chemrof
type: Ontology
IAO_0000700: chemical entity or grouping
IAO_0000700: connectivity
IAO_0000700: informational chemical entity
IAO_0000700: is part or whole
IAO_0000700: material
IAO_0000700: owl class
IAO_0000700: reaction
IAO_0000700: reaction grouping class
IAO_0000700: specificity mixin
IAO_0000700: state
license: https://creativecommons.org/publicdomain/zero/1.0/
title: Chemical Entities Mixtures and Reactions Ontological Framework
version: 0.0.1
generation date: 2022-09-06T11:54:56
metamodel version: 1.7.0
source file: chemrof.yaml
source file date: 2022-09-06T11:54:43
source file size: 83955

AZE notation html
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: chemical representation
definition: E.g. 12 /6C

acid anion grouping class
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: name
subclass of: grouping class for acids or bases
definition: A molecule grouping class that groups the different ion forms of the base of an acid
examples: Example(value='citrate', description=None)
examples: Example(value='pimelate', description=None)

acid base conflation class
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: acid base
  on property: has physiological base
subclass of: grouping class for acids or bases
definition: A molecule grouping class that can groups an acid together with all its conjugate bases. physiological
examples: Example(value='citrate/citric acid', description=None)

amino acid sequence interval
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: amino acid sequence string
  on property: has sequence representation
subclass of: sequence interval

atom anion
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: elemental charge
subclass of: anion state
subclass of: monoatomic ion
definition: A monoatomic ion that is negative

atom cation
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: elemental charge
subclass of: cation state
subclass of: monoatomic ion
definition: A monoatomic ion that is positive, e.g Cu(2+)
examples: Example(value='Helium(2+)', description='1S/He/q+2')

atom grouping by periodic table block
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: periodic table block
  on property: in periodic table block
subclass of: atom grouping by periodic table placement
definition: Example: group 13 atom

atom grouping by periodic table group
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: periodic table group
  on property: in periodic table group
subclass of: atom grouping by periodic table placement
definition: Example: p-block atom

atom grouping by property
type: Class
type: class_definition
subclass of: atom grouping class
definition: Example: metal atom

chemical grouping by charge
type: Class
type: class_definition
subclass of: Restriction
  all values from: molecule grouping class
  on property: subtype of
subclass of: Restriction
  max qualified cardinality: 1
  on class: Uriorcurie
  on property: has charge state
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical entity
  on property: charge agnostic entity
subclass of: grouping class
definition: A grouping class that refines a charge-neutral entity
examples: Example(value='copper cation', description=None)

chemical salt by anion
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: name
subclass of: chemical salt grouping class
definition: A grouping class for a chemical salt named by anion
examples: Example(value='chloride salt', description=None)

chemical salt by cation
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: name
subclass of: chemical salt grouping class
definition: A grouping class for a chemical salt named by cation
examples: Example(value='sodium salt', description=None)

chirality center
type: Class
type: class_definition
subclass of: stereocenter
definition: a stereocenter consisting of an atom holding a set of ligands (atoms or groups of atoms) in a spatial arrangement which is not superimposable on its mirror image.

copolymer
type: Class
type: class_definition
subclass of: Restriction
  all values from: macromolecule
  on property: polymer of
subclass of: monomolecular polymer
alternative label: heteropolymer
definition: a polymer with a more than one type of repeating unit
examples: Example(value='PEVA', description=None)
examples: Example(value='styrene-butadiene rubber', description='The repeat units based on styrene and 1,3-butadiene form two repeating units, which can alternate in any order in the macromolecule, making the polymer thus a random copolymer.')

DNA sequence interval
type: Class
type: class_definition
subclass of: nucleotide sequence interval

entity with atoms enumerated
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi chemical sublayer
subclass of: specificity mixin
subclass of: mixin
definition: A mixin for an entity that consists of one or more atoms where the atoms and the number of occurrences is counted (corresponding to the chemical layer in InChI)

entity with charge specified
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi charge sublayer
subclass of: specificity mixin
subclass of: mixin
definition: A mixin for an entity where the charge is explicitly specified (corresponding to the /q layer in InChI)

entity with connectivity specificied
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi atom connections sublayer
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi hydrogen connections sublayer
subclass of: specificity mixin
subclass of: mixin
definition: A mixin for an entity that consists of two or more atom occurrences where the connectivity is specified (corresponding to the /c layer in InChI)

entity with isotope specified
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi isotopic layer
subclass of: specificity mixin
subclass of: mixin
definition: A mixin for an entity where the charge is explicitly specified (corresponding to the /q layer in InChI)

entity with stereochemistry specified
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi stereochemical double bond sublayer
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi tetrahedral stereochemical sublayer
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi stereochemical type sublayer
subclass of: specificity mixin
subclass of: mixin
definition: A mixin for an entity where the stereochemistry is explicitly specified (corresponding to the /t, m/, and /s layers in InChI)

ester
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical entity
  on property: has parent alcohol
subclass of: Restriction
  max qualified cardinality: 1
  on class: Bronsted acid
  on property: has parent acid
subclass of: molecule
definition: An ester is a chemical compound derived from an acid (organic or inorganic) in which at least one –OH hydroxyl group is replaced by an –O– alkyl (alkoxy) group
examples: Example(value='butyl ethanoate', description='has parent alcohol butanol and has parent acid acetic acid')

fully specified atom
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: elemental charge
subclass of: Restriction
  max qualified cardinality: 1
  on class: count
  on property: neutron number
subclass of: atom
alternative label: atomic species
alternative label: chemical species of an element
definition: An atom type that has atomic number, charge, and neutron number stated (equivalently: protons + mass + charge)
note: {'chemical species of an element': 'Specific form of an element defined as to isotopic composition, electronic or oxidation state, and/or complex or molecular structure https://goldbook.iupac.org/terms/view/CT06859'}
examples: Example(value='Helium-4(2+)', description='The atom that is equivalent to an alpha particle 1S/He/q+2/i1+0')

functional group
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: molecule
  on property: is substitutent group from
subclass of: molecular component

general acid base grouping class
type: Class
type: class_definition
subclass of: grouping class for acids or bases
definition: A molecule grouping class that can groups an acid together with all its conjugate bases. physiological
examples: Example(value='tricarboxylic acid/tricarboxylic acid anion', description=None)

glycan
type: Class
type: class_definition
subclass of: macromolecule
alternative label: polysaccharides
definition: A macromolecule consisting of a large number of monosaccharides linked glycosidically
note: Glycans composed of a single type of monosaccharide residue (homopolysaccharide, synonym homoglycan) are named by replacing the ending '-ose' of the sugar by '-an', e.g. mannans, fructans, xylans, arabinans
examples: Example(value='https://www.glycoepitope.jp/epitopes/EP0311', description='GalNAc(b1-4)[Neu5Ac(a2-3)]Gal(b1)')

homopolymer
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: macromolecule
  on property: polymer of
subclass of: monomolecular polymer
definition: a polymer with a single type of repeating unit
examples: Example(value='polystyrene', description='composed only of styrene-based repeat units')

is part
type: Class
type: class_definition
subclass of: is part or whole

is whole
type: Class
type: class_definition
subclass of: is part or whole

isobar
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: mode of formation
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: decay mode
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: decay energy
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical element
  on property: has element
subclass of: Restriction
  max qualified cardinality: 1
  on class: number of years
  on property: half life
subclass of: Restriction
  max qualified cardinality: 1
  on class: isotope
  on property: decay product
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical entity
  on property: isobar of
subclass of: Restriction
  max qualified cardinality: 1
  on class: count
  on property: nucleon number
subclass of: nuclide
definition: Isobars are atoms (nuclides) of different chemical elements that have the same number of nucleons.
examples: Example(value='isobar-40', description='Any nuclide with a mass number of 40: 40S, 40Cl, 40Ar, 40K, and 40Ca')

isomerase reaction
type: Class
type: class_definition
subclass of: reaction
definition: A reaction that converts a molecule from one isomer to another.

lipid
type: Class
type: class_definition
subclass of: macromolecule

material grouping class
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: material
  on property: classifies
subclass of: grouping class
definition: A grouping class that classifies materials
examples: Example(value='MREO', description='mixed rare earth oxides')

mineral
type: Class
type: class_definition
subclass of: material

moiety
type: Class
type: class_definition
subclass of: molecular component
definition: a named part of a molecule. In some instances moieties may be composed of yet smaller moieties and functional groups

molecular cation
type: Class
type: class_definition
subclass of: cation state
subclass of: polyatomic ion
definition: A polyatomic ion that is positive

molecular derivative grouping class
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical entity
  on property: derivative of
subclass of: Restriction
  max qualified cardinality: 1
  on class: molecule
  on property: classifies
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: name
subclass of: molecule grouping class
definition: A grouping class defined as a derivative of another molecule or molecular grouping class
examples: Example(value='D-ornithine derivative', description=None)
examples: Example(value='oxoacid derivative', description=None)

molecular species
type: Class
type: class_definition
subclass of: molecule
definition: A molecule in which the units are identical. Example: methyl

molecular subsequence
type: Class
type: class_definition
subclass of: polymer part

molecule grouping class defined by addition of a group
type: Class
type: class_definition
subclass of: Restriction
  all values from: chemical group
  on property: has group
subclass of: Restriction
  max qualified cardinality: 1
  on class: polyatomic entity
  on property: derivative of
subclass of: molecule grouping class
definition: A grouping class defined in terms of a derivative of a molecule and the addition of a group
examples: Example(value='acetyl xylan', description=None)

molecule grouping class defined by components
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical entity or grouping
  on property: has part
subclass of: molecule grouping class
definition: A grouping class defined as an exhaustive list of components
examples: Example(value='nucleoside', description='A nucleoside consists of a nucleobase and a five-carbon sugar (ribose or 2-deoxyribose)')
examples: Example(value='nucleotide', description='a nucleotide is composed of a nucleobase, a five-carbon sugar, and one or more phosphate groups')

monomer
type: Class
type: class_definition
subclass of: polymer part
alternative label: momomer species

monomeric polymeric grouping class
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical entity
  on property: has repeat unit
subclass of: generalized molecular structure class
examples: Example(value='polynucleotide', description='A polynucleotide molecule is a biopolymer composed of 13 or more nucleotide monomers covalently bonded in a chain')

nanostructure
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: nanostructure_morphology_enum
  on property: has morphological category
subclass of: material
definition: A nanostructure is a structure of intermediate size between microscopic and molecular structures. Nanostructural detail is microstructure at nanoscale.
examples: Example(value='Zinc oxide (ZnO) nanorod', description='A nanostructure that has rod morphology and is composed of zinc oxide')
examples: Example(value='platinum copper nanoparticle', description='A nanostructure that is made from platinum and copper atoms')

natural product
type: Class
type: class_definition
subclass of: molecule

non species molecule
type: Class
type: class_definition
subclass of: molecule
definition: A molecule in which the units are not identical. TODO: move this higher

peptide
type: Class
type: class_definition
subclass of: macromolecule

protein
type: Class
type: class_definition
subclass of: macromolecule

RNA sequence interval
type: Class
type: class_definition
subclass of: nucleotide sequence interval

racemic mixture
type: Class
type: class_definition
subclass of: Restriction
  on class: enantiomer
  on property: has right enantiomer
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: IUPAC name
subclass of: Restriction
  on class: enantiomer
  on property: has left enantiomer
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: molecule
  on property: chirality agnostic form
subclass of: precise chemical mixture
alternative label: racemate
alternative label: racemic mixture of enantiomers
definition: a chemical compound that has equal amounts of left- and right-handed enantiomers of a chiral molecule. An example is Thalidomide

radionuclide
type: Class
type: class_definition
subclass of: nuclide
alternative label: radioactive isotope
alternative label: radioactive nuclide
definition: an atom that has excess nuclear energy, making it unstable
examples: Example(value='radioactive isotope', description=None)

small molecule
type: Class
type: class_definition
subclass of: molecule
definition: A molecule characterized by availability in small-molecule databases

standard inchi object
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi proton sublayer
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi hydrogen connections sublayer
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi chemical sublayer
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi stereochemical double bond sublayer
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi atom connections sublayer
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi charge sublayer
subclass of: Restriction
  on class: String
  on property: inchi version string
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi isotopic layer
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi stereochemical type sublayer
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi tetrahedral stereochemical sublayer
subclass of: inchi object

supramolecular polymer
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical entity
  on property: has repeat unit
subclass of: Restriction
  max qualified cardinality: 1
  on class: macromolecule
  on property: polymer of
subclass of: molecular complex
definition: polymeric arrays of monomeric units that are connected by reversible and highly directional secondary interactions–that is, non-covalent bonds

tanimoto similarity
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: Float
  on property: score
subclass of: molecule pairwise similarity
alternative label: Jaccard similarity
alternative label: Tanimoto coefficient

uncharged atom
type: Class
type: class_definition
subclass of: atom ionic form
subclass of: uncharged
definition: An atom type that has no charge

uncharged molecule
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: elemental charge
subclass of: molecule
subclass of: uncharged
definition: A molecule that has no charge

atomically connected to
type: ObjectProperty
type: slot_definition
domain: atom occurrence
range: atom occurrence

bond energy
type: ObjectProperty
type: slot_definition
domain: atomic bond
range: Float
alternative label: average bond enthalpy
alternative label: mean bond enthalpy
definition: the measure of bond strength in a chemical bond.

bond length
type: ObjectProperty
type: slot_definition
domain: atomic bond
range: Float
definition: the average distance between nuclei of two bonded atoms in a molecule

canonical smiles string
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: smiles string
definition: A deterministic SMILES string. Note there is no unique system for canonical smiles strings

carbbank representation
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: carboydrate representation
definition: The carbohydrate structure format used by the Complex Carbohydrate Structure Database (CCSD) originally developed at the University of Georgia. This is a 2D structure where bars and hyphens are used to indicate linkages, and monosaccharides are specified in the following order, separated by hyphens: anomer - configuration symbol - monosaccharide abbreviation.

curly smiles string
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: chemical formula
alternative label: CurlySMILES
definition: CurlySMILES is a chemical line notation which extends SMILES with annotations for storage, retrieval and modeling of interlinked, coordinated, assembled and adsorbed molecules in supramolecular structures and nanodevices. https://jcheminf.biomedcentral.com/articles/10.1186/1758-2946-3-1

empirical formula
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: chemical formula
definition: A chemical formula where numbers denote relative proportion of atoms. E.g. CH2O for glucose

enantiomer of
type: ObjectProperty
type: slot_definition
domain: molecule
range: molecule
sub property of: stereoisomer of
alternative label: enantiomorph of
definition: a stereoisomer relationship where the two forms are mirror images of one another

epimer of
type: ObjectProperty
type: slot_definition
domain: molecule
range: molecule
sub property of: diastereoisomers of
definition: A diastereoisomer of relationship in which the isomers differ at only one stereocenter

extended smiles string
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: smiles string
alternative label: CXSMILES

functional isomer of
type: ObjectProperty
type: slot_definition
domain: molecule
range: molecule
sub property of: structural isomer of
alternative label: functional group isomer of
definition: structural isomers that have the same molecular formula (that is, the same number of atoms of the same elements), but the atoms are connected in different ways so that the groupings are dissimilar.

generalized empirical formula
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: chemical formula
definition: A variant of an empirical formula where numbers are replaced by generic ns; e.g. CnH2n+2 for alkane

glycoct condensed
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: carboydrate representation
definition: This is a multiline format used by GlycomeDB, among others, and uses a graph notation to represent glycans, similar to KCF. Monosaccharides are specified more strictly to be able to map the monosaccharides between different representations. Substituents, such as N-acetyl, are specified as separate nodes from their basetypes and are linked together in the edge section. If newlines are removed, this format can be made linear.

glycominds linearcode representation
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: carboydrate representation
definition: A linear notation proposed by GlycoMinds, Ltd., where monosaccharides are indicated by a one- or two-letter code, linkages are indicated by “a” or “b” for anomers and a single number for the carbon number linkage on the reducing end, and branches are indicated by parentheses. This format is the most compact among existing formats, and several databases use a modified form of this format to accommodate additional codes and varying carbohydrate structures (such as ambiguous structures).

has cyclic structure
type: ObjectProperty
type: slot_definition
domain: molecule
range: Boolean
sub property of: chemical property
definition: true if the molecule possesses a cycle in the atom connectivity graph

has molfile location
type: ObjectProperty
type: slot_definition
range: file location
sub property of: information property
definition: Location of a MolFile representing a chemical structure

has polymer repeat units
type: ObjectProperty
type: slot_definition
range: polymer repeat unit
definition: Relation between a polymer and all instances of a repeated polymeric unit

has rauxinfo representation
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: chemical representation
alternative label: RAuxInfo
definition: Auxhiliary information on top of a RInChi
note: A half-reaction, such as a RInChI with starting materials and no identified products, is a valid RInChI

inchi fixed H layer
type: ObjectProperty
type: slot_definition
range: String
sub property of: inchi sublayer

inchi key string
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: hashed chemical formula
definition: A hashed representation of an InChi string
hash of: inchi string

inchi reconnected layer
type: ObjectProperty
type: slot_definition
range: String
sub property of: inchi sublayer

isomeric smiles string
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: smiles string
alternative label: iso-SMILES
definition: A SMILES string that distinguishes between isomeric forms. E.g. [13C] for carbon-13

isotone of
type: ObjectProperty
type: slot_definition
domain: isotope
range: isotope
sub property of: alternate form of
definition: relationship that holds between two isotones, always holds if the isotones have a different atomic number and the same neutron number.

kegg chemical function representation
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: carboydrate representation
definition: A multiline format used by the KEGG GLYCAN database and represents glycans as graphs. Monosaccharides are represented as nodes, and glycosidic linkages are represented as edges. Each node is given a unique number, and x- and y- coordinates are specified such that the glycan structure can be drawn on a 2D plane. Edge information uses the node numbers to specify anomeric and carbon number information. Monosaccharide names are specified as text, and no particular rules are specified to represent these names.

linucs representation
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: carboydrate representation
definition: A unique linear notation proposed and used by GLYCOSCIENCES.de, with the reducing end specified on the left. Monosaccharides, written according to CarbBank rules, are surrounded by square brackets and anomers, and stereochemistry is specified and separated by hyphens. Glycosidic linkages are also surrounded by hyphens, and carbon numbers of the linkages are separated by the plus sign. Branches are indicated by curly brackets.

long rinchi key string
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: rinchi key string

lychi string
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: chemical formula

molar cohesive energy
type: ObjectProperty
type: slot_definition
range: String
sub property of: thermophysical property

molar value
type: ObjectProperty
type: slot_definition
range: String
sub property of: thermophysical property

molecular formula
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: chemical formula
alternative label: Hill notation
alternative label: chemical formula
definition: A chemical formula where numbers denote atom count. E.g. C6H12O6 for glucose

next in homologous series from
type: ObjectProperty
type: slot_definition
domain: molecule
range: molecule
definition: Next in a sequence of compounds with the same functional group and similar chemical properties in which the members of the series can be branched or unbranched. E.g. ethane (C2H6) next in homologous series from methane (CH4)

nuclear isomer of
type: ObjectProperty
type: slot_definition
domain: isotope
range: isotope
sub property of: alternate form of
definition: relationship that holds between two nuclear isomers, always holds if the isomers have the same nucleon number but different energy states

position isomer of
type: ObjectProperty
type: slot_definition
domain: molecule
range: molecule
sub property of: structural isomer of
alternative label: regioisomerism isomer of
definition: a functional group or other substituent changes position on a parent structure.

selfies string
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: chemical formula
alternative label: SELFIES

short rinchi key string
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: rinchi key string

skeletal isomer of
type: ObjectProperty
type: slot_definition
domain: molecule
range: molecule
sub property of: structural isomer of
alternative label: chain isomer of
definition: components of the (usually carbon) skeleton are distinctly re-ordered to create different structures. Pentane exists as three isomers: n-pentane (often called simply "pentane"), isopentane (2-methylbutane) and neopentane (dimethylpropane).

tautomer of
type: ObjectProperty
type: slot_definition
domain: molecule
range: molecule
sub property of: structural isomer of
definition: structural isomers (constitutional isomers) of chemical compounds that readily interconvert. Examples: a neutral amino acid and its zwitterion

transitive conjugatated form of
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical entity
sub property of: derivative of
transitive closure of: direct conjugatated from

wurcs representation
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: carboydrate representation

subset_definition
type: Class

molecular electronic absorption spectroscopy
type: ObjectProperty
type: slot_definition
range: String
sub property of: molecular property

molecular spectroscopy by energy state
type: ObjectProperty
type: slot_definition
range: String
sub property of: molecular property

molecular spectroscopy
type: ObjectProperty
type: slot_definition
range: String
sub property of: molecular property

molecular replacement
type: ObjectProperty
type: slot_definition
range: String
sub property of: molecular property

molecular mass
type: ObjectProperty
type: slot_definition
range: String
sub property of: molecular property

molecular size
type: ObjectProperty
type: slot_definition
range: String
sub property of: molecular property

molecular hydration
type: ObjectProperty
type: slot_definition
range: String
sub property of: molecular property

molecular shape
type: ObjectProperty
type: slot_definition
range: String
sub property of: molecular property

molecular charge
type: ObjectProperty
type: slot_definition
range: String
sub property of: molecular property

molecular structure
type: ObjectProperty
type: slot_definition
range: String
sub property of: molecular property

molecular heat capacity
type: ObjectProperty
type: slot_definition
range: String
sub property of: molecular property

molecular electronic spectroscopy
type: ObjectProperty
type: slot_definition
range: String
sub property of: molecular property

amino acid sequence string
type: Class
type: type_definition
subclass of: Restriction
  on data range: string
  on property: value
  qualified cardinality: 1

chemical group
type: Class
type: class_definition
subclass of: molecular component
alternative label: chemical functional group
alternative label: functional group
alternative label: group

chemical salt
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: cation state
  on property: has cationic component
subclass of: Restriction
  max qualified cardinality: 1
  on class: anion state
  on property: has anionic component
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: elemental charge
subclass of: precise chemical mixture
definition: a chemical compound consisting of an ionic assembly of cations and anions.
note: in SIO falls under molecular complex? Also in biolink
examples: Example(value='sodium carbonate CHEBI:29377', description=None)

DNA sequence string
type: Class
type: type_definition
subclass of: Restriction
  on data range: string
  on property: value
  qualified cardinality: 1

fully covalently bonded
type: Class
type: class_definition
subclass of: connectivity
definition: All pairs of atoms in this entity are transitively connected via covalent bonds

generalized molecular structure class
type: Class
type: class_definition
subclass of: molecule grouping class
definition: A molecule grouping class that can be written using a chemical formula using variables (e.g. n), or arithmetic expressions uing variables (e.g. 2n+2), plus optionally constraints on those variables (e.g. n>3). An example is alkane; CnH2n+2, which groups specific molecules such as methane
examples: Example(value='monosaccharide', description=None)

imprecise chemical mixture
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: file location
  on property: has mixfile location
subclass of: Restriction
  all values from: proportional part
  on property: has proportional parts
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical encoding
  on property: has minchi representation
subclass of: chemical mixture
alternative label: portion of matter
definition: A macroscopic polyatomic entity that consists of multiple chemical entities where the stoichiometry is not specified and the spatial arrangement of the ingredients is not defined. Examples include coal, tea tree oil, toothpaste, organometallic compounds, heterogeneous metals
note: although the stoichiometry is not known rough percentage parts can be provided
examples: Example(value='toothpaste (sodium fluoride 0.243 w/v%[active] + H2O[inactive] + ... )', description=None)

inchi object
type: Class
type: class_definition
subclass of: informational chemical entity
definition: A representation of an InChI string as an object, composed of distinct sublayers

location
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: owl class
  on property: owl subclass of
subclass of: owl class

molecular anion
type: Class
type: class_definition
subclass of: anion state
subclass of: polyatomic ion
definition: A polyatomic ion that is negative

molecular complex
type: Class
type: class_definition
subclass of: precise chemical mixture
alternative label: complex of molecular entities
alternative label: molecule complex
alternative label: poly molecular composite entity
definition: A molecular complex is a chemical complex composed of at least one weakly interacting molecule.[SIO] Examples: chromosome, double-standed DNA, protein-containing macromolecular complex
note: In SIO, molecular complex is an only child of chemical complex, which is under chemical substance. chemical complex is defined as A chemical complex is a chemical substance composed of a weakly connected molecules and ions in a known stoichiometry.
note: In bioptop, molecule complex is a sibling of structured biological entity under poly molecular composite entity

molecular component grouping class
type: Class
type: class_definition
subclass of: Restriction
  all values from: molecular component grouping class
  on property: subtype of
subclass of: Restriction
  max qualified cardinality: 1
  on class: molecular component
  on property: classifies
subclass of: grouping class
definition: A grouping class that classifies molecular components. Example: inorganic anion group

molecule pairwise similarity
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: molecule
  on property: right molecule
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: score
subclass of: Restriction
  max qualified cardinality: 1
  on class: molecule
  on property: left molecule
subclass of: similarity

periodic table placement
type: Class
type: class_definition
subclass of: informational chemical entity

polymer repeat unit
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: count
  on property: degree of polymerization
subclass of: Restriction
  max qualified cardinality: 1
  on class: Float
  on property: mass
subclass of: Restriction
  max qualified cardinality: 1
  on class: molecule
  on property: repetition of
subclass of: relational chemical entity
definition: An abstract part of a polymer that is all instances of a repeated monomer of a single type

reaction grouping class
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: reaction
  on property: classifies
definition: A grouping class for reactions, for example, dehalogenase; breaking of covalent bond

similarity
type: Class
type: class_definition
subclass of: relational chemical entity
definition: A relationship between two or more entities that is quantified based on their similarity

stereoisomer
type: Class
type: class_definition
subclass of: molecule

subatomic particle
type: Class
type: class_definition
subclass of: chemical entity
definition: A chemical entity below the granularity of an atom.

weakly bonded
type: Class
type: class_definition
subclass of: connectivity
definition: Not covalently bonded

absolute configuration
type: ObjectProperty
type: slot_definition
range: String

acidity
type: ObjectProperty
type: slot_definition
range: Float

allotropic analog of
type: ObjectProperty
type: slot_definition
domain: allotrope
range: allotrope
sub property of: alternate form of
definition: relationship that holds between two allotropes, where both allotropes are allotropes of the same element

boiling point in celcius
type: ObjectProperty
type: slot_definition
range: Float

bond angle
type: ObjectProperty
type: slot_definition
range: Float

bond length in angstroms
type: ObjectProperty
type: slot_definition
range: Float
definition: the average distance between nuclei of two bonded atoms in a molecule. It is a transferable property of a bond between atoms of fixed types, relatively independent of the rest of the molecule.

bond order
type: ObjectProperty
type: slot_definition
domain: atomic bond
range: Integer
definition: the number of electron pairs (bonds) between a pair of atoms

bond type
type: ObjectProperty
type: slot_definition
range: bond_type_enum

charge agnostic entity
type: ObjectProperty
type: slot_definition
range: chemical entity

chirality agnostic form
type: ObjectProperty
type: slot_definition
range: molecule

classification relationship
type: ObjectProperty
type: slot_definition
range: String

classified by
type: ObjectProperty
type: slot_definition
domain: owl class
range: owl class
sub property of: chemical to chemical relationship
sub property of: owl subclass of
inverse of: classifies
definition: A subtype_of relationship holds between I and C if I is a specific entity of type C. Here I and C denotes instances of OWL classes, where I is a specific class and C is a grouping class
examples: Example(value=None, description='glucose classified by monosaccharide')

composed of
type: ObjectProperty
type: slot_definition
range: chemical entity

coordination number
type: ObjectProperty
type: slot_definition
range: Integer
alternative label: coordination
definition: The number of atoms bonded to the atom of interest. [https://doi.org/10.1021%2Fed083p791]

degree of polymerization
type: ObjectProperty
type: slot_definition
range: count

description
type: ObjectProperty
type: slot_definition
range: String

diastereoisomers of
type: ObjectProperty
type: slot_definition
domain: molecule
range: molecule
sub property of: stereoisomer of
alternative label: diastereomers of
definition: A stereoisomer non-mirror image non-identical stereoisomers
note: Diastereomers differ from enantiomers in that the latter are pairs of stereoisomers that differ in all stereocenters and are therefore mirror images of one another

direction
type: ObjectProperty
type: slot_definition
range: String
definition: One of l->r, r->l, bidirectional, neutral

electron configuration
type: ObjectProperty
type: slot_definition
range: String

enantiomer form of
type: ObjectProperty
type: slot_definition
domain: owl class
range: molecule
sub property of: owl subclass of
definition: Example: R-thalidomide is the enantiomer form of 2-(2,6-dioxopiperidin-3-yl)-1H-isoindole-1,3(2H)-dione

energy level
type: ObjectProperty
type: slot_definition
range: String
alternative label: energy state
definition: e.g. ground, stable

formal charge
type: ObjectProperty
type: slot_definition
range: Integer
alternative label: charge
definition: The charge remaining on an atom when all ligands are removed homolytically. [https://doi.org/10.1021%2Fed083p791]

hard or soft
type: ObjectProperty
type: slot_definition
range: hard_or_soft_enum

has acid form
type: ObjectProperty
type: slot_definition
domain: acid base
range: Bronsted acid
sub property of: conjugate base of
definition: connects a base to the acid form. E.g. citrate(3-) has acid form citric acid

has atoms
type: ObjectProperty
type: slot_definition
domain: molecule
range: atom
sub property of: has part
definition: Relation between a molecule and the atoms it contains. Note that this is a shortcut relation: for granular representations go via atom occurrences

has bonding structure
type: ObjectProperty
type: slot_definition
range: String
definition: The pattern in which the atoms are bonded; e.g. hexagonal lattice, sheets, etc

has bonds
type: ObjectProperty
type: slot_definition
domain: molecule
range: atomic bond

has charge state
type: ObjectProperty
type: slot_definition
range: Uriorcurie

has chemical role
type: ObjectProperty
type: slot_definition
range: chemical role

has derivative
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical entity
sub property of: alternate form of
inverse of: derivative of

has group
type: ObjectProperty
type: slot_definition
domain: atom
range: molecule
sub property of: has submolecules
definition: Relation between a molecule and the groups it contains

has higher charge from
type: ObjectProperty
type: slot_definition
range: String
sub property of: has different charge state from

has left enantiomer
type: ObjectProperty
type: slot_definition
range: enantiomer

has lower charge from
type: ObjectProperty
type: slot_definition
range: String
sub property of: has different charge state from

has minchi representation
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: chemical representation
alternative label: MInChi
definition: Proposed new Mixtures InChI

has mixfile location
type: ObjectProperty
type: slot_definition
range: file location
sub property of: information property
definition: Location of a MixFile representing a chemical mixture

has morphological category
type: ObjectProperty
type: slot_definition
range: nanostructure_morphology_enum
definition: e.g. rod, sheet

has parent acid
type: ObjectProperty
type: slot_definition
range: Bronsted acid

has parent alcohol
type: ObjectProperty
type: slot_definition
range: chemical entity

has physiological base
type: ObjectProperty
type: slot_definition
domain: Bronsted acid
range: acid base
sub property of: acid form of
alternative label: deprotonated form of
definition: connects an acid to the base that is stable at physiological pH. E.g. citric acid has physiological base citrate(3-)

has physiologically stable form
type: ObjectProperty
type: slot_definition
range: String
alternative label: has Ph 7.3 mapping
definition: connects an element to the equivalent form that is physiologically stable at pH 7.3

has proportional parts
type: ObjectProperty
type: slot_definition
domain: imprecise chemical mixture
range: proportional part
alternative label: has ingredients
definition: Relationship between a complex mixture and its parts

has reaction smiles representation
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: chemical formula
alternative label: reaction SMILES

has right enantiomer
type: ObjectProperty
type: slot_definition
range: enantiomer

has rinchi representation
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: chemical formula
alternative label: RInChi
definition: Proposed Reactions InChI
note: A half-reaction, such as a RInChI with starting materials and no identified products, is a valid RInChI
examples: Example(value='C2H4O2/c1-2(3)4/h1H3,(H,3,4)!C2H6O/c1-2-3/h3H,2H2,1H3<>C4H8O2/c1-3-6-4(2)5/h3H2,1- 2H3!H2O/h1H2<>H2O4S/c1-5(2,3)4/h(H2,1,2,3,4):', description='hydrolysis of ethyl acetate')
examples: Example(value='RInChI=1.00.1S /layer2<>layer3<>layer4/d+/u2-0-1', description=None)

has role
type: ObjectProperty
type: slot_definition
range: ingredient_role_enum

has stereocenter
type: ObjectProperty
type: slot_definition
range: stereocenter

has subtype
type: ObjectProperty
type: slot_definition
domain: owl class
range: String
sub property of: chemical to chemical relationship
inverse of: subtype of

inchi proton sublayer
type: ObjectProperty
type: slot_definition
range: String
sub property of: inchi sublayer

inchi string
type: ObjectProperty
type: slot_definition
title: InChi
domain: chemical entity
range: chemical encoding
sub property of: chemical formula

inchi version string
type: ObjectProperty
type: slot_definition
range: String
sub property of: inchi component

is balanced
type: ObjectProperty
type: slot_definition
range: Boolean

is branched
type: ObjectProperty
type: slot_definition
range: Boolean

is diastereoselective
type: ObjectProperty
type: slot_definition
range: Boolean

is fully characterized
type: ObjectProperty
type: slot_definition
range: Boolean
definition: False if includes R-groups

is organic
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: Boolean
definition: An organic molecule is a molecule composed of organic atoms (at least carbon, hydrogen, and optionally oxygen, phosphorus, nitrogen, sulfur) [SIO]

is radical
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: Boolean

is stereo
type: ObjectProperty
type: slot_definition
range: Boolean

is substitutent group from
type: ObjectProperty
type: slot_definition
range: molecule

is transport
type: ObjectProperty
type: slot_definition
range: Boolean

isobar of
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical entity
sub property of: alternate form of
definition: equal mass number (Z1 + N1 = Z2 + N2)

isotope of
type: ObjectProperty
type: slot_definition
domain: isotope
range: isotope
sub property of: alternate form of
definition: relationship that holds between two isotopes, always holds if the isotopes have the same atomic number and a different neutron number.

left molecule
type: ObjectProperty
type: slot_definition
range: molecule

left participants
type: ObjectProperty
type: slot_definition
range: reaction participant

maximum percentage
type: ObjectProperty
type: slot_definition
range: Float

melting point in celcius
type: ObjectProperty
type: slot_definition
range: Float

minimal percentage
type: ObjectProperty
type: slot_definition
range: Float

monoisotopic mass
type: ObjectProperty
type: slot_definition
range: Float

nucleon number
type: ObjectProperty
type: slot_definition
domain: atom
range: count
sub property of: subatomic particle count
alternative label: mass number
definition: number of nucleons in an atom. proton number plus neutron number.

occurrence of
type: ObjectProperty
type: slot_definition
range: atom

optical configuration
type: ObjectProperty
type: slot_definition
range: String

oxidation number
type: ObjectProperty
type: slot_definition
range: Integer
alternative label: oxidation
alternative label: oxidation state
definition: The charge remaining on an atom when all ligands are removed heterolytically in their closed form, with the electrons being transferred to the more electronegative partner; homonuclear bonds do not contribute to the oxidation number. [https://doi.org/10.1021%2Fed083p791]

participant
type: ObjectProperty
type: slot_definition
range: chemical entity

polymer architecture type
type: ObjectProperty
type: slot_definition
range: String
definition: morphological structure of a polymer

reaction center
type: ObjectProperty
type: slot_definition
range: String

relative configuration
type: ObjectProperty
type: slot_definition
range: String

repetition of
type: ObjectProperty
type: slot_definition
range: molecule
definition: the macromolecule that is repeated

right molecule
type: ObjectProperty
type: slot_definition
range: molecule

right participants
type: ObjectProperty
type: slot_definition
range: reaction participant

smarts string
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: chemical formula
examples: Example(value='[#1,#6:60][C@@:6]12[CX4:7][CX4H2,CX4H0:8]([CX4H3,CX4H2,#1:80])([CX4H3,CX4H2,#1:81])[CX3:9](=[CX3H2:10])[C@@:11]1([C:1](=[O:2])[CX4,c:4][CX4,c:3][CX4,c,O,NX3!r3:5]2)[C:99]#[N:97]>>[C:10]#[C:9][*:8]([*:80])([*:81])[C:7][C@@:6]1([*:60])[*:5][*:3][*:4][C:1](=[O:2])[C:11]1[C:99]#[N:97]', description=None)

standard atomic weight
type: ObjectProperty
type: slot_definition
range: Float

stoichiometry
type: ObjectProperty
type: slot_definition
range: Integer

torsional angle
type: ObjectProperty
type: slot_definition
range: Float

type
type: ObjectProperty
type: slot_definition
range: periodic_table_block_enum

valence
type: ObjectProperty
type: slot_definition
range: Integer
alternative label: atom valency
alternative label: valency
definition: the number of electrons that an atom uses in bonding [https://doi.org/10.1021%2Fed083p791]
note: example: In in ammonia, nitrogen has a valence of 3, each each hydrogen has a valency of 1
note: example: In methane, carbon has a valence of 4, and each hydrogen has a valency of 1
note: forumla: number of bonds + formal charge
note: forumla: number of electrons in valence shell of free atom – number of non-bonding electrons on atom in molecule
note: todo: determine if this is in CHEBI and how to map

electron
type: Class
type: subatomic_particle_type

Higgs boson
type: Class
type: subatomic_particle_type

hydron
type: Class
type: subatomic_particle_type

proton
type: Class
type: subatomic_particle_type

deuteron
type: Class
type: subatomic_particle_type

triton
type: Class
type: subatomic_particle_type

photon
type: Class
type: subatomic_particle_type

antimuon
type: Class
type: subatomic_particle_type

alpha particle
type: Class
type: subatomic_particle_type

helion
type: Class
type: subatomic_particle_type

neutron
type: Class
type: subatomic_particle_type

electron neutrino
type: Class
type: subatomic_particle_type

positron
type: Class
type: subatomic_particle_type

fundamental particle
type: Class
type: subatomic_particle_type

atomic nucleus
type: Class
type: subatomic_particle_type

nucleon
type: Class
type: subatomic_particle_type

d-block
type: Class
type: periodic_table_block_enum

f-block
type: Class
type: periodic_table_block_enum

s-block
type: Class
type: periodic_table_block_enum

p-block
type: Class
type: periodic_table_block_enum

lepton
type: Class
type: subatomic_particle_type

baryon
type: Class
type: subatomic_particle_type

fermion
type: Class
type: subatomic_particle_type

boson
type: Class
type: subatomic_particle_type

composite particle
type: Class
type: subatomic_particle_type

hadron
type: Class
type: subatomic_particle_type

meson
type: Class
type: subatomic_particle_type

quark
type: Class
type: subatomic_particle_type

nuclear particle
type: Class
type: subatomic_particle_type

pi meson
type: Class
type: subatomic_particle_type

pi positive meson
type: Class
type: subatomic_particle_type

pi minus meson
type: Class
type: subatomic_particle_type

pi zero meson
type: Class
type: subatomic_particle_type

neutrino
type: Class
type: subatomic_particle_type

muon neutrino
type: Class
type: subatomic_particle_type

tau neutrino
type: Class
type: subatomic_particle_type

tau lepton
type: Class
type: subatomic_particle_type

muon
type: Class
type: subatomic_particle_type

hyperon
type: Class
type: subatomic_particle_type

up quark
type: Class
type: subatomic_particle_type

down quark
type: Class
type: subatomic_particle_type

strange quark
type: Class
type: subatomic_particle_type

charm quark
type: Class
type: subatomic_particle_type

bottom quark
type: Class
type: subatomic_particle_type

top quark
type: Class
type: subatomic_particle_type

Delta baryon
type: Class
type: subatomic_particle_type

nanotube
type: Class
type: nanostructure_morphology_enum

nanoparticle
type: Class
type: nanostructure_morphology_enum

nanorod
type: Class
type: nanostructure_morphology_enum

nanotubosome
type: Class
type: nanostructure_morphology_enum

quantum dot
type: Class
type: nanostructure_morphology_enum

nanofibre
type: Class
type: nanostructure_morphology_enum

nanocrystal
type: Class
type: nanostructure_morphology_enum

nanoribbon
type: Class
type: nanostructure_morphology_enum

nanosheet
type: Class
type: nanostructure_morphology_enum

nanowire
type: Class
type: nanostructure_morphology_enum

aromatic
type: Class
type: bond_type_enum

double
type: Class
type: bond_type_enum

hydrogen
type: Class
type: bond_type_enum

covalent
type: Class
type: bond_type_enum

quadruple
type: Class
type: bond_type_enum

single
type: Class
type: bond_type_enum

triple
type: Class
type: bond_type_enum

atomic number
type: ObjectProperty
type: slot_definition
domain: atom
range: count
sub property of: subatomic particle count
alternative label: Z
alternative label: proton number
definition: number of protons in an atom

Metallic
type: Class
type: element_metallic_classification

Non-Metallic
type: Class
type: element_metallic_classification

Semi-Metallic
type: Class
type: element_metallic_classification

allotrope
type: Class
type: class_definition
subclass of: Restriction
  on class: String
  on property: has bonding structure
  qualified cardinality: 1
subclass of: Restriction
  on class: chemical element
  on property: allotropic analog of
  qualified cardinality: 1
subclass of: molecule
definition: A molecule consisting of atoms of the same element
examples: Example(value='diamond', description=None)
examples: Example(value='dioxygen', description=None)

atom grouping by periodic table placement
type: Class
type: class_definition
subclass of: atom grouping class

atom grouping class
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: atom
  on property: classifies
subclass of: Restriction
  all values from: molecule grouping class
  on property: subtype of
subclass of: grouping class
definition: A grouping class that classifies atoms. For example, metal atom

atom ionic form
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: elemental charge
subclass of: partially specified atom
alternative label: atom ionic species
definition: an atom type in which only charge state is specified, designated by the element followed by charge
examples: Example(value='chloride Cl-', description=None)

ionic
type: Class
type: bond_type_enum

metal-metal
type: Class
type: bond_type_enum

polycentric
type: Class
type: bond_type_enum

salt bridge
type: Class
type: bond_type_enum

charge state
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: elemental charge
subclass of: state
subclass of: mixin
definition: Applies to entities that have a charge state, which may be positive, negative, or neutral

chemical entity or grouping
type: Class
type: class_definition
subclass of: mixin

chemical mixture
type: Class
type: class_definition
subclass of: polyatomic entity
definition: A polyatomic entity that consists of two or more parts that are weakly bound, may be of known or unknown stoichiometry

chemical role
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: owl class
  on property: owl subclass of
subclass of: owl class
alternative label: role
definition: A characteristic of a chemical entity that is realized under particular conditions

chemical salt grouping class
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: has cationic component
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: has anionic component
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical salt
  on property: classifies
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: name
subclass of: molecule grouping class
definition: A grouping class for a chemical salt
examples: Example(value='sodium chloride', description=None)

Alkali_Earth
type: Class
type: element_family_enum

Alkaline_Earth
type: Class
type: element_family_enum

Halogen
type: Class
type: element_family_enum

Metalloids
type: Class
type: element_family_enum

Noblegas
type: Class
type: element_family_enum

Non-Metal
type: Class
type: element_family_enum

Other_Metal
type: Class
type: element_family_enum

Rare_Earth
type: Class
type: element_family_enum

Transition
type: Class
type: element_family_enum

borderline
type: Class
type: hard_or_soft_enum

hard
type: Class
type: hard_or_soft_enum

soft
type: Class
type: hard_or_soft_enum

active ingredient
type: Class
type: ingredient_role_enum

excipient
type: Class
type: ingredient_role_enum

inactive ingredient
type: Class
type: ingredient_role_enum

solvent
type: Class
type: ingredient_role_enum

monoatomic ion
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical element
  on property: has element
subclass of: atom ionic form
subclass of: charged
alternative label: charged atom
definition: An atom type that has a charge
note: this is mass-number neutral, so there can be no mass associated with a monatomic ion instance

monomolecular polymer
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical entity
  on property: has repeat unit
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: polymer architecture type
subclass of: Restriction
  max qualified cardinality: 1
  on class: Boolean
  on property: is branched
subclass of: Restriction
  max qualified cardinality: 1
  on class: macromolecule
  on property: polymer of
subclass of: macromolecule
alternative label: oligo or polymer
alternative label: polymer
definition: A macromolecule composed of repeating subunits. Examples: cellulose

nucleotide sequence interval
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: DNA sequence string
  on property: has sequence representation
subclass of: sequence interval

g-block
type: Class
type: periodic_table_block_enum

polyatomic ion
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical entity
  on property: conjugate acid of
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: elemental charge
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical entity
  on property: conjugate base of
subclass of: charged
subclass of: molecule
alternative label: polyatomic ion species
definition: A molecule that has a charge. For example, nitrate is a molecular and ionic species; its formula is (NO3-).

polymer part
type: Class
type: class_definition
subclass of: molecular component

proportional part
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: Float
  on property: minimal percentage
subclass of: Restriction
  max qualified cardinality: 1
  on class: ingredient_role_enum
  on property: has role
subclass of: Restriction
  max qualified cardinality: 1
  on class: Float
  on property: maximum percentage
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical entity
  on property: composed of
subclass of: relational chemical entity
definition: A part of a complex mixture that is of uniform composition

sequence interval
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: sequence string
  on property: has sequence representation
subclass of: molecular component
definition: a chain of connected monomers in a linear polymer - for example, a sub-region of an amino acid or nucleotide sequence.
note: - includes an interval corresponding to the whole molecule as an edge case

sequence string
type: Class
type: type_definition
subclass of: Restriction
  on data range: string
  on property: value
  qualified cardinality: 1

state
type: Class
type: class_definition
subclass of: mixin

uncharged
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: elemental charge
subclass of: charge state
subclass of: mixin
alternative label: neutral charge
definition: Applies to entities that are uncharged, i.e. have an elemental charge of zero

acid form of
type: ObjectProperty
type: slot_definition
domain: Bronsted acid
range: acid base
sub property of: conjugate acid of
alternative label: protonated form of
definition: connects an acid to any of the the base anions. E.g. citric acid acid form of citrate(1-),citrate(2-),citrate(3-)

chemical isomer of
type: ObjectProperty
type: slot_definition
domain: molecule
range: molecule
sub property of: alternate form of
alternative label: isomer of
definition: a relationship that holds between two forms of a parent molecule with identical chemical formulas but distinct arrangements of atoms in space

decay energy
type: ObjectProperty
type: slot_definition
domain: isotope
range: String
sub property of: chemical property

decay mode
type: ObjectProperty
type: slot_definition
domain: isotope
range: String
sub property of: chemical property

decay product
type: ObjectProperty
type: slot_definition
domain: isotope
range: isotope
sub property of: chemical property

direct conjugatated form of
type: ObjectProperty
type: SymmetricProperty
type: slot_definition
domain: chemical entity
range: chemical entity
sub property of: derivative of

half life
type: ObjectProperty
type: slot_definition
domain: isotope
range: number of years
sub property of: chemical property

has anionic component
type: ObjectProperty
type: slot_definition
range: String
sub property of: has ionic component

has atom occurrences
type: ObjectProperty
type: slot_definition
range: atom occurrence

has cationic component
type: ObjectProperty
type: slot_definition
range: String
sub property of: has ionic component

has different charge state from
type: ObjectProperty
type: slot_definition
range: String

has ionic component
type: ObjectProperty
type: slot_definition
range: String
sub property of: has part

hashed chemical formula
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: chemical representation
definition: A hashed version of a chemical formula

id
type: ObjectProperty
type: slot_definition
range: String
sub property of: information property

in periodic table block
type: ObjectProperty
type: slot_definition
range: periodic table block

in periodic table group
type: ObjectProperty
type: slot_definition
range: periodic table group

inchi charge sublayer
type: ObjectProperty
type: slot_definition
range: String
sub property of: inchi sublayer

inchi component
type: ObjectProperty
type: slot_definition
range: String
sub property of: information property
definition: A part of an InChI object

inchi hydrogen connections sublayer
type: ObjectProperty
type: slot_definition
range: String
sub property of: inchi sublayer in main layer
definition: Describes how many hydrogen atoms are connected to each of the other atoms.

inchi isotopic layer
type: ObjectProperty
type: slot_definition
range: String
sub property of: inchi sublayer

inchi stereochemical double bond sublayer
type: ObjectProperty
type: slot_definition
range: String
sub property of: inchi sublayer

inchi stereochemical type sublayer
type: ObjectProperty
type: slot_definition
range: String
sub property of: inchi sublayer

inchi tetrahedral stereochemical sublayer
type: ObjectProperty
type: slot_definition
range: String
sub property of: inchi sublayer

mass
type: ObjectProperty
type: slot_definition
range: Float

mode of formation
type: ObjectProperty
type: slot_definition
domain: isotope
range: String
sub property of: chemical property

neutron number
type: ObjectProperty
type: slot_definition
domain: atom
range: count
sub property of: subatomic particle count
alternative label: N
definition: number of neutrons in an atom

property of atom
type: ObjectProperty
type: slot_definition
domain: atom
range: String
sub property of: chemical property

rinchi key string
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: hashed chemical formula
definition: A hashed representation of a RInChi string
hash of: has rinchi representation

score
type: ObjectProperty
type: slot_definition
range: String

stereoisomer of
type: ObjectProperty
type: slot_definition
domain: molecule
range: molecule
sub property of: chemical isomer of
alternative label: spatial isomer of
definition: a relationship that holds between two forms of the 'same' molecule with identical chemical formulas but different bonds

thermophysical property
type: ObjectProperty
type: slot_definition
range: String
sub property of: chemical property

subatomic particle
type: Class
type: subatomic_particle_type

IUPAC name
type: ObjectProperty
type: slot_definition
range: String
sub property of: information property

anion state
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: elemental charge
subclass of: charged
subclass of: mixin
alternative label: negatively charged state
definition: This mixin is applied on an entity (atom or molecule) that is negatively charged

cation state
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: elemental charge
subclass of: charged
subclass of: mixin
alternative label: positively charged state
definition: This mixin is applied on an entity (atom or molecule) that is positively charged

connectivity
type: Class
type: class_definition
subclass of: mixin
definition: Abstract grouping for slots that related chemical entities via a connectivity relationships

element_metallic_classification
type: Class
type: EnumDefinition
union of: Metallic
union of: Non-Metallic
union of: Semi-Metallic
permissible values: Metallic
permissible values: Non-Metallic
permissible values: Semi-Metallic

file location
type: Class
type: type_definition
subclass of: Restriction
  on data range: anyURI
  on property: value
  qualified cardinality: 1

grouping class for acids or bases
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical entity
  on property: conjugate base of
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical entity
  on property: conjugate acid of
subclass of: molecule grouping class

informational chemical entity
type: Class
type: class_definition

is part or whole
type: Class
type: class_definition
subclass of: mixin

nuclide
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: energy level
subclass of: partially specified atom
alternative label: nuclear species
alternative label: nucleide
definition: an atomic species characterized by the specific constitution of its nucleus
examples: Example(value='https://en.wikipedia.org/wiki/Isotopes_of_tantalum#Tantalum-180m', description=None)

number of years
type: Class
type: type_definition
subclass of: Restriction
  on data range: int
  on property: value
  qualified cardinality: 1

partially specified atom
type: Class
type: class_definition
subclass of: atom
definition: An atom type that only has a subset of properties (has atomic number, charge, and neutron number) stated

periodic table block
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: periodic_table_block_enum
  on property: type
subclass of: periodic table placement
definition: A block of the periodic table is a set of elements unified by the orbitals their valence electrons or vacancies lie in

periodic table group
type: Class
type: type_definition
subclass of: Restriction
  on data range: int
  on property: value
  qualified cardinality: 1

precise chemical mixture
type: Class
type: class_definition
subclass of: chemical mixture
subclass of: weakly bonded
alternative label: chemical substance (SIO)
definition: A polyatomic entity that consists of two or more parts that are weakly bound, and of known stoichiometry

reaction
type: Class
type: class_definition
subclass of: Restriction
  on class: chemical encoding
  on property: has rinchi representation
  qualified cardinality: 1
subclass of: Restriction
  all values from: reaction participant
  on property: left participants
subclass of: Restriction
  all values from: reaction participant
  on property: right participants
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: direction
subclass of: Restriction
  max qualified cardinality: 1
  on class: Boolean
  on property: is diastereoselective
subclass of: Restriction
  max qualified cardinality: 1
  on class: Boolean
  on property: is stereo
subclass of: Restriction
  max qualified cardinality: 1
  on class: Boolean
  on property: is balanced
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: smarts string
subclass of: Restriction
  max qualified cardinality: 1
  on class: Boolean
  on property: is transport
subclass of: Restriction
  max qualified cardinality: 1
  on class: Boolean
  on property: is fully characterized
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: description
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical encoding
  on property: has reaction smiles representation
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: reaction center
definition: reaction

stereocenter
type: Class
type: class_definition
subclass of: location
subclass of: owl class
alternative label: stereogenic center
definition: a particular instance of a stereogenic element that is geometrically a point, bearing different substituents, such that interchanging any two substituents leads to a stereoisomer

has element
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical element
sub property of: alternate form of

has repeat unit
type: ObjectProperty
type: slot_definition
range: chemical entity

has sequence representation
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: sequence string
sub property of: chemical representation

has submolecules
type: ObjectProperty
type: slot_definition
domain: molecule
range: molecule
sub property of: has part
definition: Relation between a molecule and the molecules it is made from.

inchi atom connections sublayer
type: ObjectProperty
type: slot_definition
range: String
sub property of: inchi sublayer in main layer
definition: The atoms in the chemical formula (except for hydrogens) are numbered in sequence; this sublayer describes which atoms are connected by bonds to which other ones.

inchi chemical sublayer
type: ObjectProperty
type: slot_definition
range: String
sub property of: inchi sublayer in main layer
definition: the main chemical formula

inchi sublayer in main layer
type: ObjectProperty
type: slot_definition
range: String
sub property of: inchi sublayer
definition: The main layer consists of chemical formula, atom connections, and hydrogen atoms. Example: CH3O/c1-2/h1H3/q-1

smiles string
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: chemical formula
definition: A string encoding of a molecular graph, no chiral or isotopic information. There are usually a large number of valid SMILES which represent a given structure. For example, CCO, OCC and C(O)C all specify the structure of ethanol.
note: a problematic set of structures to describe using SMILES notation is those which cannot be easily described using molecular graphs (see “Limitations of molecular graph representations” section), such as organometallic compounds and ionic salts.

subatomic particle count
type: ObjectProperty
type: slot_definition
domain: atom
range: String
sub property of: property of atom

symbol
type: ObjectProperty
type: slot_definition
range: String
sub property of: information property
definition: short symbol for chemical entity, e.g. K, C-16

charged
type: Class
type: class_definition
subclass of: charge state
subclass of: mixin
alternative label: ion
alternative label: ionic state
definition: Applies to entities that are charged, either positive or negative

enantiomer
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: absolute configuration
subclass of: Restriction
  max qualified cardinality: 1
  on class: molecule
  on property: enantiomer form of
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: relative configuration
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: optical configuration
subclass of: stereoisomer
definition: one of two stereoisomers of a chiral molecule that are mirror images. Example: R-thalidomide
note: key= (enantiomer form of, absolute configuration)
note: key= (enantiomer form of, inchi tetrahedral stereochemical sublayer)

material
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical entity
  on property: has part
definition: A substance composed of one or more chemical entities

polyatomic entity
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi atom connections sublayer
subclass of: chemical entity
definition: Any chemical entity consisting of more than one atom.

reaction participant
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: stoichiometry
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical entity
  on property: participant
subclass of: relational chemical entity
definition: Instances of this link a reaction to a chemical entity participant

conjugate acid of
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical entity
sub property of: direct conjugatated form of
sub property of: has higher charge from
inverse of: conjugate base of
alternative label: is conjugate acid of (chebi)

conjugate base of
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical entity
sub property of: direct conjugatated form of
sub property of: has lower charge from
inverse of: conjugate acid of
alternative label: is conjugate base of (chebi)
definition: connects the base form of an acid to an acid. Also connects the different charge states of the base. Example: the different charge states of lactate (CHEBI:24996) conjugate base of lactic acid (CHEBI:28358)
editorial note: sometimes chebi hops over a state skipping an intermediate

polymer of
type: ObjectProperty
type: slot_definition
range: macromolecule
sub property of: has part

structural isomer of
type: ObjectProperty
type: slot_definition
domain: molecule
range: molecule
sub property of: chemical isomer of
alternative label: constitutional isomer
definition: a relationship that holds between two forms of the 'same' molecule with identical chemical formulas but different bonding patterns

acid base
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: Bronsted acid
  on property: has acid form
subclass of: molecular anion
definition: A conugate base of an acid with charge specified. Example: citrate(3-)

atom occurrence
type: Class
type: class_definition
subclass of: Restriction
  on class: atom
  on property: occurrence of
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: oxidation number
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: formal charge
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: coordination number
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: valence
subclass of: owl class
subclass of: relational chemical entity
definition: An occurrence of an atom in the context of a particular molecule. For example, one of two occurrences of oxygen in nitrate

atomic bond
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: Float
  on property: bond length in angstroms
subclass of: Restriction
  max qualified cardinality: 1
  on class: Float
  on property: bond angle
subclass of: Restriction
  all values from: atom occurrence
  on property: has atom occurrences
subclass of: Restriction
  max qualified cardinality: 1
  on class: bond_type_enum
  on property: bond type
subclass of: Restriction
  max qualified cardinality: 1
  on class: Float
  on property: torsional angle
subclass of: Restriction
  max qualified cardinality: 1
  on class: Integer
  on property: bond order
subclass of: owl class
subclass of: relational chemical entity
alternative label: bond
alternative label: chemical bond
definition: A connection between two atoms. Note this is the reified form of 'atomically connected to'.

chemical element
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: Float
  on property: melting point in celcius
subclass of: Restriction
  max qualified cardinality: 1
  on class: Float
  on property: standard atomic weight
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: electron configuration
subclass of: Restriction
  max qualified cardinality: 1
  on class: Float
  on property: boiling point in celcius
subclass of: Restriction
  max qualified cardinality: 1
  on class: Float
  on property: monoisotopic mass
subclass of: Restriction
  max qualified cardinality: 1
  on class: Float
  on property: mass
subclass of: Restriction
  max qualified cardinality: 1
  on class: periodic table group
  on property: in periodic table group
subclass of: Restriction
  max qualified cardinality: 1
  on class: periodic table block
  on property: in periodic table block
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: has physiologically stable form
subclass of: Restriction
  all values from: stereocenter
  on property: has stereocenter
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: symbol
subclass of: partially specified atom
alternative label: element
alternative label: generic atom
definition: generic form of an atom, with unspecified neutron or charge
examples: Example(value='carbon', description=None)
examples: Example(value='nickel', description=None)

hard_or_soft_enum
type: Class
type: EnumDefinition
union of: hard
union of: soft
union of: borderline
permissible values: borderline
permissible values: hard
permissible values: soft

derivative of
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical entity
sub property of: alternate form of
inverse of: has derivative

Bronsted acid
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: hard_or_soft_enum
  on property: hard or soft
subclass of: Restriction
  all values from: acid base
  on property: acid form of
subclass of: Restriction
  max qualified cardinality: 1
  on class: Float
  on property: acidity
subclass of: molecule
definition: A molecule capable of donating a hydron to an acceptor. Example: citric acid

grouping class
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: owl class
  on property: owl subclass of
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical entity
  on property: classifies
subclass of: Restriction
  all values from: grouping class
  on property: subtype of
subclass of: Restriction
  on class: String
  on property: id
  qualified cardinality: 1
subclass of: owl class
definition: A non-specific entity. For example "amino acid" is a grouping for "serine", "leucine" etc; ester is a grouping for nitroglycerin; alkane is a grouping for pentane, butane, methane, etc

ingredient_role_enum
type: Class
type: EnumDefinition
union of: active ingredient
union of: inactive ingredient
union of: excipient
union of: solvent
permissible values: active ingredient
permissible values: excipient
permissible values: inactive ingredient
permissible values: solvent

molecular component
type: Class
type: class_definition
subclass of: polyatomic entity
alternative label: molecular part
alternative label: submolecule
definition: A proper part of a molecule that is larger than an atom

relational chemical entity
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: owl class
  on property: owl subclass of
subclass of: owl class
definition: A reified relationship

specificity mixin
type: Class
type: class_definition
subclass of: mixin

carboydrate representation
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: chemical representation

chemical to chemical relationship
type: ObjectProperty
type: slot_definition
range: String

subtype of
type: ObjectProperty
type: slot_definition
domain: owl class
range: owl class
sub property of: chemical to chemical relationship
sub property of: owl subclass of
inverse of: has subtype
alternative label: metasubclass of
definition: A subtype_of relationship holds between C and P if C is a more specialized form of P. Here C and P denotes instances of OWL classes, where C and P both function as grouping class
narrow match: subClassOf

name
type: ObjectProperty
type: slot_definition
range: String
sub property of: information property
definition: name of chemical entity. E.g. nickel, carbon-16

periodic_table_block_enum
type: Class
type: EnumDefinition
union of: s-block
union of: p-block
union of: d-block
union of: f-block
union of: g-block
permissible values: d-block
permissible values: f-block
permissible values: s-block
permissible values: p-block
permissible values: g-block

chemical representation
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: information property
alternative label: has chemical encoding

has part
type: ObjectProperty
type: slot_definition
range: String
sub property of: chemical to chemical relationship
definition: basic parthood relations

information property
type: ObjectProperty
type: slot_definition
range: String

type_definition
type: Class

value
type: DatatypeProperty

count
type: Class
type: type_definition
subclass of: Restriction
  on data range: int
  on property: value
  qualified cardinality: 1

element_family_enum
type: Class
type: EnumDefinition
union of: Alkali_Earth
union of: Alkaline_Earth
union of: Halogen
union of: Metalloids
union of: Noblegas
union of: Non-Metal
union of: Other_Metal
union of: Rare_Earth
union of: Transition
permissible values: Alkali_Earth
permissible values: Alkaline_Earth
permissible values: Halogen
permissible values: Metalloids
permissible values: Noblegas
permissible values: Non-Metal
permissible values: Other_Metal
permissible values: Rare_Earth
permissible values: Transition

molecule grouping class
type: Class
type: class_definition
subclass of: Restriction
  all values from: molecule grouping class
  on property: subtype of
subclass of: Restriction
  max qualified cardinality: 1
  on class: molecule
  on property: classifies
subclass of: grouping class
definition: A grouping class that classifies molecules. Example: carbohydrate, monosaccharide, amino acid, polyacrylamide
note: Molecular grouping classes are typically defined by elemental composition and structure as well as chemical properties
note: Unlike an actual molecule, a molecule grouping class will not have an inchi or properties such as mass
examples: Example(value='nucleobase', description=None)

alternate form of
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical entity
sub property of: chemical to chemical relationship
definition: A relationship between two entities of the same type

chemical property
type: ObjectProperty
type: slot_definition
range: String

classifies
type: ObjectProperty
type: slot_definition
domain: owl class
range: String
sub property of: chemical to chemical relationship
inverse of: classified by

inchi sublayer
type: ObjectProperty
type: slot_definition
range: String
sub property of: inchi component

owl subclass of
type: ObjectProperty
type: slot_definition
domain: owl class
range: owl class
sub property of: classification relationship
alternative label: is a
definition: Holds between C and P if C owl:subClassOf P. Note that in this model, most classes are metaclasses (see 'owl class'), where these metaclasses may represent *groupings* or specific countable elements or species. We provide two different sub-properties of subclass of for two cases: (1) subtype_of, which connects grouping classes (e.g. alkane is_a hydrocarbon; alpha-amino-acid is_a amino-acid), (2) classified_by, which connects a specific element to a grouping class (e.g. methane is_a hydrocarbon; iron is_a metal; serine is_a amino-acid)
narrow match: terminologyfamily

macromolecule
type: Class
type: class_definition
subclass of: Restriction
  all values from: molecule
  on property: has submolecules
subclass of: molecule
definition: A large molecule, such as a polymer, lipid, or macrocycle
note: check on classification of lipids

chemical formula
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: chemical encoding
sub property of: chemical representation
definition: A generic grouping for miolecular formulae and empirical formulae

elemental charge
type: ObjectProperty
type: slot_definition
domain: chemical entity
range: Integer
sub property of: property of atom
definition: number of protons minus number of electrons

nanostructure_morphology_enum
type: Class
type: EnumDefinition
union of: nanotube
union of: nanoparticle
union of: nanorod
union of: nanotubosome
union of: quantum dot
union of: nanofibre
union of: nanocrystal
union of: nanoribbon
union of: nanosheet
union of: nanowire
permissible values: nanotube
permissible values: nanoparticle
permissible values: nanorod
permissible values: nanotubosome
permissible values: quantum dot
permissible values: nanofibre
permissible values: nanocrystal
permissible values: nanoribbon
permissible values: nanosheet
permissible values: nanowire

molecular property
type: ObjectProperty
type: slot_definition
range: String
sub property of: chemical property

atom
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: subatomic particle
  on property: has part
subclass of: Restriction
  max qualified cardinality: 1
  on class: count
  on property: atomic number
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: symbol
subclass of: chemical entity
alternative label: atomic species
alternative label: chemical species of an element
definition: A chemical entity consisting of exactly one atomic nucleus and the electron(s) orbiting it.
note: {'chemical species of an element': 'Specific form of an element defined as to isotopic composition, electronic or oxidation state, and/or complex or molecular structure https://goldbook.iupac.org/terms/view/CT06859'}

bond_type_enum
type: Class
type: EnumDefinition
union of: covalent
union of: aromatic
union of: single
union of: double
union of: triple
union of: quadruple
union of: hydrogen
union of: ionic
union of: polycentric
union of: metal-metal
union of: salt bridge
permissible values: aromatic
permissible values: double
permissible values: hydrogen
permissible values: covalent
permissible values: quadruple
permissible values: single
permissible values: triple
permissible values: ionic
permissible values: metal-metal
permissible values: polycentric
permissible values: salt bridge

isotope
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: isotope
  on property: decay product
subclass of: Restriction
  max qualified cardinality: 1
  on class: count
  on property: neutron number
subclass of: Restriction
  max qualified cardinality: 1
  on class: number of years
  on property: half life
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: decay energy
subclass of: Restriction
  max qualified cardinality: 1
  on class: isotope
  on property: isotope of
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: decay mode
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical element
  on property: has element
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: mode of formation
subclass of: nuclide
definition: A specific subtype of an atom with a specified neutron number
note: Wikidata has isotope as a subclass of nuclide, but nuclide has no instances that are not isotope instances.
examples: Example(value='1H (protium)', description=None)
examples: Example(value='2H (deuterium)', description=None)
examples: Example(value='https://en.wikipedia.org/wiki/Carbon-12', description=None)

owl class
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: owl class
  on property: owl subclass of
subclass of: mixin
alternative label: metaclass
alternative label: second order class
alternative label: species
definition: instances of this class mixin are OWL Classes

chemical encoding
type: Class
type: type_definition
subclass of: Restriction
  on data range: string
  on property: value
  qualified cardinality: 1

subatomic_particle_type
type: Class
type: EnumDefinition
union of: proton
union of: alpha particle
union of: tau neutrino
union of: positron
union of: muon
union of: hyperon
union of: boson
union of: fermion
union of: baryon
union of: top quark
union of: hydron
union of: muon neutrino
union of: nuclear particle
union of: pi minus meson
union of: pi meson
union of: nucleon
union of: triton
union of: deuteron
union of: neutrino
union of: meson
union of: quark
union of: Higgs boson
union of: fundamental particle
union of: electron neutrino
union of: subatomic particle
union of: tau lepton
union of: photon
union of: up quark
union of: antimuon
union of: strange quark
union of: Delta baryon
union of: pi zero meson
union of: hadron
union of: bottom quark
union of: composite particle
union of: atomic nucleus
union of: electron
union of: neutron
union of: lepton
union of: helion
union of: charm quark
union of: down quark
union of: pi positive meson
permissible values: electron
permissible values: Higgs boson
permissible values: hydron
permissible values: proton
permissible values: deuteron
permissible values: triton
permissible values: photon
permissible values: antimuon
permissible values: alpha particle
permissible values: helion
permissible values: neutron
permissible values: electron neutrino
permissible values: positron
permissible values: fundamental particle
permissible values: atomic nucleus
permissible values: nucleon
permissible values: lepton
permissible values: baryon
permissible values: fermion
permissible values: boson
permissible values: subatomic particle
permissible values: composite particle
permissible values: hadron
permissible values: meson
permissible values: quark
permissible values: nuclear particle
permissible values: pi meson
permissible values: pi positive meson
permissible values: pi minus meson
permissible values: pi zero meson
permissible values: neutrino
permissible values: muon neutrino
permissible values: tau neutrino
permissible values: tau lepton

molecule
type: Class
type: class_definition
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: has part
subclass of: Restriction
  max qualified cardinality: 1
  on class: Boolean
  on property: is organic
subclass of: Restriction
  all values from: atomic bond
  on property: has bonds
subclass of: Restriction
  all values from: atom occurrence
  on property: has atom occurrences
subclass of: Restriction
  all values from: atom
  on property: has atoms
subclass of: Restriction
  all values from: molecule
  on property: has submolecules
subclass of: fully covalently bonded
subclass of: polyatomic entity
alternative label: molecular entity
alternative label: monomolecular entity
definition: A chemical entity that consists of two or more atoms where all atoms are connected via covalent bonds.
examples: Example(value='cysteine', description=None)
examples: Example(value='dioxygen', description=None)
examples: Example(value='phosphene', description=None)

chemical entity
type: Class
type: class_definition
subclass of: Restriction
  on class: String
  on property: id
  qualified cardinality: 1
subclass of: Restriction
  max qualified cardinality: 1
  on class: Boolean
  on property: is radical
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical role
  on property: has chemical role
subclass of: Restriction
  max qualified cardinality: 1
  on class: chemical encoding
  on property: inchi string
subclass of: Restriction
  max qualified cardinality: 1
  on class: owl class
  on property: owl subclass of
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: name
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: inchi chemical sublayer
subclass of: Restriction
  max qualified cardinality: 1
  on class: String
  on property: IUPAC name
subclass of: owl class
alternative label: chemical
alternative label: chemical species
alternative label: specific chemical entity
definition: An entity that can be described using using chemical properties.
note: Does not encompass chemical grouping classes, such as "amino acid". Use the class ChemicalGrouping for this.
note: Encompasses subatomic particles through to macromolecular structures.
note: In common chemical usage generic and specific chemical names (such as radical or hydroxide ion) or chemical formulae refer either to a chemical species or to a molecular entity[https://goldbook.iupac.org/terms/view/CT01038]

class_definition
type: Class

slot_definition
type: Class