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AFT Molecular Scale - Perspective (REC/2021/03)

Metadata

URI
http://purl.allotrope.org/voc/afo/perspective/REC/2021/03/molecular-scale
Publisher(s)
None
Contributor(s)
None
Modified
2021-03-29T12:00:00+00:00
Issued
2021-03-29T12:00:00+00:00
Version Information
REC/2021/03
Version URI
http://purl.allotrope.org/voc/afo/perspective/REC/2021/03/molecular-scale
Imports
http://purl.allotrope.org/voc/afo/REC/2021/03/curation
http://purl.allotrope.org/voc/bfo/REC/2018/04/bfo-2-0
http://purl.allotrope.org/voc/skos/REC/2018/10/skos
License & Rights
http://purl.allotrope.org/voc/iupac-license
http://purl.allotrope.org/voc/©
Ontology RDF
RDF (turtle)

Description

Perspective taxonomy of materal entities of molecular granularity or smaller, as discussed in chemistry, mostly a subset of ChEBI

Table of Contents

  1. Classes
  2. Object Properties
  3. Datatype Properties
  4. Annotation Properties
  5. Named Individuals
  6. Namespaces
  7. Legend

Overview

Pictures say 1,000 words
Figure 1: Ontology overview

Classes

ionc # Classes

URI http://purl.allotrope.org/ontologies/material#AFM_0000077
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_0000161c
af-m:AFM_0000189c

anionc # Classes

URI http://purl.allotrope.org/ontologies/material#AFM_0000161
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

cationc # Classes

URI http://purl.allotrope.org/ontologies/material#AFM_0000189
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

nucleusc # Classes

URI http://purl.allotrope.org/ontologies/material#AFM_0000226
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

electronc # Classes

URI http://purl.allotrope.org/ontologies/material#AFM_0000418
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

protonc # Classes

URI http://purl.allotrope.org/ontologies/material#AFM_0001023
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

neutronc # Classes

URI http://purl.allotrope.org/ontologies/material#AFM_0001027
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_33253c
cdao:CHEBI_36347c

atomc # Classes

URI http://purl.allotrope.org/ontologies/material#AFM_0001028
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

molecular entity qualityc # Classes

URI http://purl.allotrope.org/ontologies/quality#AFQ_0000252
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 cdao:PATO_0002193c
af-q:AFQ_0000256c
af-q:AFQ_0000257c
cdao:PATO_0002186c
af-q:AFQ_0000263c
af-q:AFQ_0000319c
af-q:AFQ_0000265c
cdao:PATO_0002070c

molecular mass (molecular quality)c # Classes

URI http://purl.allotrope.org/ontologies/quality#AFQ_0000256
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

mass-to-charge ratio (molecular quality)c # Classes

URI http://purl.allotrope.org/ontologies/quality#AFQ_0000257
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

molecular formula (molecular quality)c # Classes

URI http://purl.allotrope.org/ontologies/quality#AFQ_0000263
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

electron energyc # Classes

URI http://purl.allotrope.org/ontologies/quality#AFQ_0000264
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

Electron energy is the translational energy that electrons acquire when accelerated in an electric field. [IUPAC]

Super-classes cdao:BFO_0000019c

isotopic distribution (molecular quality)c # Classes

URI http://purl.allotrope.org/ontologies/quality#AFQ_0000265
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

chemical shift (molecular quality)c # Classes

URI http://purl.allotrope.org/ontologies/quality#AFQ_0000319
Description

The fractional variation of the resonance frequency of a nucleus in nuclear magnetic resonance (NMR) spectroscopy in consequence of its magnetic environment. [IUPAC]

Super-classes af-q:AFQ_0000252c

ion facetc # Classes

URI http://purl.allotrope.org/ontologies/result#AFR_0001857
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

charge statec # Classes

URI http://purl.allotrope.org/ontologies/result#AFR_0001859
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

molecular entity facetc # Classes

URI http://purl.allotrope.org/ontologies/result#AFR_0001951
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

molecular formulac # Classes

URI http://purl.allotrope.org/ontologies/result#AFR_0001952
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

water (molecule)c # Classes

URI http://purl.obolibrary.org/obo/CHEBI_15377
Description

An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms. [CHEBI]

Super-classes cdao:CHEBI_25367c

dioxygen (molecule)c # Classes

URI http://purl.obolibrary.org/obo/CHEBI_15379
Description

An elemental molecule consisting of two bivalently-bonded oxygen atoms. [Allotrope]

Super-classes cdao:CHEBI_25367c

ammonia (molecule)c # Classes

URI http://purl.obolibrary.org/obo/CHEBI_16134
Description

An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. [CHEBI]

Super-classes cdao:CHEBI_25367c

methane (molecule)c # Classes

URI http://purl.obolibrary.org/obo/CHEBI_16183
Description

A one-carbon compound in which the carbon is attached by single bonds to four hydrogen atoms. [CHEBI]

Super-classes cdao:CHEBI_25367c

carbon dioxide (molecule)c # Classes

URI http://purl.obolibrary.org/obo/CHEBI_16526
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

nitrate ionc # Classes

URI http://purl.obolibrary.org/obo/CHEBI_17632
Description

A nitrogen oxoanion formed by loss of a proton from nitric acid. [CHEBI]

Super-classes af-m:AFM_0000161c

dinitrogen (molecule)c # Classes

URI http://purl.obolibrary.org/obo/CHEBI_17997
Description

An elemental molecule consisting of two trivalently-bonded nitrogen atoms. [CHEBI]

Super-classes cdao:CHEBI_25367c

dihydrogen (molecule)c # Classes

URI http://purl.obolibrary.org/obo/CHEBI_18276
Description

An elemental molecule consisting of two hydrogens joined by a single bond. [CHEBI]

Super-classes cdao:CHEBI_25367c

molecular entityc # Classes

URI http://purl.obolibrary.org/obo/CHEBI_23367
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_0000077c
cdao:CHEBI_25367c
af-m:AFM_0001028c

moleculec # Classes

URI http://purl.obolibrary.org/obo/CHEBI_25367
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_15377c
cdao:CHEBI_16183c
cdao:CHEBI_15379c
cdao:CHEBI_18276c
cdao:CHEBI_17997c
cdao:CHEBI_16526c
cdao:CHEBI_16134c

photonc # Classes

URI http://purl.obolibrary.org/obo/CHEBI_30212
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

nucleonc # Classes

URI http://purl.obolibrary.org/obo/CHEBI_33253
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_0001027c
af-m:AFM_0001023c

helium (atom)c # Classes

URI http://purl.obolibrary.org/obo/CHEBI_33681
Description

An atom of the chemical element Helium. [Allotrope]

Super-classes af-m:AFM_0001028c

leptonc # Classes

URI http://purl.obolibrary.org/obo/CHEBI_36338
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

baryonc # Classes

URI http://purl.obolibrary.org/obo/CHEBI_36339
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

fermionc # Classes

URI http://purl.obolibrary.org/obo/CHEBI_36340
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_36338c
cdao:CHEBI_36339c

bosonc # Classes

URI http://purl.obolibrary.org/obo/CHEBI_36341
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

subatomic particlec # Classes

URI http://purl.obolibrary.org/obo/CHEBI_36342
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_36340c
cdao:CHEBI_36347c

nuclear particlec # Classes

URI http://purl.obolibrary.org/obo/CHEBI_36347
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_0000226c
af-m:AFM_0001027c

silver(1+) ionc # Classes

URI http://purl.obolibrary.org/obo/CHEBI_49468
Description

An silver(1+) ion is a +1 charged silver cation. [Allotrope]

Super-classes af-m:AFM_0000189c

affinityc # Classes

URI http://purl.obolibrary.org/obo/PATO_0002070
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

polarity (molecular quality)c # Classes

URI http://purl.obolibrary.org/obo/PATO_0002186
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

electric charge (molecular quality)c # Classes

URI http://purl.obolibrary.org/obo/PATO_0002193
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_0002196c
cdao:PATO_0002195c
cdao:PATO_0002194c

neutral chargec # Classes

URI http://purl.obolibrary.org/obo/PATO_0002194
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

positive chargec # Classes

URI http://purl.obolibrary.org/obo/PATO_0002195
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

negative chargec # Classes

URI http://purl.obolibrary.org/obo/PATO_0002196
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

LicenseDocumentc # Classes

URI http://purl.org/dc/terms/LicenseDocument
Members http://purl.allotrope.org/voc/iupac-license
http://purl.allotrope.org/voc/creative-commons-attribution-license

RightsStatementc # Classes

URI http://purl.org/dc/terms/RightsStatement
Members http://purl.allotrope.org/voc/iupac-copyright
http://purl.allotrope.org/voc/copyright
http://purl.allotrope.org/voc/attribution

Object Properties

OBI_0000643op # OPs

URI http://purl.obolibrary.org/obo/OBI_0000643

closeMatchop # OPs

URI http://www.w3.org/2004/02/skos/core#closeMatch

exactMatchop # OPs

URI http://www.w3.org/2004/02/skos/core#exactMatch

Datatype Properties

namedp # DPs

URI http://xmlns.com/foaf/0.1/name

Annotation Properties

AFX_0002794ap # APs

URI http://purl.allotrope.org/ontologies/property#AFX_0002794

AFX_0002795ap # APs

URI http://purl.allotrope.org/ontologies/property#AFX_0002795

AFX_0002796ap # APs

URI http://purl.allotrope.org/ontologies/property#AFX_0002796

AFX_0002798ap # APs

URI http://purl.allotrope.org/ontologies/property#AFX_0002798

AFX_0002808ap # APs

URI http://purl.allotrope.org/ontologies/property#AFX_0002808

AFX_0002809ap # APs

URI http://purl.allotrope.org/ontologies/property#AFX_0002809

AFX_0002811ap # APs

URI http://purl.allotrope.org/ontologies/property#AFX_0002811

IAO_0000115ap # APs

URI http://purl.obolibrary.org/obo/IAO_0000115

IAO_0000412ap # APs

URI http://purl.obolibrary.org/obo/IAO_0000412

descriptionap # APs

URI http://purl.org/dc/terms/description

hasVersionap # APs

URI http://purl.org/dc/terms/hasVersion

replacesap # APs

URI http://purl.org/dc/terms/replaces

sourceap # APs

URI http://purl.org/dc/terms/source

titleap # APs

URI http://purl.org/dc/terms/title

minQualifiedCardinalityap # APs

URI http://www.w3.org/2002/07/owl#minQualifiedCardinality

definitionap # APs

URI http://www.w3.org/2004/02/skos/core#definition

prefLabelap # APs

URI http://www.w3.org/2004/02/skos/core#prefLabel

Named Individuals

Derivative works attributionni

Class(es)
dct:RightsStatement
URI http://purl.allotrope.org/voc/attribution
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. ******************************************************************************

Copyright © 2015-2020 Allotrope Foundationni

Class(es)
dct:RightsStatement
URI http://purl.allotrope.org/voc/copyright
Description Copyright © 2015-2020 Allotrope Foundation

Creative Commons Attribution 4.0 International Public Licenseni

Class(es)
dct:LicenseDocument
URI http://purl.allotrope.org/voc/creative-commons-attribution-license
Description This work is licensed under a Creative Commons Attribution 4.0 International License http://creativecommons.org/licenses/by/4.0/. THESE MATERIALS ARE PROVIDED "AS IS" AND ALLOTROPE EXPRESSLY DISCLAIMS ALL WARRANTIES, EXPRESS, IMPLIED OR STATUTORY, INCLUDING, WITHOUT LIMITATION, THE WARRANTIES OF NON-INFRINGEMENT, TITLE, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. Copyright © 2015-2020 Allotrope Foundation

iupac-licenseni

Class(es)
dct:LicenseDocument
URI http://purl.allotrope.org/voc/iupac-license
Description Reproduced by permission of International Union of Pure and Applied Chemistry

Namespaces

default (:)
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bfo
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cdao
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chebi
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chmo
http://purl.obolibrary.org/obo/CHMO
dct
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foaf
http://xmlns.com/foaf/0.1/
formats
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iao
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obi
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ops
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ore
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org
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owl
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pato
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pav
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prov
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qudt
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rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
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ro
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sdo
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sio
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skos
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time
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void
http://rdfs.org/ns/void#
xsd
http://www.w3.org/2001/XMLSchema#

Legend

cClasses
opObject Properties
fpFunctional Properties
dpData Properties
dpAnnotation Properties
pProperties
niNamed Individuals