PeakForest descriptors used for analytical instrument metadata
MS metadata help
Descriptors definition and corresponding uri
| Descriptors | Definition | Ontology uri |
|---|---|---|
| additional axis unit | The unit of measurement of the second dimension of a 2D NMR dataset. | http://nmrML.org/nmrCV#NMR:1400093 |
| atmospheric pressure chemical ionization (APCI) | Chemical ionization that takes place at atmospheric pressure as opposed to the reduced pressure is normally used for chemical ionization. | http://purl.obolibrary.org/obo/MS_1000070 |
| author | Main creator(s) of a written work (use on works, not humans); use P2093 when Wikidata item is unknown or does not exist | https://www.wikidata.org/wiki/Property:P50 |
| buffer solution / NMR Buffer | Missing def. | http://nmrML.org/nmrCV#NMR:1000331 |
| chemical ionization (CI) | The formation of a new ion by the reaction of a neutral species with an ion. The process may involve transfer of an electron, a proton or other charged species between the reactants. When a positive ion results from chemical ionization the term may be used without qualification. When a negative ion results the term negative ion chemical ionization should be used. Note that this term is not synonymous with chemi-ionization. | http://purl.obolibrary.org/obo/MS_1000071 |
| chemical shift | Chemical shift is the resonance frequency of a nucleus related to a chemical shift standard. in ppm along x-axis | http://nmrML.org/nmrCV#NMR:1000223 |
| chromatography column | A chromatography column is a type of column that contains a stationary phase for chromatographic separation of compounds. [Allotrope] | http://purl.allotrope.org/ontologies/equipment#AFE_0000217 |
| chromatography separation | A technique by which molecules are separated by chemical and physical properties such as hydrophobicity or vapour pressure. | http://purl.obolibrary.org/obo/MS_1002270 |
| concentration | The concentration of a chemical compound. | http://edamontology.org/data_2140 |
| CPMG or carr purcell meiboom gill pulse sequence | 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 | http://nmrML.org/nmrCV#NMR:1400167 |
| data | Quantities, characters, or symbols on which operations are performed by a computer | https://www.wikidata.org/wiki/Q494756 |
| Data acquisition | Sum of methods of simultaneous or sequential time measurement and counting for measurable or quantifiable data and groups of contiguous data | https://www.wikidata.org/wiki/Q1172399 |
| Date / calendar date | Particular day represented within a calendar system | https://www.wikidata.org/wiki/Q205892 |
| decoupling method | 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://nmrML.org/nmrCV#NMR:1000044 |
| derivation method | Missing def. | |
| electron ionization (EI) | The ionization of an atom or molecule by electrons that are typically accelerated to energies between 50 and 150 eV. Usually 70 eV electrons are used to produce positive ions. The term 'electron impact' is not recommended. | http://purl.obolibrary.org/obo/MS_1000389 |
| electronvolt (eV) | A non-SI unit of energy (eV) defined as the energy acquired by a single unbound electron when it passes through an electrostatic potential difference of one volt. An electronvolt is equal to 1.602 176 53(14) x 10^-19 J. | http://purl.obolibrary.org/obo/UO_0000266 |
| electrospray ionization (ESI) | A process in which ionized species in the gas phase are produced from an analyte-containing solution via highly charged fine droplets, by means of spraying the solution from a narrow-bore needle tip at atmospheric pressure in the presence of a high electric field. When a pressurized gas is used to aid in the formation of a stable spray, the term pneumatically assisted electrospray ionization is used. The term ion spray is not recommended. | http://purl.obolibrary.org/obo/MS_1000073 |
| f1 axis | Missing def. | http://nmrML.org/nmrCV#NMR:1000209 |
| f2 axis | Missing def. | http://nmrML.org/nmrCV#NMR:1000210 |
| FID fourier transformation | missing def. | http://nmrML.org/nmrCV#NMR:1000070 |
| field strength | The intensity of an electric, magnetic, or other field. | http://nmrML.org/nmrCV#NMR:1400027 |
| flow rate | A physical quality inhering in a bearer by virtue of the bearer's motion characteristic. | http://purl.obolibrary.org/obo/PATO_0001574 |
| gas chromatography separation | Gas chromatography (GC) is a separation technique in which the mobile phase is a gas. | http://purl.obolibrary.org/obo/MS_1002272 |
| HSQC NMR spectrum or heteronuclear single quantum coherence spectrum | Missing def. | http://nmrML.org/nmrCV#NMR:1000107 |
| InChI | Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation. | http://edamontology.org/format_1197 |
| InChIKey | The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound. An InChIKey identifier is not human- nor machine-readable but is more suitable for web searches than an InChI chemical structure specification. | http://edamontology.org/format_1199 |
| ionization type | The method by which gas phase ions are generated from the sample. | http://purl.obolibrary.org/obo/MS_1000008 |
| irradiation frequency | The frequency of the RF radiation used to irradiate an NMR sample. | http://nmrML.org/nmrCV#NMR:1400026 |
| JRES spectrum | Missing def. | http://nmrML.org/nmrCV#NMR:1000086 |
| liquid chromatography separation | Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid. | http://purl.obolibrary.org/obo/MS_1002271 |
| lock substance / field frequency lock | Missing def. | http://nmrML.org/nmrCV#NMR:1000166 |
| m/z / mass-to-charge ratio | Three-character symbol m/z is used to denote the quantity formed by dividing the mass of an ion in unified atomic mass units by its charge number (regardless of sign). The symbol is written in italicized lower case letters with no spaces. Note 1: The term mass-to-charge-ratio is deprecated. Mass-to-charge ratio has been used for the abscissa of a mass spectrum, although the quantity measured is not the quotient of the ion's mass to its electric charge. The three-character symbol m/z is recommended for the quantity that is the independent variable in a mass spectrum Note 2: The proposed unit thomson (Th) is deprecated. | http://purl.obolibrary.org/obo/MS_1000040 |
| Magnetic field strength | Missing def. | http://nmrML.org/nmrCV#NMR:1400253 |
| Mass analyzer type | Mass analyzer separates the ions according to their mass-to-charge ratio. | http://purl.obolibrary.org/obo/MS_1000443 |
| Matrix (context: sample / biology) | In biology, matrix (plural: matrices) is the material (or tissue) in between a eukaryotic organism's cells. The structure of connective tissues is an extracellular matrix. Finger nails and toenails grow from matrices. It is found in various connective tissues. It is generally used as a jelly-like structure instead of cytoplasm in connective tissue. | https://en.wikipedia.org/wiki/Matrix_(biology) |
| molecule common name / Molecule name | Name of a specific molecule. | http://edamontology.org/data_0984 |
| NMR probe | 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. | http://nmrML.org/nmrCV#NMR:1400014 |
| NMR pulse sequence | A sequence of excitation pulses. | http://nmrML.org/nmrCV#NMR:1400037 |
| NMR raw data file format | Describes the type of file and its content. | http://nmrML.org/nmrCV#NMR:1000577 |
| NMR sample tube | Sortal dimensions are Vendor, Size (Diameter, length), Material (glass, quarz, pyrex ...), Frequency, Concentricity, OD and ID | http://nmrML.org/nmrCV#NMR:1400132 |
| NMR Solvent | Missing def. | http://nmrML.org/nmrCV#NMR:1000330 |
| 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. | http://nmrML.org/nmrCV#NMR:1000350 |
| number of data points | Missing def. | http://nmrML.org/nmrCV#NMR:1000176 |
| number of scans | The number of repeat scans performed and summed to create the data set for an NMR sample. | http://nmrML.org/nmrCV#NMR:1400087 |
| ownership | Legal concept; relationship between a legal person and property conferring exclusive control | https://www.wikidata.org/wiki/Q6498684 |
| PeakForest | Comprehensive infrastructure to organize, curate and share a multi- instrument spectral library for metabolomics data annotation developed and distributed by the French National infrastructure in metabolomics and fluxomics (MetaboHUB). | http://purl.obolibrary.org/obo/MS_1003232 |
| pH (potential of hydrogen) | Quantity of dimension one used to express on a scale from 0 to 14 the amount-of-substance concentration of hydrogen ion of dilute aqueous solution, calculated as the logarithm of the reciprocal of hydrogen-ion concentration in gram atoms per liter. [Definition Source: NCI] | http://purl.obolibrary.org/obo/NCIT_C45997 |
| raw data file | Data file that contains original data as generated by an instrument, although not necessarily in the original data Format (i.e. an original raw file converted to a different format is still a raw data file). | http://purl.obolibrary.org/obo/MS_1003083 |
| Raw file format | Uncompressed file format, in general | https://www.wikidata.org/wiki/Q3930596 |
| reference standard | The compound that produced the peak used to reference a spectrum during data pre-processing. | http://nmrML.org/nmrCV#NMR:1400032 |
| relative retention time | Relative retention time is a ratio quality of the adjusted or net retention time of a component relative to that of a Standard, obtained under identical conditions. [Allotrope] | http://purl.allotrope.org/ontologies/quality#AFQ_0000019 |
| relaxation delay | The delay between repeat scans to allow nuclei to relax back to their steady state. | http://nmrML.org/nmrCV#NMR:1400090 |
| retention time | A chromatography peak facet that indicates the elapsed time between the injection of the sample and the maximum Detector response attributed to the peak (analyte band). [Allotrope] | http://purl.allotrope.org/ontologies/result#AFR_0001089 |
| S-lens voltage | Potential difference setting of the Thermo Scientific S-lens stacked-ring ion guide in volts. | http://purl.obolibrary.org/obo/MS_1001913 |
| sample temperature in magnet | The temperature of an NMR sample whilst in the magnet of an NMR instrument. | http://nmrML.org/nmrCV#NMR:1400025 |
| sample volume | missing def. | http://nmrML.org/nmrCV#NMR:1000005 |
| Software | Missing def. | http://nmrML.org/nmrCV#NMR:1400213 |
| solvent | A liquid that can dissolve other substances (solutes) without any change in their chemical composition. | http://purl.obolibrary.org/obo/CHEBI_46787 |
| Source temperature | The temperature of the source of a mass spectrometer. | http://purl.obolibrary.org/obo/MS_1002041 |
| spectral projection axis | missing def. | http://nmrML.org/nmrCV#NMR:1000208 |
| sweep width / spectrum width | Missing def. | http://nmrML.org/nmrCV#NMR:1000175 |
| template | Sample document that already has some elements prepared in a word processing environment | https://www.wikidata.org/wiki/Q3307269 |
| Validator / biocurator | Scientist who curates, collects, annotates, and validates information that is disseminated by biological and model organism databases | https://www.wikidata.org/wiki/Q4914736 |
| window function for apodization | Missing def. | http://nmrML.org/nmrCV#NMR:1400068 |
| window function parameter | A parameter to a window function. | http://nmrML.org/nmrCV#NMR:1400096 |
| x-axis unit | 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). | http://nmrML.org/nmrCV#NMR:1400091 |
| y-axis unit | Missing def. | http://nmrML.org/nmrCV#NMR:1400092 |
References
Ontology mapping is done through EBI OLS Web services. (Reference: We are currently preparing a manuscript for the new OLS. In the meantime you can cite "Jupp S. et al. (2015) A new Ontology Lookup Service at EMBL-EBI. In: Malone, J. et al. (eds.) Proceedings of SWAT4LS International Conference 2015".)