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 defneed synonym: 2D hadamard TOCSY hadamard total correlation spectroscopy pulse sequence defneed 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 defneed NMR instrument parameter set defneed 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 defneed NMR software defneed 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 defneed 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 defneed 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.