
Keyword assigned by a data curator.
MSI:MI
value-type:xsd:string
The allowed value-type for this CV term.
Parameters used in the NMR spectrometry acquisition.
value-type:xsd:string
NMR
NMR:1001954
NMR acquisition parameter
NMR:1001954
Parameters used in the NMR spectrometry acquisition.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
A unique identifier for a metabolite in the HMDB database (HMDB00001).
value-type:xsd:integer
NMR
NMR:1002000
HMDB identifier
NMR:1002000
A unique identifier for a metabolite in the HMDB database (HMDB00001).
MSI:NMR
value-type:xsd:integer
The allowed value-type for this CV term.
Chenomx software for data acquisition and analysis.
NMR
NMR:1002001
Chenomx software
NMR:1002001
Chenomx software for data acquisition and analysis.
MSI:NMR
Chenomx software for data analysis.
http://www.chenomx.com/software/
NMR
NMR:1002002
Chenomx NMR Suite software
NMR:1002002
Chenomx software for data analysis.
MSI:NMR
file=xsd:IDREF.
NMR
NMR:1002003
The nativeID must be the same as the source file ID.
Varian FID format
NMR:1002003
file=xsd:IDREF.
MSI:NMR
The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format.
NMR
NMR:1002004
NMR spectrometer file format
NMR:1002004
The format of the file being used. This could be a instrument or vendor specific proprietary file format or a converted open file format.
MSI:NMR
Simple text file of peaks.
NMR
NMR:1002005
text file
NMR:1002005
Simple text file of peaks.
MSI:PI
Parameter file used to configure the acquisition of raw data on the instrument.
NMR
NMR:1002006
acquisition parameter file
NMR:1002006
Parameter file used to configure the acquisition of raw data on the instrument.
MSI:NMR
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
as designated Experiment type on http://www.bmrb.wisc.edu/tools/choose_pulse_info.php
NMR
NMR:1002007
NMR spectrum
NMR:1002007
Conversion of a file format to Metabolomics Standards Initiative nmrData file format.
NMR
NMR:1002008
conversion to nmrML
NMR:1002008
Conversion of a file format to Metabolomics Standards Initiative nmrData file format.
MSI:NMR
Conversion of a file format to JCAMP-DX file format.
NMR
NMR:1002009
conversion to JCAMP-DX
NMR:1002009
Conversion of a file format to JCAMP-DX file format.
MSI:NMR
value-type:xsd:string
NMR
NMR:1002010
NMR solvent information
NMR:1002010
value-type:xsd:string
The allowed value-type for this CV term.
pH.
value-type:xsd:string
NMR
NMR:1002011
pH
NMR:1002011
pH.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
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.
https://github.com/nmrML/nmrML/issues/29#issue
value-type:xsd:string
NMR
NMR:1002013
chemical shift reference
NMR:1002013
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.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
A bin for a spectrum.
value-type:xsd:string
bucketed spectrum descriptor
NMR
NMR:1002014
binned spectrum descriptor
NMR:1002014
A bin for a spectrum.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
Bin label.
value-type:xsd:string
NMR
NMR:1002015
bin label
NMR:1002015
Bin label.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
Bin start.
value-type:xsd:decimal
NMR
NMR:1002016
bin start
NMR:1002016
Bin start.
MSI:NMR
value-type:xsd:decimal
The allowed value-type for this CV term.
Bin end.
value-type:xsd:decimal
NMR
NMR:1002017
bin end
NMR:1002017
Bin end.
MSI:NMR
value-type:xsd:decimal
The allowed value-type for this CV term.
Bin area.
value-type:xsd:decimal
NMR
NMR:1002018
bin area
NMR:1002018
Bin area.
MSI:NMR
value-type:xsd:decimal
The allowed value-type for this CV term.
Name of metabolite.
value-type:xsd:string
NMR
NMR:1002020
assigned chemical compound name
NMR:1002020
Name of metabolite.
MSI:NMR
value-type:xsd:string
The allowed value-type for this CV term.
value-type:xsd:decimal
NMR
NMR:1002021
assigned chemical compound concentration
NMR:1002021
value-type:xsd:decimal
The allowed value-type for this CV term.
Hilbert transformation based scaling
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...
optional part of NMR instrument
TODO: Discuss "obligatory_part_of".
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.
autosampler
http://www.chem.wisc.edu/areas/reich/plt/windnmr.htm
multiplicity
multiplicity feature
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
projected spectrum
binned spectrum
def: A post-processed NMR spectrum in which the y-values of the datapoints have been summed based on periodic ranges of the x-axis values.
bucketed spectrum
TODO: has spectral post processing parameter
defneed
peak-picked spectrum
TODO: has spectral post processing parameter.
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
cardinal part of NMR instrument
def: A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers.
acquisition computer
def: Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile “single point of failure” that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency.
altdef: The instrument that transmits and recieves radiofrequency to and from the NMR sample.
NMR probe
def: A component of an NMR instrument that controls the activities of the other components.
console
TODO: same as or part of acquisition computer?
tempdef: The number of data points in a data set.
number of acquisition data points
def: A frequency used during Hadamard encoding.
hadamard frequency
def: The axis onto which the spectrum was projected.
projection axis
90 degree pulse duration
ninety degree pulse duration
The duration of the excitation pulse needed to rotate the magnetisation vector by 90 degrees.
def: A digital sampling interval.
alsprcls: time interval
dwell time
def: The temperature of an item of analysis material whilst in an autosampler.
sample temperature in autosampler
def: The temperature of an NMR sample whilst in the magnet of an NMR instrument.
sample temperature in magnet
def: The frequency of the RF radiation used to irradiate an NMR sample.
irradiation frequency
def: The intensity of an electric, magnetic, or other field.
field strength
def: The rate at which an item of analysis material is spun.
spinning rate
def: An indication of whether the nucleus being studied is the acquitsition nucleus.
decoupled nucleus flag
def: A compound added to a sample to alter its pH value.
buffer information
reference compound
reference standard
def: The compound that produced the peak used to reference a spectrum during data pre-processing.
calibration compound
http://www.nmrnotes.org/NMRPages/refcomps.html
https://github.com/nmrML/nmrML/issues/31
https://github.com/nmrML/nmrML/issues/33
chemical shift reference compound
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.
chemical shift standard
def: The compound that produced a peak that is measured to assess the quality of a data set.
quality check compound signal
http://www.bmrb.wisc.edu/tools/choose_pulse_info.php
https://github.com/nmrML/nmrML/issues/40
def: A sequence of excitation pulses.
NMR pulse sequence
May later import from
http://purl.obolibrary.org/obo/CHMO_0001841
See also http://www.jcamp-dx.org/protocols/NMR%20Pulse%20Sequences%20PAC%2079(11)%20pp1748-1764%202001.pdf
nmr-spectrum data processing
post-FT data processing
def: Automatic or manual procedures performed upon pre-processed NMR data sets that aim to summarise them or annotate them with speculative values.
frequency domain data processing
pre-FT data processing
def: The post acquisition process of producing or refining a spectrum from raw data.
defprov: Daniel Schober
time domain data processing
def: A data transformation that converts an NMR input data set into an output data set in a tracable and useful manner.
NMR data processing
tempdef: A non FT based method for converting from the time to the frequency domain.
non-fourier FID transformation
TODO:Exclusion guided definition.
https://github.com/nmrML/nmrML/issues/37
tempdef: A data processing which alteres a data file for a specific purpose.
defprov: Daniel Schober
data encoding
tempdef:GFT NMR allows for rapid multidimensional FT NMR spectral information gathering, avoiding sampling limitations without compromising on the precision of chemicalshift.
defprov: ttp://www.nsm.buffalo.edu/Research/GFT/szyperski_publications_1st_page/Szyperski%2067.pdf
synonym: GFT-projection
G matrix fourier transform projection
defneed
synonym: TPPI
time proportional phase incrementation
def: A method for quadrature detection.
synonym: S-TPPI
states-time proportional phase incrementation
defneed
Hadamard encoding
http://www.magnet.fsu.edu/library/publications/NHMFL_Publication-6859.pdf
defneed
Frydman encoding
defneed
echo anti-echo coherence selection
def: An Instrument which is used to carry out a NMR analysis of some sample.
synonym: NMR instrument
NMR instrument
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
NMR instrument acquisition parameter set
method
defneed
data transformation
altspcls: process ???
Philippe Rocca Serra
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.
http://stats.stackexchange.com/questions/35591/normalization-vs-scaling
normalisation
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.
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
pre-acquisition water suppression
A function applied to a FID to increase the signal-to-noise ratio or the resolution.
http://www.uwyo.edu/wheelernmr/nmr/window_functions.pdf
https://github.com/nmrML/nmrML/issues/39
https://github.com/nmrML/nmrML/issues/67
apodization function
window function for apodization
The exponential function used to multiply a FID by to produce a desitred amount of line broadening.
exponential apodization
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.
exponential multiplication window function
gaussian broadening
defneed
Gaussian window function
sine
sine bell window function
defneed
sine window function
QSINE
defneed
sine squared window
def: A method for eliminating or reducing the noise in a spectrum.
spectral denoising
def: A method of flattening the baseline of a spectrum.
baseline correction
A method of spectral projection.
spectral projection
defneed
maximum intensity projection
def: .A projection method that sums the intensities of a pre-processed 2D J-resolved NMR spectrum to obtain a projected spectrum.
altdef: The adding of spectra together to produce a composite avergaed spectrum.
summation projection
def: 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.
zero order phase correction
defneed
first order phase correction
defneed
symmetrisation
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.
acquisition nucleus
def: A feature of a peak that is measured to assess the quality of a data set.
quality check peak feature
def: The number of repeat scans performed and summed to create the data set for an NMR sample.
number of scans
def: The number of scans whose data is not summed to create the data set for an NMR sample, but that are carried out to establish the steady-state of relaxation for the nuclei.
number of steady state scans
def: A scheme for producing a numerical representation of the environment of an atom.
atom environment encoding
def: The delay between repeat scans to allow nuclei to relax back to their steady state.
relaxation delay
def: The units of measure for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum.
altdef: The units used to represent either time domain (for a FID) or the frequency domain (for a spectrum).
x-axis unit
defneed
y-axis unit
def: The unit of measurement of the second dimension of a 2D NMR dataset.
additional axis unit
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 start value
tempdef: The end value for the x-axis of a (1D or 2D) FID, (1D or 2D) pre-processed spectrum, 2D projected spectrum, and (1D or 2D) post-processed spectrum.
x end value
def: A parameter to a window function.
window function parameter
Philippe Rocca-Serra
http://www.chem.wisc.edu/areas/reich/nmr/08-tech-01-relax.htm.
Hans J. Reich 2015, University of Wisconsin
defneed
line broadening
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.
Philippe Rocca-Serra
http://www.chem.wisc.edu/areas/reich/nmr/08-tech-01-relax.htm.
Hans J. Reich 2015, University of Wisconsin
defneed
line sharpening
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.
defneed
parameter
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 spectral projection parameter set
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
NMR data post-processing parameter set
TODO: altsprcls: process, not clear wether set is plural (list) or process.
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
NMR quality check parameter set
excitation sculpting
tempdef: A data processing technique used to suppress the water peak in a spectrum in order to get clearer results.
defprov: Daniel Schober
post-acquisition water suppression
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
hankel singular value decomposition
defneed
convolution
defneed
polynomial fitting
def: A computational method that archieves water suppression via wavlet multi resolution analysis.
WaveWat
defneed
synonym: NMR data pre-processing parameter set
NMR data pre-processing parameter set
def: The process of ensuring the quality of the raw data that results from an NMR analysis.
synonym: NMR quality check
NMR quality check
def: A reference is a label which refers to data elsewhere, as opposed to containing the data itself. Accessing the value that a reference refers to is called dereferencing it. References are fundamental in constructing many data structures and in exchanging information between different parts of programs and databases.
reference
FID file reference
def: A reference to a file containing the raw FID.
synonym: FID file reference
FID file
def: A reference to a description of a pulse sequence in the literature.
pulse sequence literature reference
def: A reference to a file containing a specfication of the shape of an excitation pulse.
shaped pulse file
def: A reference to a file containing a specification of a pulse sequence.
pulse sequence file
def: A reference to a file of data pre-processing parameters produced by the machine.
processing parameter file
PRS: rename 'reference' to 'identifier'
def: A reference to information on the provenance of the NMR sample.
synonym: NMR sample reference
NMR sample identifier
def: A result of an NMR quality check.
synonym: NMR quality check result
NMR quality check descriptor
def: A sample that has been prepared for chemical analysis by NMR. NMR samples are usually liquid solutions contained in glass tubes. NMR solution sample volume ranges from 50ul to 5ml depending on the NMR probe. Sample concentrations of solute for 1H NMR are usually in the range of 100ug to 5g, with 10 to 50mg being typical. NMR is not a chemical trace analysis technique. The NMR signal of solids and gases can be recorded but to measure solid-state NMR additional specialized hardware is required.
synonym: NMR sample
NMR sample
tempdef: A sample introduction parameter is a parameter that describes the particular method of introducing the sample under investigation into the NMR instrument.
sample introduction parameter
defneed
synonym: MAS rotor
magic angle spinning rotor
defneed
flow probe
The sample-tube holds the NMR sample and sits in the NMR probe. It is usually a glass tube of 5-20mm diameter.
http://en.wikipedia.org/wiki/NMR_tube
https://github.com/nmrML/nmrML/issues/54
sample tube
sortal dimensions are Vendor, Size (Diameter, length), Material (glass, quarz, pyrex ...), Frequency, Concentricity, OD and ID
NMR sample tube
def: A software artifact used during data pre-processing.
spectrum pre-processing software
def: A software artifact used during spectral post-processing.
spectrum post-processing software
defneed
peak picking
binning
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.
for bucket parameters see 'binned spectrum descriptor'
bucketing
presaturation of the solvent resonance
defneed
synonym: presaturation
presat pulse sequence
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
water suppression enhanced through T1 effects
WET
NOESY presat
tempdef: The presat for an nuclear overhauser and exchange spectroscopy experiment. A 2D method used to map NOE correlations between protons within a molecule. The nuclear Overhauser effect (NOE) causes changes in peak areas, as a secondary effect of decoupling.
defprov: Daniel Schober
synonym: NOESY-presat
nuclear overhauser and exchange spectroscopy-presat
defneed
watergate
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
coherence pathway rejection
defneed
flip-back watergate
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 pulse sequence
tempdef: A jump and return 1-1 pulse sequence method is a jump and return method that uses one 90 degree pulse and one 90 degree return puls to make fast exchanging protons visible, first described by Plateau,P. and Gueron,M. (1982) J. Am. Chem. Soc., 104, 7310–7311. Compared to the 1-3-3-1 method it has a lower receiver gain and the dispersive tail of water interferes with the signals of interest.
jump and return 1-1
tempdef:A jump and return 1-3-3-1 pulse sequence method is a jump and return method that uses a 1-3-3-1 pulse sequence to make fast exchanging protons visible. Compared to the 1-1 method it has better water suppression (higher receiver gain) capabilities, but with offset-dependent phase distortion (unsuitable for 2D).
jump and return 1-3-3-1
defneed
synonym: 1D spectrum
1D spectrum
defneed
synonym: 2D spectrum
2D spectrum
defneed
synonym: 1D NMR acquisition parameter set
1D NMR acquisition parameter set
defneed
synonym: 2D NMR acquisition parameter set
2D NMR acquisition parameter set
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
carr purcell meiboom gill pulse sequence
CPMG
TCOSY pulse sequence
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
total correlation spectroscopy pulse sequence
def: One dimensional (referring to a FID, pre-processed spectrum, or post-processed spectrum).
synonym: 1D
1D pulse sequence
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
J-resolved pulse sequence
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synonym: 2D hadamard TOCSY
hadamard total correlation spectroscopy pulse sequence
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synonym: 1D diffusion edited
diffusion edited pulse sequence
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.
NMR magnet
defneed
Bruker NMR magnet
defneed
UltraShield
Ultrastabilized
US 2
??? How to model "hoch 2"?
UltraShield Plus
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
Bruker CryoProbe
def: Samples that are neither solid nor liquid, being of biological, chemical, and/or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Bruker’s high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject/insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g., 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used.
defprov: Bruker website
altdef: High resolution MAS (hr-MAS) provides an easy means of obtaining high resolution spectra for a variety of samples that would otherwise result in poorly resolved spectra. The addition of an hr-MAS probe and a MAS pneumatic unit to a standard high resolution spectrometer is all that is needed to open the gate to the world of hr-MAS spectroscopy and gain access to a vast amount of highly interesting samples.
synonyms: High resolution MAS, hr-MAS
high resolution magic angle spin probe
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
solid magic angle spinning probe
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
1mm MicroProbe
def: Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes.
defprov: Bruker website
synonym: flow HR-probe
flow high resolution probe
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NMR instrument parameter set
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AVANCE II spectrometer
TODO: May need no definition
defneed
Bruker NMR instrument
https://www.bruker.com/de/products/mr/nmr.html
For metabolism studies, and analysis of complex mixtures.
Metabolic Profiler instrument
NMR Instruments using hyphenated analytical techniques combining mass spectrometry and chromatograph.
Hyphenated NMR instrument
Capillary LC-NMR
def: The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats.
defprov: Bruker website
NMR Case
defneed
NMR tube washing system
def: In today's fast-paced research environment, NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean™ system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material.
defprov: Bruker website
Bruker AutoClean
def: The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data.
defprov: Bruker website
synonym: Bruker Efficient Sample Transfer NMR
Bruker BEST NMR
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
SampleRail
def: Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation.
The SampleJet utilizes the modern-day industry standard for sample arrangements—the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement.
defprov: Bruker website
SampleJet
defneed
Bruker autosampler
def: The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit.
defprov: Bruker website
B-ACS
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
Bruker MATCH
def: A NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the NMR sample.
NMR sample holder
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NMR software
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Bruker NMR software
TODO: May need no definition.
Bruker TopSpin software
SampleTrack software
Paravision software
AURELIA software
AUREMOL software
AMIX VIEWER & AMIX-TOOLS
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
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
high resolution probe with ATM
defneed
micro imaging probe
JEOL NMR instrument
JNM-ECX Series FT NMR instrument
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
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
Delta NMR software
https://www.bruker.com/products/mr/nmr/probes/probes.html
Bruker NMR probe
defneed
JEOL NMR probe
CapNMR probe
Varian NMR instrument
Varian MERCURY
Varian INOVA
Varian UNITY
Varian VXR
Varian GEMINI
AMX instrument
AC instrument
liquid NMR probe
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solid NMR probe
defneed
NMR imaging probe
tecmag console
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
DISCOVERY console
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
tecmag EAGLE probe
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APOLLO console
tecmag NMR instrument
CAT
defneed
magnetic field strength
defneed
vendor
TODO: Belongs in Ref Ontol.
A manufacturer that produces (and eventually sells) NMR instruments.
NMR instrument manufacturer
defneed
Bruker
TODO: May not need definition due to its instance character.
Varian
JEOL
MR Resources
tecmag
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.
sample temperature information
Doty Scientific
Wilmad
JS Research
data file
file
Any data file as generated by some acquisition computer or console.
This is a class annotation exemplifying skos usage. We assume the rdfs:label to capture the skos:preferedLabel.
an FID raw data file
In the NMR case a file generated by an NMR acquisition computer, console or NMR processing software.
Acorn NMR Inc
LC NMR
liquid chromatography NMR
Includes the connection to a high-resolution TOF-LC-MS system.
LC MS NMR
SPE NMR
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.
solid phase extraction NMR
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.
Capillary LC-NMR
direct detection probe
indirect detection probe
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
continuous wave NMR
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
fourier transformation NMR instrument
NMR software data format
ChemMagnetics format
GE Omega format
JEOL Lambda format
JEOL Alpha format
Jeol Delta format
JEOL generic format
JEOL AL95 format
JEOL EX format
TecMag format
Varian VNMR format
Galactic format
Felix format
JCAMP DX format
Lybrics format
Nuts format
MACNMR format
Nicolet GE/QE-300 format
m
J-coupler
multiplet feature
ThermoMattson
FOSS
Jasco
Agilent Technologies
micromass
Waters
ThermoNicolet
Perkin Elmer
OceanOptics
ThermoFinnigan
Applied Biosystems
TX
Net CDF format
Bruker DISNMR format
Bruker UXNMR/XWIN-NMR format
Bruker WIN NMR format
acdlabs
BFO:0000001
entity
Entity
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
per discussion with Barry Smith
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
BFO:0000002
continuant
Continuant
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
BFO:0000003
occurrent
Occurrent
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
per discussion with Barry Smith
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
BFO:0000004
ic
IndependentContinuant
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
BFO:0000006
s-region
SpatialRegion
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
per discussion with Barry Smith
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
BFO:0000008
t-region
TemporalRegion
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
per discussion with Barry Smith
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
BFO:0000009
2d-s-region
TwoDimensionalSpatialRegion
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
two-dimensional spatial region
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
BFO:0000011
st-region
SpatiotemporalRegion
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
spatiotemporal region
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
BFO:0000015
process
Process
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
process
p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
BFO:0000016
disposition
Disposition
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
BFO:0000017
realizable
RealizableEntity
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
realizable entity
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
BFO:0000018
0d-s-region
ZeroDimensionalSpatialRegion
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
zero-dimensional spatial region
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
BFO:0000019
quality
Quality
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
quality
quality
a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
BFO:0000020
sdc
SpecificallyDependentContinuant
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the role of being a doctor
the shape of this hole.
the smell of this portion of mozzarella
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
specifically dependent continuant
b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
per discussion with Barry Smith
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
BFO:0000023
role
Role
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
BFO:0000024
fiat-object-part
FiatObjectPart
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
fiat object part
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
BFO:0000026
1d-s-region
OneDimensionalSpatialRegion
an edge of a cube-shaped portion of space.
A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
one-dimensional spatial region
A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
BFO:0000027
object-aggregate
ObjectAggregate
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
object aggregate
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
BFO:0000028
3d-s-region
ThreeDimensionalSpatialRegion
a cube-shaped region of space
a sphere-shaped region of space,
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
three-dimensional spatial region
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
BFO:0000029
site
Site
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
BFO:0000030
object
Object
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
object
object
b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
BFO:0000031
gdc
GenericallyDependentContinuant
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
generically dependent continuant
b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
BFO:0000034
function
Function
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
BFO:0000035
p-boundary
ProcessBoundary
the boundary between the 2nd and 3rd year of your life.
p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
process boundary
p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
BFO:0000038
1d-t-region
OneDimensionalTemporalRegion
the temporal region during which a process occurs.
BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
one-dimensional temporal region
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
BFO:0000040
material
MaterialEntity
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
BFO:0000140
cf-boundary
ContinuantFiatBoundary
b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
Every continuant fiat boundary is located at some spatial region at every time at which it exists
(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
continuant fiat boundary
b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
BFO:0000141
immaterial
ImmaterialEntity
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
BFO:0000142
1d-cf-boundary
OneDimensionalContinuantFiatBoundary
The Equator
all geopolitical boundaries
all lines of latitude and longitude
the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
the median sulcus of your tongue
a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
one-dimensional continuant fiat boundary
a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
BFO:0000144
process-profile
ProcessProfile
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
process profile
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
BFO:0000145
r-quality
RelationalQuality
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
a marriage bond, an instance of requited love, an obligation between one person and another.
b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
relational quality
b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
BFO:0000146
2d-cf-boundary
TwoDimensionalContinuantFiatBoundary
a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
two-dimensional continuant fiat boundary
a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
BFO:0000147
0d-cf-boundary
ZeroDimensionalContinuantFiatBoundary
the geographic North Pole
the point of origin of some spatial coordinate system.
the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
zero-dimensional continuant fiat boundary
zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
requested by Melanie Courtot
a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
BFO:0000148
0d-t-region
ZeroDimensionalTemporalRegion
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
BFO:0000182
history
History
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
history
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
owl:Thing
1.1.0
en
http://nmrml.org/examples/
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.
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
solvent suppression method-->solvent suppression method
encoding scheme (Quadrature detection method)-->encoding method
window function parameter-->window function parameter
CVParamWithUnitType occurrences:
CVParamWithUnitType is currently not used in the xsd and dangling ! I assume ValueWithUnitType substitutes it ?
UserParamType occurrences:
No CV terms needed
ValueWithUnitType occurrences:
These will have to be used from the Unit ontology.
Annick Moing
Catherine Deborde
Daniel Jacob
Daniel Schober
Joseph Cruz
Michael Wilson
Philippe Rocca-Serra
Reza Salek
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, Antonio; Klein, Matthias; Lewis, Ian; Luchinat, Claudio; Jones, Andrew; Grauslys, Arturas; Larralde, Martin; Yokochi, Masashi; Kobayashi, Naohiro; Porzel, Andrea; Griffin, Julian; Viant, Mark; Wishart, David; Steinbeck, Christoph; Salek, Reza; Neumann, Steffen
Steffen Neumann
Nuclear magnetic resonance (NMR) data annotation as required by the msi sanctioned open access nmrML XML format developed by the COSMOS EU project.
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).)
Creative Commons Public Domain Mark 1.0
nuclear magnetic resonance CV
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.
https://github.com/nmrML/nmrML/issues
Daniel Schober
https://github.com/nmrML/nmrML
https://github.com/nmrML/nmrML/tree/master/ontologies
https://groups.google.com/forum/?hl=en#!forum/nmrml/join
http://www.metabolomics-msi.org/
http://phenomenal-h2020.eu/home/
http://www.cosmos-fp7.eu/WP2
OBO-Edit 2.2
Daniel Schober
2017-10-19T10:11:26Z
1.2
dschober
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.
http://www.metabolomicscentre.ca/nmrML/msi-nmr.obo
1.1.0
http://nmrml.org/cv/
BFO 2 Reference: BFO does not claim to provide complete coverage of entities of all types. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning - coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation.
BFO 2 Reference: BFO's treatment of continuants and occurrents - as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality - earlier called the 'SNAP' and 'SPAN' perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science.
BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. 'Entity' is an example of a primitive term. Primitive terms in a highest-level ontology such as BFO are terms that are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms.
Alan Ruttenberg
Albert Goldfain
Barry Smith
Bill Duncan
Bjoern Peters
Chris Mungall
David Osumi-Sutherland
Fabian Neuhaus
Holger Stenzhorn
James A. Overton
Janna Hastings
Jie Zheng
Jonathan Bona
Larry Hunter
Leonard Jacuzzo
Ludger Jansen
Mark Ressler
Mathias Brochhausen
Mauricio Almeida
Melanie Courtot
Pierre Grenon
Randall Dipert
Ron Rudnicki
Selja Seppälä
Stefan Schulz
Thomas Bittner
Werner Ceusters
Yongqun "Oliver" He
Please see the project site https://github.com/BFO-ontology/BFO, the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel, the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx. This ontology is generated from a specification at https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/ and with the code that generates the OWL version in https://github.com/BFO-ontology/BFO/tree/master/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif.
The BSD license on the BFO project site refers to code used to build BFO.
This BFO 2.0 version represents a major update to BFO and is not strictly backwards compatible with BFO 1.1. The previous OWL version of BFO, version 1.1.1 will remain available at http://ifomis.org/bfo/1.1 and will no longer be updated. The BFO 2.0 OWL is a classes-only specification. The incorporation of core relations has been held over for a later version.