http://purl.allotrope.org/voc/afo/perspective/REC/2020/12/molecular-scale
Perspective taxonomy of materal entities of molecular granularity or smaller, as discussed in chemistry, mostly a subset of ChEBI
URI | http://purl.allotrope.org/ontologies/material#AFM_0000077 |
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Source | IUPAC. Compendium of Chemical Terminology, 2nd ed. (the "Gold Book"). Compiled by A. D. McNaught and A. Wilkinson. Blackwell Scientific Publications, Oxford (1997). |
Description |
An ion is an atomic or molecular particle having a net electric charge. [IUPAC] |
Super-classes |
cdao:CHEBI_23367c |
Sub-classes |
af-m:AFM_0000189c af-m:AFM_0000161c |
URI | http://purl.allotrope.org/ontologies/material#AFM_0000161 |
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Description |
An anion (-) is an ion with more electrons than protons, giving it a net negative charge (since electrons are negatively charged and protons are positively charged). [Wikipedia] |
Super-classes |
af-m:AFM_0000077c |
Sub-classes |
cdao:CHEBI_17632c |
URI | http://purl.allotrope.org/ontologies/material#AFM_0000189 |
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Description |
A cation (+) is an ion with fewer electrons than protons, giving it a positive charge. [Wikipedia] |
Super-classes |
af-m:AFM_0000077c |
Sub-classes |
cdao:CHEBI_49468c |
URI | http://purl.allotrope.org/ontologies/material#AFM_0000226 |
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Source | PAC, 1982, 54, 1533 (Glossary of terms used in nuclear analytical chemistry (Provisional)) |
Description |
The positively charged central portion of an atom, excluding the orbital electrons. [IUPAC] |
Super-classes |
cdao:CHEBI_36347c |
URI | http://purl.allotrope.org/ontologies/material#AFM_0000418 |
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Source | https://en.wikipedia.org/wiki/Electron |
Description |
Elementary particle not affected by the strong force having a spin quantum number 1/2, a negative elementary charge and a rest mass of 0.000 548 579 903(13) u. [IUPAC] |
Super-classes |
cdao:CHEBI_36338c |
URI | http://purl.allotrope.org/ontologies/material#AFM_0001023 |
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Source | Green Book, 2nd ed.: IUPAC Quantities, Units and Symbols in Physical Chemistry. Second Edition, Blackwell Scientific Publications, Oxford, 1993. |
Description |
A proton is a nuclear particle of charge number +1, spin quantum number of 1/2 and rest mass of 1.00727647012 u. [IUPAC] |
Super-classes |
cdao:CHEBI_36347c cdao:CHEBI_33253c |
URI | http://purl.allotrope.org/ontologies/material#AFM_0001027 |
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Source | IUPAC Green Book, 2nd ed., p. 93 |
Description |
A neutron is a nuclear particle of zero charge, spin quantum number 1/2 and a mass of 1.00866490414 u. [IUPAC] |
Super-classes |
cdao:CHEBI_36347c cdao:CHEBI_33253c |
URI | http://purl.allotrope.org/ontologies/material#AFM_0001028 |
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Source | IUPAC Red Book, p. 35 |
Description |
An atom is a smallest particle still characterizing a chemical element. It consists of a nucleus of a positive charge carrying almost all its mass (more than 99.9%) and Z electrons determining its size. [IUPAC] |
Super-classes |
cdao:CHEBI_23367c |
Sub-classes |
cdao:CHEBI_33681c |
URI | http://purl.allotrope.org/ontologies/quality#AFQ_0000252 |
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Description |
A molecular quality is a chemical quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc. [Allotrope] |
Super-classes |
cdao:BFO_0000019c |
Sub-classes |
af-q:AFQ_0000257c af-q:AFQ_0000263c cdao:PATO_0002186c cdao:PATO_0002070c af-q:AFQ_0000265c cdao:PATO_0002193c af-q:AFQ_0000256c |
URI | http://purl.allotrope.org/ontologies/quality#AFQ_0000256 |
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Description |
Molecular mass is a molecular quality inhered in a molecular entity that expresses its mass relative to 1/12 of the mass of an unbound neutral atom of carbon-12 in its nuclear and electronic ground state and at rest. [Allotrope] |
Super-classes |
af-q:AFQ_0000252c |
URI | http://purl.allotrope.org/ontologies/quality#AFQ_0000257 |
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Description |
Mass-to-charge ratio is a molecular quality that expresses the ratio of the molecular mass to the charge number of a molecular entity. [Allotrope] |
Scope Notes |
This quality is itself a ratio of relative qualities, the molecular mass is relative to the unified atomic mass unit and the electric charge to the elementary charge. [Allotrope] |
Super-classes |
af-q:AFQ_0000252c |
URI | http://purl.allotrope.org/ontologies/quality#AFQ_0000263 |
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Description |
A molecular formula is a molecular quality that inheres in a molecular entity by the relative amount of component atoms. [Allotrope] |
Super-classes |
af-q:AFQ_0000252c |
URI | http://purl.allotrope.org/ontologies/quality#AFQ_0000264 |
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Source | K. K. Murray, R. K. Boyd, M. N. Eberlin, G. J. Langley, L. Li and Y. Naito, Pure Appl. Chem., 2013, 85, 1515-1609 |
Description |
Electron energy is the translational energy that electrons acquire when accelerated in an electric field. [IUPAC] |
Super-classes |
cdao:BFO_0000019c |
URI | http://purl.allotrope.org/ontologies/quality#AFQ_0000265 |
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Description |
Isotopic distribution is a molecular quality inhered in a molecule by the distribution of different isotopes in the molecule. [Allotrope] |
Super-classes |
af-q:AFQ_0000252c |
URI | http://purl.allotrope.org/ontologies/result#AFR_0001857 |
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Description |
An ion facet is a molecular facet that is about some ion. [Allotrope] |
Super-classes |
af-r:AFR_0001951c |
Sub-classes |
af-r:AFR_0001859c |
URI | http://purl.allotrope.org/ontologies/result#AFR_0001859 |
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Description |
Charge state is a facet that is about the electrical charge of an ion. It is single or multiple and positive or negatively charged. [Allotrope] |
Super-classes |
af-r:AFR_0001857c |
URI | http://purl.allotrope.org/ontologies/result#AFR_0001951 |
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Description |
A molecular entity facet is a facet that is about some molecular entity such as atoms, ions or molecules. [Allotrope] |
Super-classes |
af-r:AFR_0000923c |
Sub-classes |
af-r:AFR_0001857c af-r:AFR_0001952c |
URI | http://purl.allotrope.org/ontologies/result#AFR_0001952 |
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Description |
A molecular formula is a molecular entity facet which identifies each constituent element by its chemical symbol and indicates the number of atoms of each element found in each discrete molecular entity of that compound. [CHEMINF] |
Super-classes |
af-r:AFR_0001951c |
URI | http://purl.obolibrary.org/obo/CHEBI_15377 |
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Description |
An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms. [CHEBI] |
Super-classes |
cdao:CHEBI_25367c |
URI | http://purl.obolibrary.org/obo/CHEBI_15379 |
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Description |
An elemental molecule consisting of two bivalently-bonded oxygen atoms. [Allotrope] |
Super-classes |
cdao:CHEBI_25367c |
URI | http://purl.obolibrary.org/obo/CHEBI_16134 |
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Description |
An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. [CHEBI] |
Super-classes |
cdao:CHEBI_25367c |
URI | http://purl.obolibrary.org/obo/CHEBI_16183 |
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Description |
A one-carbon compound in which the carbon is attached by single bonds to four hydrogen atoms. [CHEBI] |
Super-classes |
cdao:CHEBI_25367c |
URI | http://purl.obolibrary.org/obo/CHEBI_16526 |
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Description |
A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. [CHEBI] |
Super-classes |
cdao:CHEBI_25367c |
URI | http://purl.obolibrary.org/obo/CHEBI_17632 |
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Description |
A nitrogen oxoanion formed by loss of a proton from nitric acid. [CHEBI] |
Super-classes |
af-m:AFM_0000161c |
URI | http://purl.obolibrary.org/obo/CHEBI_17997 |
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Description |
An elemental molecule consisting of two trivalently-bonded nitrogen atoms. [CHEBI] |
Super-classes |
cdao:CHEBI_25367c |
URI | http://purl.obolibrary.org/obo/CHEBI_18276 |
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Description |
An elemental molecule consisting of two hydrogens joined by a single bond. [CHEBI] |
Super-classes |
cdao:CHEBI_25367c |
URI | http://purl.obolibrary.org/obo/CHEBI_23367 |
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Source | PAC, 1994, 66, 1077. (Glossary of terms used in physical organic chemistry (IUPAC Recommendations 1994)) on page 1142 |
Description |
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. [IUPAC] |
Super-classes |
cdao:BFO_0000040c |
Sub-classes |
af-m:AFM_0001028c af-m:AFM_0000077c cdao:CHEBI_25367c |
URI | http://purl.obolibrary.org/obo/CHEBI_25367 |
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Source | PAC, 1994, 66, 1077. (Glossary of terms used in physical organic chemistry (IUPAC Recommendations 1994)) on page 1143 |
Description |
A molecule is a polyatomic molecular entity that is an electrically neutral entity consisting of more than one atom. [Allotrope] |
Super-classes |
cdao:CHEBI_23367c |
Sub-classes |
cdao:CHEBI_16183c cdao:CHEBI_16134c cdao:CHEBI_17997c cdao:CHEBI_16526c cdao:CHEBI_15379c cdao:CHEBI_18276c cdao:CHEBI_15377c |
URI | http://purl.obolibrary.org/obo/CHEBI_30212 |
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Source | PAC, 1996, 68, 2223. 'Glossary of terms used in photochemistry (IUPAC Recommendations 1996)' on page 2262 |
Description |
A photon is a particle of zero charge, zero rest mass, spin quantum number 1, energy hν and momentum hν/c (h is the Planck constant, ν the frequency of radiation and c the speed of light), carrier of electromagnetic force. [IUPAC] |
Super-classes |
cdao:CHEBI_36341c |
URI | http://purl.obolibrary.org/obo/CHEBI_33253 |
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Source | https://en.wikipedia.org/wiki/Nucleon |
Description |
A nucleon is either a proton or a neutron. [Wikipedia] |
Super-classes |
cdao:CHEBI_36339c |
Sub-classes |
af-m:AFM_0001023c af-m:AFM_0001027c |
URI | http://purl.obolibrary.org/obo/CHEBI_33681 |
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Description |
An atom of the chemical element Helium. [Allotrope] |
Super-classes |
af-m:AFM_0001028c |
URI | http://purl.obolibrary.org/obo/CHEBI_36338 |
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Description |
Lepton is a fermion that does not experience the strong force (strong interaction). [CHEBI] |
Super-classes |
cdao:CHEBI_36340c |
Sub-classes |
af-m:AFM_0000418c |
URI | http://purl.obolibrary.org/obo/CHEBI_36339 |
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Source | https://en.wikipedia.org/wiki/Baryon |
Description |
Baryon is a fermion that does experience the strong force (strong interaction). [CHEBI] |
Super-classes |
cdao:CHEBI_36340c |
Sub-classes |
cdao:CHEBI_33253c |
URI | http://purl.obolibrary.org/obo/CHEBI_36340 |
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Source | https://en.wikipedia.org/wiki/Fermion |
Description |
Particle of half-integer spin quantum number following Fermi-Dirac statistics. [CHEBI] |
Super-classes |
cdao:CHEBI_36342c |
Sub-classes |
cdao:CHEBI_36339c cdao:CHEBI_36338c |
URI | http://purl.obolibrary.org/obo/CHEBI_36341 |
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Source | https://en.wikipedia.org/wiki/Boson |
Description |
A boson is a particle that follows Bose–Einstein statistics. [Wikipedia] |
Super-classes |
cdao:CHEBI_36342c |
Sub-classes |
cdao:CHEBI_30212c |
URI | http://purl.obolibrary.org/obo/CHEBI_36342 |
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Description |
A subatomic particle is a material that is below the scale of an atom. [Allotrope] |
Super-classes |
cdao:BFO_0000040c |
Sub-classes |
cdao:CHEBI_36341c cdao:CHEBI_36347c cdao:CHEBI_36340c |
URI | http://purl.obolibrary.org/obo/CHEBI_36347 |
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Description |
A nuclear particle is a nucleus or any of its constituents in any of their energy states. [CHEBI] |
Super-classes |
cdao:CHEBI_36342c |
Sub-classes |
af-m:AFM_0001023c af-m:AFM_0001027c af-m:AFM_0000226c |
URI | http://purl.obolibrary.org/obo/CHEBI_49468 |
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Description |
An silver(1+) ion is a +1 charged silver cation. [Allotrope] |
Super-classes |
af-m:AFM_0000189c |
URI | http://purl.obolibrary.org/obo/PATO_0002070 |
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Description |
Affinity is a molecular quality that arises from the molecular attraction exerted between two atoms or compounds. [PATO] |
Super-classes |
af-q:AFQ_0000252c |
URI | http://purl.obolibrary.org/obo/PATO_0002186 |
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Description |
Polarity is a molecular quality that inheres in a molecular entity by virtue of whether or not the molecular entity has a separation of electric charge which leads to the molecule having an electric dipole. [PATO] |
Super-classes |
af-q:AFQ_0000252c |
URI | http://purl.obolibrary.org/obo/PATO_0002193 |
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Description |
Electric charge is a molecular quality that inheres in a molecular entity by virtue of the overall electric charge of the molecule, which is due to a comparison between the total number of electrons and the total number of protons. [PATO] |
Super-classes |
af-q:AFQ_0000252c |
Sub-classes |
cdao:PATO_0002195c cdao:PATO_0002194c cdao:PATO_0002196c |
URI | http://purl.obolibrary.org/obo/PATO_0002194 |
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Description |
Neutral charge is a quality which inheres in a molecular entity by virtue of the molecular entity possessing the same amount of electrons overall as protons, thus having an overall neutral charge. [PATO] |
Super-classes |
cdao:PATO_0002193c |
URI | http://purl.obolibrary.org/obo/PATO_0002195 |
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Description |
Positive charge is a quality which inheres in a molecular entity by virtue of the molecular entity possessing more protons overall than electrons, thus having an overall positive charge. [PATO] |
Super-classes |
cdao:PATO_0002193c |
URI | http://purl.obolibrary.org/obo/PATO_0002196 |
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Description |
Negative charge is a quality which inheres in a molecular entity by virtue of the molecular entity possessing more electrons overall than protons, thus having an overall negative charge. [PATO] |
Super-classes |
cdao:PATO_0002193c |
URI | http://purl.org/dc/terms/LicenseDocument |
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Description | These taxonomies contain material or may constitute derivative works of material which may be subject to copyright by one of the following organizations. By using these taxonomies, you agree to the following terms and conditions applicable to its contents: ****************************************************************************** Copyright Notice and Terms for IUPAC Gold Book ______________________________________________________________________________ Copyright © 1998, Regents of the University of California All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ****************************************************************************** Copyright Notice and Terms for PSI-MS (Proteomics Standards Initiative - Mass Spectrometry) Mass spectrometer output files and spectra interpretation _____________________________________________________________________________ Created by Matt Chambers, Andreas Bertsch, Marius Kallhardt, Eric Deutsch Fredrik Levander, Pierre-Alain Binz, and Gerhard Mayer. Publisher: HUPO Proteomics Standards Initiative Mass Spectrometry Standards Working Group and HUPO Proteomics Standards Initiative Proteomics Informatics Working Group. This work is used pursuant to a Creative Commons license available here: http://creativecommons.org/licenses/by/3.0/legalcode ****************************************************************************** Attribution Notice for National Center for Biomedical Ontology materials. This work contains material from the Cell Ontology and Clinical Measurement Ontology, available here: http://bioportal.bioontology.org/. ****************************************************************************** Attribution Notice for ChEBI This work contains material from the European Bioinformatics Institute’s ChEBI database. ****************************************************************************** Attribution Notice for Quantities Units Dimensions Data Types (http://www.qudt.org/) This work contains content from www.qudt.org and is used pursuant to a Creative Commons License available here: http://creativecommons.org/licenses/by-sa/3.0/us/legalcode. The original work may have been modified. ****************************************************************************** Copyright and Attribution Notice for Dublin Core Metadata Initiative Document This work contains material from the following DCMI document used pursuant to a creative commons license available here: https://creativecommons.org/licenses/by/4.0/legalcode. This material may have been modified or changed. Timestamped URL: http://dublincore.org/documents/2012/06/14/dcmi-terms/ Date Issued: 2012-06-14 Document Status: This is a DCMI Recommendation. Copyright © 1995-2015 DCMI. All Rights Reserved. DCMI liability, trademark/service mark, document use and software licensing rules apply. ****************************************************************************** |
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Description | Copyright (c) 2019 International Union of Pure Applied Chemistry |
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Description | Reproduced by permission of International Union of Pure and Applied Chemistry |
http://purl.allotrope.org/voc/afo/perspective/REC/2020/12/molecular-scale
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c | Classes |
op | Object Properties |
fp | Functional Properties |
dp | Data Properties |
dp | Annotation Properties |
p | Properties |
ni | Named Individuals |