AZE_notation_html
type: DatatypeProperty
title: AZE notation html
sub property of: chemical_representation
definition: E.g. <super>12</super>/6C
in scheme: chemrof

AcidAnionGroupingClass
type: Class
title: acid anion grouping class
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ate$
  on property: name
subclass of: Restriction
  min cardinality: 0
  on property: name
subclass of: GroupingClassForAcidsOrBases
definition: A molecule grouping class that groups the different ion forms of the base of an acid
in scheme: chemrof

AcidBaseConflationClass
type: Class
title: acid base conflation class
subclass of: GroupingClassForAcidsOrBases
definition: A molecule grouping class that can groups an acid together with all its conjugate bases. physiological
in scheme: chemrof

AtomGroupingByPeriodicTableBlock
type: Class
title: atom grouping by periodic table block
subclass of: Restriction
  all values from: PeriodicTableBlockEnum
  on property: in_periodic_table_block
subclass of: Restriction
  max cardinality: 1
  on property: in_periodic_table_block
subclass of: Restriction
  min cardinality: 0
  on property: in_periodic_table_block
subclass of: AtomGroupingByPeriodicTablePlacement
definition: Example: group 13 atom
in scheme: chemrof

AtomGroupingByPeriodicTableGroup
type: Class
title: atom grouping by periodic table group
subclass of: Restriction
  all values from: int
  on property: in_periodic_table_group
subclass of: Restriction
  max cardinality: 1
  on property: in_periodic_table_group
subclass of: Restriction
  min cardinality: 0
  on property: in_periodic_table_group
subclass of: AtomGroupingByPeriodicTablePlacement
definition: Example: p-block atom
in scheme: chemrof

AtomGroupingByProperty
type: Class
title: atom grouping by property
subclass of: AtomGroupingClass
definition: Example: metal atom
in scheme: chemrof

ChemicalGroupingByCharge
type: Class
title: chemical grouping by charge
subclass of: Restriction
  all values from: MoleculeGroupingClass
  on property: subtype_of
subclass of: Restriction
  min cardinality: 0
  on property: subtype_of
subclass of: Restriction
  min cardinality: 0
  on property: has_charge_state
subclass of: Restriction
  max cardinality: 1
  on property: charge_agnostic_entity
subclass of: Restriction
  all values from: anyURI
  on property: has_charge_state
subclass of: Restriction
  all values from: ChemicalEntity
  on property: charge_agnostic_entity
subclass of: Restriction
  max cardinality: 1
  on property: has_charge_state
subclass of: Restriction
  min cardinality: 0
  on property: charge_agnostic_entity
subclass of: ChemicalGroupingClass
definition: A grouping class that refines a charge-neutral entity
in scheme: chemrof

ChemicalSaltByAnion
type: Class
title: chemical salt by anion
subclass of: Restriction
  max cardinality: 1
  on property: has_anionic_component
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  min cardinality: 0
  on property: name
subclass of: Restriction
  all values from: string
  on property: name
subclass of: Restriction
  min cardinality: 0
  on property: has_anionic_component
subclass of: Restriction
  all values from: string
  on property: has_anionic_component
subclass of: ChemicalSaltGroupingClass
definition: A grouping class for a chemical salt named by anion
in scheme: chemrof

ChemicalSaltByCation
type: Class
title: chemical salt by cation
subclass of: Restriction
  min cardinality: 0
  on property: name
subclass of: Restriction
  max cardinality: 1
  on property: has_cationic_component
subclass of: Restriction
  all values from: string
  on property: has_cationic_component
subclass of: Restriction
  min cardinality: 0
  on property: has_cationic_component
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  all values from: string
  on property: name
subclass of: ChemicalSaltGroupingClass
definition: A grouping class for a chemical salt named by cation
in scheme: chemrof

ChiralityCenter
type: Class
title: chirality center
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.
in scheme: chemrof

Collection
type: Class
subclass of: Restriction
  min cardinality: 0
  on property: entities
subclass of: Restriction
  all values from: DomainEntity
  on property: entities
subclass of: ClassDefinition
definition: This utility class serves to collect a set of domain entities, and to be the top level object in tree-based representations such as JSON.
in scheme: chemrof

GeneralAcidBaseGroupingClass
type: Class
title: general acid base grouping class
subclass of: GroupingClassForAcidsOrBases
definition: A molecule grouping class that can groups an acid together with all its conjugate bases. physiological
in scheme: chemrof

MolecularDerivativeGroupingClass
type: Class
title: molecular derivative grouping class
subclass of: Restriction
  max cardinality: 1
  on property: classifies
subclass of: Restriction
  max cardinality: 1
  on property: derivative_of
subclass of: Restriction
  all values from: DomainEntity
  on property: derivative_of
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  min cardinality: 0
  on property: derivative_of
subclass of: Restriction
  min cardinality: 0
  on property: classifies
subclass of: Restriction
  all values from: string
  on property: name
subclass of: Restriction
  min cardinality: 0
  on property: name
subclass of: Restriction
  all values from: Molecule
  on property: classifies
subclass of: MoleculeGroupingClass
definition: A grouping class defined as a derivative of another molecule or molecular grouping class
in scheme: chemrof

MoleculeGroupingClassDefinedByAdditionOfAGroup
type: Class
title: molecule grouping class defined by addition of a group
subclass of: Restriction
  all values from: PolyatomicEntity
  on property: derivative_of
subclass of: Restriction
  min cardinality: 0
  on property: has_group
subclass of: Restriction
  min cardinality: 0
  on property: derivative_of
subclass of: Restriction
  max cardinality: 1
  on property: derivative_of
subclass of: Restriction
  max cardinality: 1
  on property: has_group
subclass of: Restriction
  all values from: ChemicalGroup
  on property: has_group
subclass of: MoleculeGroupingClass
definition: A grouping class defined in terms of a derivative of a molecule and the addition of a group
in scheme: chemrof

MoleculeGroupingClassDefinedByComponents
type: Class
title: molecule grouping class defined by components
subclass of: Restriction
  min cardinality: 0
  on property: has_part
subclass of: Restriction
  max cardinality: 1
  on property: has_part
subclass of: Restriction
  all values from: ChemicalEntityOrGrouping
  on property: has_part
subclass of: MoleculeGroupingClass
definition: A grouping class defined as an exhaustive list of components
in scheme: chemrof

MonomericPolymericGroupingClass
type: Class
title: monomeric polymeric grouping class
subclass of: Restriction
  max cardinality: 1
  on property: has_repeat_unit
subclass of: Restriction
  min cardinality: 0
  on property: has_repeat_unit
subclass of: Restriction
  all values from: ChemicalEntity
  on property: has_repeat_unit
subclass of: GeneralizedMolecularStructureClass
in scheme: chemrof

PeriodicTablePlacement
type: Class
title: periodic table placement
subclass of: ChemicalInformation
in scheme: chemrof

StandardInchiObject
type: Class
title: standard inchi object
subclass of: Restriction
  max cardinality: 1
  on property: inchi_stereochemical_type_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_chemical_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_chemical_sublayer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^c.*
  on property: inchi_atom_connections_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_stereochemical_type_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_hydrogen_connections_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_atom_connections_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_proton_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_isotopic_layer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^p[\-]\d+
  on property: inchi_proton_sublayer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^q.*
  on property: inchi_charge_sublayer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^h.*
  on property: inchi_hydrogen_connections_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_tetrahedral_stereochemical_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_tetrahedral_stereochemical_sublayer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^[ih].*
  on property: inchi_isotopic_layer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_charge_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_proton_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_stereochemical_double_bond_sublayer
subclass of: Restriction
  min cardinality: 1
  on property: inchi_version_string
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^s.*
  on property: inchi_stereochemical_type_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_isotopic_layer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^[tm].*
  on property: inchi_tetrahedral_stereochemical_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_stereochemical_double_bond_sublayer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^1S$
  on property: inchi_version_string
subclass of: Restriction
  min cardinality: 0
  on property: inchi_hydrogen_connections_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_version_string
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^b.*
  on property: inchi_stereochemical_double_bond_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_charge_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_atom_connections_sublayer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^[A-Z0-9\.]+$
  on property: inchi_chemical_sublayer
subclass of: InchiObject
in scheme: chemrof

TanimotoSimilarity
type: Class
title: tanimoto similarity
subclass of: Restriction
  max cardinality: 1
  on property: score
subclass of: Restriction
  all values from: Datatype
    intersection of: float
    intersection of: Datatype
      on datatype: float
      with restrictions:
        min inclusive: 1e+00
    intersection of: Datatype
      on datatype: float
      with restrictions:
        max inclusive: 1e+00
  on property: score
subclass of: Restriction
  min cardinality: 0
  on property: score
subclass of: MoleculePairwiseSimilarity
alternative label: Jaccard similarity
alternative label: Tanimoto coefficient
in scheme: chemrof

atomically_connected_to
type: ObjectProperty
title: atomically connected to
domain: AtomOccurrence
range: AtomOccurrence
in scheme: chemrof

canonical_smiles_string
type: DatatypeProperty
title: canonical smiles string
sub property of: smiles_string
definition: A deterministic SMILES string. Note there is no unique system for canonical smiles strings
in scheme: chemrof

carbbank_representation
type: DatatypeProperty
title: carbbank representation
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.
in scheme: chemrof

charge
type: DatatypeProperty
in scheme: chemrof

chebi_formula
type: DatatypeProperty
sub property of: chemical_formula
definition: A CHEBI formular combines aspects of molecular and generalized molecular formulae, and may also be an atom symbol
in scheme: chemrof

curly_smiles_string
type: DatatypeProperty
title: curly smiles string
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
in scheme: chemrof

enantiomer_of
type: DatatypeProperty
title: enantiomer of
sub property of: stereoisomer_of
alternative label: enantiomorph of
definition: a stereoisomer relationship where the two forms are mirror images of one another
in scheme: chemrof

epimer_of
type: DatatypeProperty
title: epimer of
sub property of: diastereoisomers_of
definition: A diastereoisomer of relationship in which the isomers differ at only one stereocenter
in scheme: chemrof

extended_smiles_string
type: DatatypeProperty
title: extended smiles string
sub property of: smiles_string
alternative label: CXSMILES
in scheme: chemrof

functional_isomer_of
type: DatatypeProperty
title: functional isomer of
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.
in scheme: chemrof

generalized_empirical_formula
type: DatatypeProperty
title: generalized empirical formula
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
in scheme: chemrof

glycoct_condensed
type: DatatypeProperty
title: glycoct condensed
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.
in scheme: chemrof

glycominds_linearcode_representation
type: DatatypeProperty
title: glycominds linearcode representation
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).
in scheme: chemrof

has_acid_form
type: ObjectProperty
title: has acid form
domain: MoleculeByChargeState
range: MoleculeByChargeState
sub property of: conjugate_base_of
definition: connects a base to the acid form. E.g. citrate(3-) has acid form citric acid
in scheme: chemrof

has_cyclic_structure
type: DatatypeProperty
title: has cyclic structure
domain: Molecule
range: boolean
sub property of: chemical_property
definition: true if the molecule possesses a cycle in the atom connectivity graph
in scheme: chemrof
mapping relation: CHEMINF_000067

has_derivative
type: DatatypeProperty
title: has derivative
sub property of: alternate_form_of
inverse of: derivative_of
in scheme: chemrof

has_molfile_location
type: DatatypeProperty
title: has molfile location
range: anyURI
sub property of: information_property
definition: Location of a MolFile representing a chemical structure
in scheme: chemrof

has_physiologically_stable_form
type: DatatypeProperty
title: has physiologically stable form (Deprecated)
definition: Different term for the concept of a major microspecies at pH 7.3.
in scheme: chemrof

has_polymer_repeat_units
type: ObjectProperty
title: has polymer repeat units
range: PolymerRepeatUnit
definition: Relation between a polymer and all instances of a repeated polymeric unit
in scheme: chemrof

has_rauxinfo_representation
type: DatatypeProperty
title: has rauxinfo representation
sub property of: chemical_representation
alternative label: RAuxInfo
definition: Auxhiliary information on top of a RInChi
in scheme: chemrof
note: A half-reaction, such as a RInChI with starting materials and no identified products, is a valid RInChI

has_reaction_smarts_representation
type: DatatypeProperty
title: has reaction SMARTS representation
sub property of: has_reaction_representation
alternative label: reaction SMARTS
in scheme: chemrof

has_smirks_representation
type: DatatypeProperty
title: has reaction SMILES representation
sub property of: has_reaction_representation
alternative label: SMIRKS
definition: A reaction transform language that is a superset of reaction SMILES and a subset of reaction SMARTS
in scheme: chemrof

has_subtype
type: DatatypeProperty
title: has subtype
sub property of: chemical_to_chemical_relationship
inverse of: subtype_of
in scheme: chemrof

inchi2d_key_string
type: DatatypeProperty
title: inchi2d key string
sub property of: hashed_chemical_formula
alternative label: InChi2DKey
alternative label: inchi2d key
definition: A hashed representation of an InChi2D string
in scheme: chemrof
hash of: inchi2d_string

inchi2d_string
type: DatatypeProperty
title: InChi2D
sub property of: chemical_formula
alternative label: InChi
in scheme: chemrof

inchi_fixed_H_layer
type: DatatypeProperty
title: inchi fixed H layer
sub property of: inchi_sublayer
in scheme: chemrof

inchi_key_string
type: DatatypeProperty
title: inchi key string
sub property of: hashed_chemical_formula
alternative label: InChiKey
alternative label: inchi key
definition: A hashed representation of an InChi string
in scheme: chemrof
hash of: inchi_string

inchi_reconnected_layer
type: DatatypeProperty
title: inchi reconnected layer
sub property of: inchi_sublayer
in scheme: chemrof

isotone_of
type: ObjectProperty
title: isotone of
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.
in scheme: chemrof

isotopologue_of
type: ObjectProperty
title: isotopologue of
domain: Molecule
range: Molecule
sub property of: alternate_form_of
alternative label: isotopolog_of
definition: a relationship that holds between two forms of a parent molecule with identical chemical formulas but are differentiated by the number of neutrons in at least one atom
in scheme: chemrof

isotopomer_of
type: DatatypeProperty
sub property of: chemical_isomer_of
alternative label: isotopic_isomer_of
definition: isomers which differ by isotopic substitution, and which have the same number of atoms of each isotope but in a different arrangement.
in scheme: chemrof

kcat
type: DatatypeProperty
alternative label: turnover number
definition: The maximum number of substrate molecules converted to product per enzyme molecule per unit time, when the enzyme is saturated with substrate. It represents the maximum catalytic efficiency of an enzyme under ideal conditions.
in scheme: chemrof

kegg_chemical_function_representation
type: DatatypeProperty
title: kegg chemical function representation
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.
in scheme: chemrof

linucs_representation
type: DatatypeProperty
title: linucs representation
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.
in scheme: chemrof

logP6_partition_coefficient
type: DatatypeProperty
source: PhyschemPropHelp.html
sub property of: chemical_property
definition: logP partition coefficient calculated from 2D structure using contributions from pre-defined structure fragments. It corresponds to: log(Poctanol/Pwater) = log(SoluteInOctanol/SoluteInWater)
in scheme: chemrof

long_rinchi_key_string
type: DatatypeProperty
title: long rinchi key string
sub property of: rinchi_key_string
in scheme: chemrof

lychi_string
type: DatatypeProperty
title: lychi string
sub property of: chemical_formula
in scheme: chemrof

michaelis_constant
type: DatatypeProperty
alternative label: Km
definition: the substrate concentration at which the reaction rate is half of its maximum value (Vmax)
in scheme: chemrof
note: A lower Km indicates higher affinity (the enzyme needs less substrate to achieve half its maximum rate
note: Km is typically expressed in units of concentration (e.g., mol/L, μM, mM)

molar_cohesive_energy
type: DatatypeProperty
title: molar cohesive energy
sub property of: thermophysical_property
in scheme: chemrof

molar_refractivity
type: DatatypeProperty
source: PhyschemPropHelp.html
title: molar refractivity
sub property of: chemical_property
definition: Molar refractivity calculated from 2D structure using contributions from pre-defined structure fragments.
in scheme: chemrof

molar_value
type: DatatypeProperty
title: molar value
sub property of: thermophysical_property
in scheme: chemrof

molecular_charge
type: DatatypeProperty
title: molecular charge
range: integer
sub property of: molecular_property
definition: The electric charge of a molecule, typically expressed as multiples of the elementary charge.
in scheme: chemrof

molecular_electronic_absorption_spectroscopy
type: DatatypeProperty
title: molecular electronic absorption spectroscopy
sub property of: molecular_property
in scheme: chemrof

molecular_electronic_spectroscopy
type: DatatypeProperty
title: molecular electronic spectroscopy
range: string
sub property of: molecular_property
definition: A molecular property describing absorption or emission of electromagnetic radiation due to electronic transitions.
in scheme: chemrof

molecular_formula
type: DatatypeProperty
title: molecular formula
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
in scheme: chemrof
mapping relation: CHEMINF_000042

molecular_heat_capacity
type: DatatypeProperty
title: molecular heat capacity
range: float
sub property of: molecular_property
definition: The amount of heat required to raise the temperature of one mole of a molecule by one Kelvin.
in scheme: chemrof

molecular_hydration
type: DatatypeProperty
title: molecular hydration
range: integer
sub property of: molecular_property
definition: The number of water molecules associated with or bound to a molecule.
in scheme: chemrof

molecular_replacement
type: DatatypeProperty
title: molecular replacement
sub property of: molecular_property
in scheme: chemrof

molecular_shape
type: DatatypeProperty
title: molecular shape
range: string
sub property of: molecular_property
definition: The geometric configuration or three-dimensional arrangement of atoms within a molecule.
in scheme: chemrof

molecular_size
type: DatatypeProperty
title: molecular size
range: float
sub property of: molecular_property
definition: A property reflecting the spatial dimensions or volume occupied by a molecule.
in scheme: chemrof

molecular_spectroscopy
type: DatatypeProperty
title: molecular spectroscopy
sub property of: molecular_property
in scheme: chemrof

molecular_spectroscopy_by_energy_state
type: DatatypeProperty
title: molecular spectroscopy by energy state
sub property of: molecular_property
in scheme: chemrof

molecular_structure
type: DatatypeProperty
title: molecular structure
range: string
sub property of: molecular_property
definition: The specific arrangement of atoms in a molecule, usually represented by chemical notation or structural formulas.
in scheme: chemrof

next_in_homologous_series_from
type: ObjectProperty
title: next in homologous series from
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)
in scheme: chemrof

nuclear_isomer_of
type: ObjectProperty
title: nuclear isomer of
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
in scheme: chemrof

number_of_aromatic_rings
type: DatatypeProperty
source: PhyschemPropHelp.html
title: number of aromatic rings
sub property of: chemical_property
in scheme: chemrof

number_of_heavy_atoms
type: DatatypeProperty
source: PhyschemPropHelp.html
title: Heavy Atoms
sub property of: chemical_property
definition: number of of non-hydrogen atoms
in scheme: chemrof

number_of_hydrogen_bond_acceptors
type: DatatypeProperty
source: PhyschemPropHelp.html
title: number of hydrogen bond acceptors
sub property of: chemical_property
definition: number of hydrogen bond acceptors corresponding to sum of nitrogen atoms without any any implicit/explicit hydrogen atom and all oxygen atoms
in scheme: chemrof

number_of_hydrogen_bond_donors
type: DatatypeProperty
source: PhyschemPropHelp.html
title: number of hydrogen bond donors
sub property of: chemical_property
definition: number of hydrogen bond donors corresponding to sum of nitrogen and oxygen atoms with at least one implicit/explicit hydrogen atom
in scheme: chemrof

number_of_rings
type: DatatypeProperty
source: PhyschemPropHelp.html
title: number of rings
sub property of: chemical_property
in scheme: chemrof

number_of_rotatable_bonds
type: DatatypeProperty
source: PhyschemPropHelp.html
title: number of rotatable bonds
sub property of: chemical_property
definition: number of rotatable bonds corresponds to single bonds excluding following types of single bonds terminal bonds; attached to triple bonds; amide, thioamide and sulfonamide bonds.
in scheme: chemrof

object_atom_occurrence
type: ObjectProperty
title: object atom occurrence
range: AtomOccurrence
in scheme: chemrof

position_isomer_of
type: DatatypeProperty
title: position isomer of
sub property of: structural_isomer_of
alternative label: regioisomerism isomer of
definition: a functional group or other substituent changes position on a parent structure.
in scheme: chemrof

reaction_has_bidirectional_form
type: DatatypeProperty
title: reaction has bidirectional form
sub property of: variant_reaction_of
in scheme: chemrof

selfies_string
type: DatatypeProperty
title: selfies string
sub property of: chemical_formula
alternative label: SELFIES
in scheme: chemrof

short_rinchi_key_string
type: DatatypeProperty
title: short rinchi key string
sub property of: rinchi_key_string
in scheme: chemrof

skeletal_isomer_of
type: DatatypeProperty
title: skeletal isomer of
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).
in scheme: chemrof

subject_atom_occurrence
type: ObjectProperty
title: subject atom occurrence
range: AtomOccurrence
in scheme: chemrof

tautomer_of
type: DatatypeProperty
title: tautomer of
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
in scheme: chemrof

topological_polar_surface_area
type: DatatypeProperty
source: PhyschemPropHelp.html
title: topological polar surface area
sub property of: chemical_property
definition: Topological Polar Surface Area corresponding to nitrogen and oxygen atoms calculated from 2D structure using contributions from pre-defined structure fragments containing these atoms
in scheme: chemrof

transitive_conjugatated_form_of
type: DatatypeProperty
type: TransitiveProperty
title: transitive conjugatated form of
sub property of: derivative_of
in scheme: chemrof
transitive closure of: direct conjugatated from

tucan_string
type: DatatypeProperty
title: tucan string
sub property of: chemical_formula
in scheme: chemrof

van_der_waals_molecular_volume
type: DatatypeProperty
source: PhyschemPropHelp.html
title: van der waals molecular volume
sub property of: chemical_property
definition: van der Waals molecular volume calculated from 2D structure using atomic radii with adjustments for number of bonds, aromatic and non-aromatic rings
in scheme: chemrof

wurcs_representation
type: DatatypeProperty
title: wurcs representation
range: Datatype
  on datatype: string
  with restrictions:
    pattern: ^WURCS=Version/.*
sub property of: carboydrate_representation
alternative label: WURCS
in scheme: chemrof

ChemicalSimilarity
type: Class
title: similarity
subclass of: ChemicalRelationship
definition: A relationship between two or more chemical entities where there is some degree of similarity between these entities on their similarity
in scheme: chemrof

EntityWithAtomsEnumerated
type: Class
title: entity with atoms enumerated
subclass of: SpecificityMixin
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)
in scheme: chemrof

EntityWithChargeSpecified
type: Class
title: entity with charge specified
subclass of: SpecificityMixin
definition: A mixin for an entity where the charge is explicitly specified (corresponding to the /q layer in InChI)
in scheme: chemrof

EntityWithConnectivitySpecificied
type: Class
title: entity with connectivity specificied
subclass of: SpecificityMixin
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)
in scheme: chemrof

EntityWithIsotopeSpecified
type: Class
title: entity with isotope specified
subclass of: SpecificityMixin
definition: A mixin for an entity where the charge is explicitly specified (corresponding to the /q layer in InChI)
in scheme: chemrof

EntityWithStereochemistrySpecified
type: Class
title: entity with stereochemistry specified
subclass of: SpecificityMixin
definition: A mixin for an entity where the stereochemistry is explicitly specified (corresponding to the /t, m/, and /s layers in InChI)
in scheme: chemrof

GeneralizedMolecularStructureClass
type: Class
title: generalized molecular structure class
subclass of: MoleculeGroupingClass
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
in scheme: chemrof

InchiObject
type: Class
title: inchi object
subclass of: ChemicalInformation
definition: A representation of an InChI string as an object, composed of distinct sublayers
in scheme: chemrof

Location
type: Class
title: location
subclass of: ClassDefinition
definition: Abstract grouping for entities that represent abstract or concrete locations of chemical entities or their parts.
in scheme: chemrof

MaterialGroupingClass
type: Class
title: material grouping class
subclass of: Restriction
  all values from: Material
  on property: classifies
subclass of: Restriction
  max cardinality: 1
  on property: classifies
subclass of: Restriction
  min cardinality: 0
  on property: classifies
subclass of: Restriction
  all values from: MaterialGroupingClass
  on property: subtype_of
subclass of: Restriction
  min cardinality: 0
  on property: subtype_of
subclass of: PhysicochemicalEntityGroupingClass
definition: A grouping class that classifies materials
in scheme: chemrof

MolecularComponentGroupingClass
type: Class
title: molecular component grouping class
subclass of: Restriction
  min cardinality: 0
  on property: classifies
subclass of: Restriction
  min cardinality: 0
  on property: subtype_of
subclass of: Restriction
  all values from: MolecularComponent
  on property: classifies
subclass of: Restriction
  max cardinality: 1
  on property: classifies
subclass of: Restriction
  all values from: MolecularComponentGroupingClass
  on property: subtype_of
subclass of: ChemicalGroupingClass
definition: A grouping class that classifies molecular components. Example: inorganic anion group
in scheme: chemrof

MoleculePairwiseSimilarity
type: Class
title: molecule pairwise similarity
subclass of: Restriction
  min cardinality: 0
  on property: left_molecule
subclass of: Restriction
  all values from: Molecule
  on property: left_molecule
subclass of: Restriction
  min cardinality: 0
  on property: right_molecule
subclass of: Restriction
  max cardinality: 1
  on property: left_molecule
subclass of: Restriction
  all values from: float
  on property: score
subclass of: Restriction
  max cardinality: 1
  on property: right_molecule
subclass of: Restriction
  max cardinality: 1
  on property: score
subclass of: Restriction
  all values from: Molecule
  on property: right_molecule
subclass of: Restriction
  min cardinality: 0
  on property: score
subclass of: ChemicalSimilarity
in scheme: chemrof

PolymerRepeatUnit
type: Class
title: polymer repeat unit
subclass of: Restriction
  min cardinality: 0
  on property: repetition_of
subclass of: Restriction
  all values from: float
  on property: mass
subclass of: Restriction
  max cardinality: 1
  on property: mass
subclass of: Restriction
  max cardinality: 1
  on property: degree_of_polymerization
subclass of: Restriction
  all values from: int
  on property: degree_of_polymerization
subclass of: Restriction
  all values from: Molecule
  on property: repetition_of
subclass of: Restriction
  min cardinality: 0
  on property: mass
subclass of: Restriction
  max cardinality: 1
  on property: repetition_of
subclass of: Restriction
  min cardinality: 0
  on property: degree_of_polymerization
subclass of: ChemicalRelationship
definition: An abstract part of a polymer that is all instances of a repeated monomer of a single type
in scheme: chemrof

ReactionGroupingClass
type: Class
title: reaction grouping class
subclass of: Restriction
  max cardinality: 1
  on property: classifies
subclass of: Restriction
  min cardinality: 0
  on property: classifies
subclass of: Restriction
  all values from: Reaction
  on property: classifies
subclass of: Restriction
  min cardinality: 0
  on property: subtype_of
subclass of: Restriction
  all values from: ReactionGroupingClass
  on property: subtype_of
subclass of: GroupingClass
definition: A grouping class for reactions, for example, dehalogenase; breaking of covalent bond
in scheme: chemrof

classification_relationship
type: DatatypeProperty
title: classification relationship
in scheme: chemrof

classified_by
type: ObjectProperty
title: classified by
domain: OwlClass
range: OwlClass
sub property of: chemical_to_chemical_relationship
sub property of: owl_subclass_of
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
in scheme: chemrof

diastereoisomers_of
type: DatatypeProperty
title: diastereoisomers of
sub property of: stereoisomer_of
alternative label: diastereomers of
definition: A stereoisomer non-mirror image non-identical stereoisomers
in scheme: chemrof
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

has_higher_charge_from
type: DatatypeProperty
title: has higher charge from
sub property of: has_different_charge_state_from
in scheme: chemrof

has_lower_charge_from
type: DatatypeProperty
title: has lower charge from
sub property of: has_different_charge_state_from
in scheme: chemrof

major_microspecies_at_pH7_3_of
type: DatatypeProperty
sub property of: acid_form_of
inverse of: has_major_microspecies_at_pH7_3
definition: The subject of this link is the most common protonation state for this chemical at a pH of 7.3. The link may point to it's source.
in scheme: chemrof

variant_reaction_of
type: ObjectProperty
title: variant reaction of
domain: Reaction
range: Reaction
in scheme: chemrof

electron
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.

Higgs boson
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: A boson that is its own antiparticle, has no spin, zero electric charge and zero colour charge.

hydron
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: The general name for the hydrogen nucleus, to be used without regard to the hydrogen nuclear mass (either for hydrogen in its natural abundance or where it is not desired to distinguish between the isotopes).

lipid
type: Class
subclass of: MoleculeClassificationEnum
subclass of: PermissibleValue

proton
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u.

deuteron
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Nucleus of the (2)H atom.

triton
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Nucleus of the (3)H atom.

photon
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Particle of zero charge, zero rest mass, spin quantum number 1, energy hnu and momentum hnu/c (h is the Planck constant, nu the frequency of radiation and c the speed of light), carrier of electromagnetic force.

antimuon
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Elementary particle not affected by the strong force having a spin 1/2, a positive elementary charge and a rest mass of 0.113428913(17) u, or 105.658389(34) MeV.

alpha particle
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Nucleus of the (4)He atom.

helion
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Nucleus of the (3)He atom.

neutron
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Nuclear particle of zero charge, spin 1/2 and rest mass of 1.008664904(14) u.

electron neutrino
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue

positron
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Elementary particle not affected by the strong force having a spin 1/2, a positive elementary charge and a rest mass of 0.000548579903(13) u, or 0.51099906(15) MeV.

fundamental particle
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: A particle not known to have substructure.

nucleon
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Heavy nuclear particle: proton or neutron.

d-block
type: Class
subclass of: PeriodicTableBlockEnum
subclass of: PermissibleValue

f-block
type: Class
subclass of: PeriodicTableBlockEnum
subclass of: PermissibleValue

s-block
type: Class
subclass of: PeriodicTableBlockEnum
subclass of: PermissibleValue

p-block
type: Class
subclass of: PeriodicTableBlockEnum
subclass of: PermissibleValue

ester
type: Class
subclass of: MoleculeClassificationEnum
subclass of: PermissibleValue

lepton
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Lepton is a fermion that does not experience the strong force (strong interaction). The term is derived from the Greek lambdaepsilonpitauomicronsigma (small, thin).

baryon
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Baryon is a fermion that does experience the strong force (strong interaction). The term is derived from the Greek betaalpharhoupsilonsigma (heavy).

fermion
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Particle of half-integer spin quantum number following Fermi-Dirac statistics. Fermions are named after Enrico Fermi.

boson
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Particle of integer spin quantum number following Bose-Einstein statistics. Bosons are named after Satyendra Nath Bose.

composite particle
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: A subatomic particle known to have substructure (i.e. consisting of smaller particles).

hadron
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Hadron is a subatomic particle which experiences the strong force.

meson
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: A hadron with zero or integer spin; a strongly interacting boson. The term is derived from the Greek muepsilonsigmaomicronsigma (medium, middle).

quark
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Quarks comprise one of two classes of the fundamental particles. Quarks possess fractional electric charges and are not observed in free state.

nuclear particle
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: A nucleus or any of its constituents in any of their energy states.

pi meson
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: The collective name for zero-spin mesons pi(+), pi(-) and pi(0).

pi positive meson
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: A subatomic particle of charge number +1, zero spin and rest mass of 0.1498323(8) u, or 139.5679(7) MeV.

pi minus meson
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: A subatomic particle of charge number -1, zero spin and rest mass of 0.1498323(8) u, or 139.5679(7) MeV.

pi zero meson
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: A subatomic particle of zero charge, zero spin and rest mass of 0.1449008(9) u, or 134.9743(8) MeV.

neutrino
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: An elementary particle of spin 1/2, zero electric charge and negligible rest mass. Three known types (flavors) of neutrino are electron neutrino, muon neutrino and tau neutrino, named after their charged partner leptons.

muon neutrino
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue

tau neutrino
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue

tau lepton
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 1777.05 MeV.

muon
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: Elementary particle not affected by the strong force having a spin 1/2, a negative elementary charge and a rest mass of 0.113428913(17) u, or 105.658389(34) MeV.

hyperon
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: A baryon which contain one or more strange quarks. Hyperons are short-lived and heavier than nucleons.

up quark
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: A first-generation quark with a charge of +2/3. The up and down quarks are the fundamental constituents of the nucleons.

down quark
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: A first-generation quark with a charge of -1/3. The up and down quarks are the fundamental constituents of the nucleons.

strange quark
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: A second-generation quark with a charge of -1/3 and a strangeness of -1.

charm quark
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: A second-generation quark with a charge of +2/3.

bottom quark
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: A third-generation quark with a charge of -1/3.

top quark
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: A third-generation quark with a charge of +2/3.

Delta baryon
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue

nanotube
type: Class
subclass of: NanostructureMorphologyEnum
subclass of: PermissibleValue

nanoparticle
type: Class
subclass of: NanostructureMorphologyEnum
subclass of: PermissibleValue

nanorod
type: Class
subclass of: NanostructureMorphologyEnum
subclass of: PermissibleValue

nanotubosome
type: Class
subclass of: NanostructureMorphologyEnum
subclass of: PermissibleValue

quantum dot
type: Class
subclass of: NanostructureMorphologyEnum
subclass of: PermissibleValue

nanofibre
type: Class
subclass of: NanostructureMorphologyEnum
subclass of: PermissibleValue

nanocrystal
type: Class
subclass of: NanostructureMorphologyEnum
subclass of: PermissibleValue

nanoribbon
type: Class
subclass of: NanostructureMorphologyEnum
subclass of: PermissibleValue

nanosheet
type: Class
subclass of: NanostructureMorphologyEnum
subclass of: PermissibleValue

nanowire
type: Class
subclass of: NanostructureMorphologyEnum
subclass of: PermissibleValue

condensation
type: Class
subclass of: ReactionTypeEnum
subclass of: bond_formation
definition: A reaction in which two or more reactants yield a single main product with accompanying formation of a small molecule

cyclization
type: Class
subclass of: ReactionTypeEnum
subclass of: bond_formation
definition: Formation of cyclic structures from linear precursors

oxidation
type: Class
subclass of: functional_group_interconversion
subclass of: ReactionTypeEnum
definition: A functional group modification reaction where a functional group is oxidised

acylation
type: Class
subclass of: ReactionTypeEnum
subclass of: bond_formation
definition: Formation of an acyl group bond, typically involving carboxylic acid derivatives

carbon_carbon_bond_formation
type: Class
subclass of: ReactionTypeEnum
subclass of: bond_formation
definition: Reactions that form new carbon-carbon bonds

heteroatom_alkylation_arylation
type: Class
subclass of: ReactionTypeEnum
subclass of: bond_formation
definition: Alkylation or arylation of heteroatoms such as nitrogen, oxygen, or sulfur

isomerization
type: Class
subclass of: ReactionTypeEnum
subclass of: PermissibleValue
definition: Rearrangement reactions that convert one isomer to another

reduction
type: Class
subclass of: functional_group_interconversion
subclass of: ReactionTypeEnum
definition: A functional group modification reaction where a functional group is reduced

addition
type: Class
subclass of: ReactionTypeEnum
subclass of: bond_formation
definition: Reactions that add atoms or groups across multiple bonds

substitution
type: Class
subclass of: ReactionTypeEnum
subclass of: PermissibleValue
definition: A reaction step where one atom or group is replaced with another

hydrolysis
type: Class
subclass of: ReactionTypeEnum
subclass of: bond_breaking
definition: A solvolysis reaction where the solvent material is water

elimination
type: Class
subclass of: ReactionTypeEnum
subclass of: bond_breaking
definition: A molecular process where two groups are lost with concomitant formation of an unsaturation in the molecule or formation of a new ring

aromatic
type: Class
subclass of: BondTypeEnum
subclass of: PermissibleValue

double
type: Class
subclass of: BondTypeEnum
subclass of: PermissibleValue

hydrogen
type: Class
subclass of: BondTypeEnum
subclass of: PermissibleValue

covalent
type: Class
subclass of: BondTypeEnum
subclass of: PermissibleValue
definition: A covalent bond is a chemical bond that involves the sharing of pairs of electrons between atoms. This sharing results in a stable balance of attractive and repulsive forces between those atoms.

quadruple
type: Class
subclass of: BondTypeEnum
subclass of: PermissibleValue

single
type: Class
subclass of: BondTypeEnum
subclass of: PermissibleValue

triple
type: Class
subclass of: BondTypeEnum
subclass of: PermissibleValue

Metallic
type: Class
subclass of: ElementMetallicClassification
subclass of: PermissibleValue

Non-Metallic
type: Class
subclass of: ElementMetallicClassification
subclass of: PermissibleValue

Semi-Metallic
type: Class
subclass of: ElementMetallicClassification
subclass of: PermissibleValue

AminoAcidSequenceInterval
type: Class
title: amino acid sequence interval
subclass of: Restriction
  all values from: string
  on property: has_sequence_representation
subclass of: Restriction
  min cardinality: 0
  on property: has_sequence_representation
subclass of: Restriction
  max cardinality: 1
  on property: has_sequence_representation
subclass of: SequenceInterval
in scheme: chemrof

AtomAnion
type: Class
title: atom anion
subclass of: Restriction
  max cardinality: 1
  on property: elemental_charge
subclass of: Restriction
  min cardinality: 0
  on property: elemental_charge
subclass of: Restriction
  on property: mixins
  some values from: AnionState
subclass of: Restriction
  all values from: Datatype
    on datatype: integer
    with restrictions:
      max inclusive: -1
  on property: elemental_charge
subclass of: MonoatomicIon
definition: A monoatomic ion that is negative
in scheme: chemrof

AtomCation
type: Class
title: atom cation
subclass of: Restriction
  all values from: Datatype
    on datatype: integer
    with restrictions:
      min inclusive: 1
  on property: elemental_charge
subclass of: Restriction
  max cardinality: 1
  on property: elemental_charge
subclass of: Restriction
  min cardinality: 0
  on property: elemental_charge
subclass of: Restriction
  on property: mixins
  some values from: CationState
subclass of: MonoatomicIon
definition: A monoatomic ion that is positive, e.g Cu(2+)
in scheme: chemrof

AtomGroupingByPeriodicTablePlacement
type: Class
title: atom grouping by periodic table placement
subclass of: AtomGroupingClass
in scheme: chemrof

AtomGroupingClass
type: Class
title: atom grouping class
subclass of: Restriction
  min cardinality: 0
  on property: subtype_of
subclass of: Restriction
  max cardinality: 1
  on property: classifies
subclass of: Restriction
  min cardinality: 0
  on property: classifies
subclass of: Restriction
  all values from: MoleculeGroupingClass
  on property: subtype_of
subclass of: Restriction
  all values from: Atom
  on property: classifies
subclass of: ChemicalGroupingClass
definition: A grouping class that classifies atoms. For example, metal atom
in scheme: chemrof

AtomicBond
type: Class
title: atomic bond
subclass of: Restriction
  all values from: BondTypeEnum
  on property: bond_type
subclass of: Restriction
  min cardinality: 0
  on property: bond_angle
subclass of: Restriction
  min cardinality: 0
  on property: bond_energy
subclass of: Restriction
  max cardinality: 1
  on property: bond_length_in_angstroms
subclass of: Restriction
  max cardinality: 1
  on property: torsional_angle
subclass of: Restriction
  on property: mixins
  some values from: OwlClass
subclass of: Restriction
  min cardinality: 0
  on property: object
subclass of: Restriction
  all values from: float
  on property: bond_angle
subclass of: Restriction
  all values from: float
  on property: torsional_angle
subclass of: Restriction
  all values from: AtomOccurrence
  on property: object
subclass of: Restriction
  min cardinality: 0
  on property: bond_order
subclass of: Restriction
  max cardinality: 1
  on property: bond_type
subclass of: Restriction
  all values from: float
  on property: bond_energy
subclass of: Restriction
  max cardinality: 1
  on property: bond_energy
subclass of: Restriction
  min cardinality: 0
  on property: bond_type
subclass of: Restriction
  all values from: integer
  on property: bond_order
subclass of: Restriction
  max cardinality: 1
  on property: bond_order
subclass of: Restriction
  max cardinality: 1
  on property: object
subclass of: Restriction
  max cardinality: 1
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: subject
subclass of: Restriction
  min cardinality: 0
  on property: torsional_angle
subclass of: Restriction
  all values from: float
  on property: bond_length_in_angstroms
subclass of: Restriction
  min cardinality: 0
  on property: bond_length
subclass of: Restriction
  max cardinality: 1
  on property: bond_length
subclass of: Restriction
  min cardinality: 0
  on property: bond_length_in_angstroms
subclass of: Restriction
  max cardinality: 1
  on property: bond_angle
subclass of: Restriction
  all values from: AtomOccurrence
  on property: subject
subclass of: Restriction
  all values from: float
  on property: bond_length
subclass of: ChemicalRelationship
alternative label: bond
alternative label: chemical bond
definition: A connection between two atoms. Note this is the reified form of 'atomically connected to'.
in scheme: chemrof
mapping relation: CHEMINF_000063

ionic
type: Class
subclass of: BondTypeEnum
subclass of: PermissibleValue

metal-metal
type: Class
subclass of: BondTypeEnum
subclass of: PermissibleValue

polar covalent
type: Class
subclass of: BondTypeEnum
subclass of: PermissibleValue

polycentric
type: Class
subclass of: BondTypeEnum
subclass of: PermissibleValue

salt bridge
type: Class
subclass of: BondTypeEnum
subclass of: PermissibleValue

sigma
type: Class
subclass of: BondTypeEnum
subclass of: PermissibleValue

acid
type: Class
subclass of: BronstedAcidBaseRoleEnum
subclass of: PermissibleValue
definition: CHEBI:39141

base
type: Class
subclass of: BronstedAcidBaseRoleEnum
subclass of: PermissibleValue
definition: CHEBI:39142

ChemicalEntityOrGrouping
type: Class
title: chemical entity or grouping
subclass of: Mixin
in scheme: chemrof

ChemicalInformation
type: Class
title: chemical information
subclass of: ClassDefinition
in scheme: chemrof

ChemicalRole
type: Class
title: chemical role
subclass of: Restriction
  on property: mixins
  some values from: OwlClass
subclass of: ClassDefinition
alternative label: role
definition: A characteristic of a chemical entity that is realized under particular conditions
in scheme: chemrof

ChemicalSaltGroupingClass
type: Class
title: chemical salt grouping class
subclass of: Restriction
  max cardinality: 1
  on property: has_anionic_component
subclass of: Restriction
  all values from: ChemicalSalt
  on property: classifies
subclass of: Restriction
  max cardinality: 1
  on property: has_cationic_component
subclass of: Restriction
  all values from: string
  on property: has_cationic_component
subclass of: Restriction
  min cardinality: 0
  on property: has_cationic_component
subclass of: Restriction
  all values from: string
  on property: name
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  min cardinality: 0
  on property: classifies
subclass of: Restriction
  max cardinality: 1
  on property: classifies
subclass of: Restriction
  min cardinality: 0
  on property: has_anionic_component
subclass of: Restriction
  min cardinality: 0
  on property: name
subclass of: Restriction
  all values from: string
  on property: has_anionic_component
subclass of: MoleculeGroupingClass
definition: A grouping class for a chemical salt
in scheme: chemrof

Category
type: Class
subclass of: ClassificationLevelEnum
subclass of: PermissibleValue

Class
subclass of: ClassificationLevelEnum
subclass of: PermissibleValue

IsomericSubspecies
type: Class
subclass of: ClassificationLevelEnum
subclass of: Subspecies

MolecularSubspecies
type: Class
subclass of: ClassificationLevelEnum
subclass of: Subspecies

Species
type: Class
subclass of: ClassificationLevelEnum
subclass of: PermissibleValue

StructuralSubspecies
type: Class
subclass of: ClassificationLevelEnum
subclass of: Subspecies

Uncategorized
type: Class
subclass of: ClassificationLevelEnum
subclass of: PermissibleValue

Copolymer
type: Class
title: copolymer
subclass of: Restriction
  min cardinality: 0
  on property: polymer_of
subclass of: Restriction
  all values from: Thing
  on property: polymer_of
subclass of: MonomolecularPolymer
alternative label: heteropolymer
definition: a polymer with a more than one type of repeating unit
in scheme: chemrof

DNASequenceInterval
type: Class
title: DNA sequence interval
subclass of: NucleotideSequenceInterval
in scheme: chemrof

Alkali_Earth
type: Class
subclass of: ElementFamilyEnum
subclass of: PermissibleValue

Alkaline_Earth
type: Class
subclass of: ElementFamilyEnum
subclass of: PermissibleValue

Halogen
type: Class
subclass of: ElementFamilyEnum
subclass of: PermissibleValue

Metalloids
type: Class
subclass of: ElementFamilyEnum
subclass of: PermissibleValue

Noblegas
type: Class
subclass of: ElementFamilyEnum
subclass of: PermissibleValue

Non-Metal
type: Class
subclass of: ElementFamilyEnum
subclass of: PermissibleValue

Other_Metal
type: Class
subclass of: ElementFamilyEnum
subclass of: PermissibleValue

Rare_Earth
type: Class
subclass of: ElementFamilyEnum
subclass of: PermissibleValue

Transition
type: Class
subclass of: ElementFamilyEnum
subclass of: PermissibleValue

Ester
type: Class
title: ester
subclass of: Restriction
  min cardinality: 0
  on property: has_parent_alcohol
subclass of: Restriction
  all values from: MoleculeByChargeState
  on property: has_parent_acid
subclass of: Restriction
  max cardinality: 1
  on property: has_parent_acid
subclass of: Restriction
  all values from: ChemicalEntity
  on property: has_parent_alcohol
subclass of: Restriction
  max cardinality: 1
  on property: has_parent_alcohol
subclass of: Restriction
  min cardinality: 0
  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
in scheme: chemrof

FullyCovalentlyBonded
type: Class
title: fully covalently bonded
subclass of: Connectivity
definition: All pairs of atoms in this entity are transitively connected via covalent bonds
in scheme: chemrof

FullySpecifiedAtom
type: Class
title: fully specified atom
subclass of: Restriction
  min cardinality: 0
  on property: neutron_number
subclass of: Restriction
  max cardinality: 1
  on property: neutron_number
subclass of: Restriction
  all values from: int
  on property: neutron_number
subclass of: Restriction
  all values from: integer
  on property: elemental_charge
subclass of: Restriction
  min cardinality: 0
  on property: elemental_charge
subclass of: Restriction
  max cardinality: 1
  on property: elemental_charge
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)
in scheme: chemrof
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

FunctionalGroup
type: Class
title: functional group
subclass of: Restriction
  all values from: Molecule
  on property: is_substitutent_group_from
subclass of: Restriction
  min cardinality: 0
  on property: is_substitutent_group_from
subclass of: Restriction
  max cardinality: 1
  on property: is_substitutent_group_from
subclass of: MolecularComponent
in scheme: chemrof

Glycan
type: Class
title: glycan
subclass of: Macromolecule
alternative label: polysaccharides
definition: A macromolecule consisting of a large number of monosaccharides linked glycosidically
in scheme: chemrof
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

borderline
type: Class
subclass of: HardOrSoftEnum
subclass of: PermissibleValue

hard
type: Class
subclass of: HardOrSoftEnum
subclass of: PermissibleValue

soft
type: Class
subclass of: HardOrSoftEnum
subclass of: PermissibleValue

Homopolymer
type: Class
title: homopolymer
subclass of: Restriction
  all values from: Thing
  on property: polymer_of
subclass of: Restriction
  min cardinality: 0
  on property: polymer_of
subclass of: Restriction
  max cardinality: 1
  on property: polymer_of
subclass of: MonomolecularPolymer
definition: a polymer with a single type of repeating unit
in scheme: chemrof

active ingredient
type: Class
subclass of: IngredientRoleEnum
subclass of: PermissibleValue

excipient
type: Class
subclass of: IngredientRoleEnum
subclass of: PermissibleValue

inactive ingredient
type: Class
subclass of: IngredientRoleEnum
subclass of: PermissibleValue

solvent
type: Class
subclass of: IngredientRoleEnum
subclass of: PermissibleValue

Isobar
type: Class
title: isobar
subclass of: Restriction
  min cardinality: 0
  on property: decay_energy
subclass of: Restriction
  min cardinality: 0
  on property: mode_of_formation
subclass of: Restriction
  max cardinality: 1
  on property: isobar_of
subclass of: Restriction
  max cardinality: 1
  on property: mode_of_formation
subclass of: Restriction
  max cardinality: 1
  on property: decay_mode
subclass of: Restriction
  all values from: string
  on property: decay_mode
subclass of: Restriction
  all values from: int
  on property: nucleon_number
subclass of: Restriction
  max cardinality: 1
  on property: nucleon_number
subclass of: Restriction
  all values from: int
  on property: half_life
subclass of: Restriction
  all values from: ChemicalElement
  on property: has_element
subclass of: Restriction
  max cardinality: 1
  on property: decay_product
subclass of: Restriction
  min cardinality: 0
  on property: decay_product
subclass of: Restriction
  min cardinality: 0
  on property: decay_mode
subclass of: Restriction
  min cardinality: 0
  on property: nucleon_number
subclass of: Restriction
  max cardinality: 1
  on property: half_life
subclass of: Restriction
  all values from: string
  on property: mode_of_formation
subclass of: Restriction
  max cardinality: 1
  on property: decay_energy
subclass of: Restriction
  max cardinality: 1
  on property: has_element
subclass of: Restriction
  min cardinality: 0
  on property: half_life
subclass of: Restriction
  all values from: string
  on property: decay_energy
subclass of: Restriction
  min cardinality: 0
  on property: has_element
subclass of: Restriction
  all values from: Isotope
  on property: decay_product
subclass of: Restriction
  min cardinality: 0
  on property: isobar_of
subclass of: Restriction
  all values from: Thing
  on property: isobar_of
subclass of: Nuclide
definition: Isobars are atoms (nuclides) of different chemical elements that have the same number of nucleons.
in scheme: chemrof

IsomeraseReaction
type: Class
title: isomerase reaction
subclass of: Reaction
definition: A reaction that converts a molecule from one isomer to another.
in scheme: chemrof
note: This class is deprecated. Use the reaction_type slot with value 'isomerization' instead.

Mineral
type: Class
title: mineral
subclass of: Material
in scheme: chemrof

Moiety
type: Class
title: moiety
subclass of: MolecularComponent
definition: a named part of a molecule. In some instances moieties may be composed of yet smaller moieties and functional groups
in scheme: chemrof

MolecularAnion
type: Class
title: molecular anion
subclass of: Restriction
  on property: mixins
  some values from: AnionState
subclass of: PolyatomicIon
definition: A polyatomic ion that is negative
in scheme: chemrof

MolecularCation
type: Class
title: molecular cation
subclass of: Restriction
  on property: mixins
  some values from: CationState
subclass of: PolyatomicIon
definition: A polyatomic ion that is positive
in scheme: chemrof

MolecularSpecies
type: Class
title: molecular species
subclass of: Molecule
definition: A molecule in which the units are identical. Example: methyl
in scheme: chemrof

MolecularSubsequence
type: Class
title: molecular subsequence
subclass of: PolymerPart
in scheme: chemrof

MoleculeClassificationEnum
type: Class
subclass of: EnumDefinition
union of: lipid
union of: ester
in scheme: chemrof
permissible values: lipid
permissible values: ester

Monomer
type: Class
title: monomer
subclass of: PolymerPart
alternative label: momomer species
in scheme: chemrof

Nanomaterial
type: Class
source: Nanomaterials
title: nanomaterial
subclass of: Restriction
  max cardinality: 1
  on property: has_morphological_category
subclass of: Restriction
  all values from: NanostructureMorphologyEnum
  on property: has_morphological_category
subclass of: Restriction
  min cardinality: 0
  on property: has_morphological_category
subclass of: Material
definition: A material of which a single unit is sized (in at least one dimension) between 1 and 100 nm
in scheme: chemrof

NaturalProduct
type: Class
title: natural product
subclass of: Restriction
  min cardinality: 0
  on property: derived_from_organisms
subclass of: Restriction
  all values from: anyURI
  on property: derived_from_organisms
subclass of: Molecule
in scheme: chemrof

NeutralMolecule
type: Class
title: neutral molecule
subclass of: NetUnchargedMolecule
definition: A molecule that has no net charge and is not a zwitterion
in scheme: chemrof

NonSpeciesMolecule
type: Class
title: non species molecule
subclass of: Molecule
definition: A molecule in which the units are not identical. TODO: move this higher
in scheme: chemrof

Peptide
type: Class
title: peptide
subclass of: Macromolecule
in scheme: chemrof

g-block
type: Class
subclass of: PeriodicTableBlockEnum
subclass of: PermissibleValue
definition: The g-block is a hypothetical region in the periodic table of the elements.

ProportionalPart
type: Class
title: proportional part
subclass of: Restriction
  min cardinality: 0
  on property: composed_of
subclass of: Restriction
  all values from: float
  on property: minimal_percentage
subclass of: Restriction
  max cardinality: 1
  on property: maximum_percentage
subclass of: Restriction
  all values from: float
  on property: maximum_percentage
subclass of: Restriction
  max cardinality: 1
  on property: has_role
subclass of: Restriction
  min cardinality: 0
  on property: maximum_percentage
subclass of: Restriction
  min cardinality: 0
  on property: minimal_percentage
subclass of: Restriction
  all values from: ChemicalEntity
  on property: composed_of
subclass of: Restriction
  max cardinality: 1
  on property: composed_of
subclass of: Restriction
  max cardinality: 1
  on property: minimal_percentage
subclass of: Restriction
  all values from: IngredientRoleEnum
  on property: has_role
subclass of: Restriction
  min cardinality: 0
  on property: has_role
subclass of: ChemicalRelationship
definition: A part of a complex mixture that is of uniform composition
in scheme: chemrof

Protein
type: Class
title: protein
subclass of: Macromolecule
definition: A macromolecule composed of one or more polypeptide chains of amino acids that fold into a specific three-dimensional structure and perform biological functions
in scheme: chemrof

RNASequenceInterval
type: Class
title: RNA sequence interval
subclass of: NucleotideSequenceInterval
in scheme: chemrof

RacemicMixture
type: Class
title: racemic mixture
subclass of: Restriction
  max cardinality: 1
  on property: has_right_enantiomer
subclass of: Restriction
  all values from: Enantiomer
  on property: has_right_enantiomer
subclass of: Restriction
  all values from: Enantiomer
  on property: has_left_enantiomer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^rac-
  on property: IUPAC_name
subclass of: Restriction
  all values from: Molecule
  on property: chirality_agnostic_form
subclass of: Restriction
  min cardinality: 1
  on property: has_left_enantiomer
subclass of: Restriction
  max cardinality: 1
  on property: chirality_agnostic_form
subclass of: Restriction
  max cardinality: 1
  on property: has_left_enantiomer
subclass of: Restriction
  min cardinality: 0
  on property: chirality_agnostic_form
subclass of: Restriction
  min cardinality: 1
  on property: has_right_enantiomer
subclass of: Restriction
  min cardinality: 0
  on property: IUPAC_name
subclass of: Restriction
  max cardinality: 1
  on property: IUPAC_name
subclass of: PreciseChemicalMixture
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
in scheme: chemrof

Radionuclide
type: Class
title: radionuclide
subclass of: Nuclide
alternative label: radioactive isotope
alternative label: radioactive nuclide
definition: an atom that has excess nuclear energy, making it unstable
in scheme: chemrof

aromatic_heterocycle_formation
type: Class
subclass of: ReactionTypeEnum
subclass of: PermissibleValue
definition: Formation of aromatic rings containing heteroatoms

deprotection
type: Class
subclass of: ReactionTypeEnum
subclass of: PermissibleValue
definition: Removal of protecting groups to restore original functionalities

functional_group_addition
type: Class
subclass of: ReactionTypeEnum
subclass of: PermissibleValue
definition: Addition of functional groups to unsaturated bonds or reactive centers

protection
type: Class
subclass of: ReactionTypeEnum
subclass of: PermissibleValue
definition: Introduction of protecting groups to temporarily mask reactive functionalities

resolution
type: Class
subclass of: ReactionTypeEnum
subclass of: PermissibleValue
definition: Separation of enantiomers or other stereoisomers

ring_opening
type: Class
subclass of: ReactionTypeEnum
subclass of: bond_breaking
definition: Cleavage of cyclic structures to form linear products

SmallMolecule
type: Class
title: small molecule
subclass of: Molecule
definition: A molecule characterized by availability in small-molecule databases
in scheme: chemrof

State
type: Class
title: state
subclass of: Mixin
in scheme: chemrof

SubatomicParticleOccurrence
type: Class
title: subatomic particle occurrence
subclass of: Restriction
  max cardinality: 1
  on property: Count
subclass of: Restriction
  min cardinality: 1
  on property: occurrence_of
subclass of: Restriction
  max cardinality: 1
  on property: occurrence_of
subclass of: Restriction
  on property: mixins
  some values from: OwlClass
subclass of: Restriction
  all values from: SubatomicParticle
  on property: occurrence_of
subclass of: Restriction
  all values from: integer
  on property: Count
subclass of: Restriction
  min cardinality: 0
  on property: Count
subclass of: ChemicalRelationship
in scheme: chemrof

SupramolecularPolymer
type: Class
title: supramolecular polymer
subclass of: Restriction
  max cardinality: 1
  on property: has_repeat_unit
subclass of: Restriction
  min cardinality: 0
  on property: has_repeat_unit
subclass of: Restriction
  min cardinality: 0
  on property: polymer_of
subclass of: Restriction
  all values from: Macromolecule
  on property: polymer_of
subclass of: Restriction
  all values from: ChemicalEntity
  on property: has_repeat_unit
subclass of: Restriction
  max cardinality: 1
  on property: polymer_of
subclass of: MolecularComplex
definition: polymeric arrays of monomeric units that are connected by reversible and highly directional secondary interactions–that is, non-covalent bonds
in scheme: chemrof

UnchargedAtom
type: Class
title: uncharged atom
subclass of: Restriction
  on property: mixins
  some values from: Uncharged
subclass of: AtomIonicForm
definition: An atom type that has no charge
in scheme: chemrof
mapping relation: COB_0000043

WeaklyBonded
type: Class
title: weakly bonded
subclass of: Connectivity
definition: Not covalently bonded
in scheme: chemrof

Zwitterion
type: Class
title: zwitterion
subclass of: NetUnchargedMolecule
definition: A molecule that has both a positive and negative charges but is net neutral
in scheme: chemrof

derived_from_organisms
type: DatatypeProperty
in scheme: chemrof

direct_conjugatated_form_of
type: DatatypeProperty
type: SymmetricProperty
title: direct conjugatated form of
sub property of: derivative_of
in scheme: chemrof

entities
type: ObjectProperty
in scheme: chemrof

has_atom_occurrences
type: ObjectProperty
title: has atom occurrences
range: AtomOccurrence
definition: An individuated atom in the context of a chemical structure.
in scheme: chemrof

has_atoms
type: ObjectProperty
title: has atoms
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
in scheme: chemrof

has_bonds
type: ObjectProperty
title: has bonds
domain: Molecule
range: AtomicBond
in scheme: chemrof

has_different_charge_state_from
type: DatatypeProperty
title: has different charge state from
in scheme: chemrof

has_ionic_component
type: DatatypeProperty
title: has ionic component
sub property of: has_part
in scheme: chemrof

has_proportional_parts
type: ObjectProperty
title: has proportional parts
domain: ImpreciseChemicalMixture
range: ProportionalPart
alternative label: has ingredients
definition: Relationship between a complex mixture and its parts
in scheme: chemrof

has_stereocenter
type: ObjectProperty
title: has stereocenter
range: Stereocenter
in scheme: chemrof

inchi_component
type: DatatypeProperty
title: inchi component
sub property of: information_property
definition: A part of an InChI object
in scheme: chemrof

left_participants
type: ObjectProperty
title: left participants
range: ReactionParticipant
in scheme: chemrof

pka_ionization_constant
type: DatatypeProperty
title: pKa ionization constant
range: float
sub property of: molecular_property
definition: The negative logarithm of the acid dissociation constant (Ka) for ionizable groups in a molecule. Multiple pKa values may exist for molecules with multiple ionizable groups.
in scheme: chemrof
note: For molecules with multiple ionizable groups, this field can contain multiple values
note: Lower pKa values indicate stronger acids
note: Standard conditions: aqueous solution at 25°C

right_participants
type: ObjectProperty
title: right participants
range: ReactionParticipant
in scheme: chemrof

rinchi_key_string
type: DatatypeProperty
title: rinchi key string
sub property of: hashed_chemical_formula
definition: A hashed representation of a RInChi string
in scheme: chemrof
hash of: has_rinchi_representation

stereoisomer_of
type: DatatypeProperty
title: stereoisomer of
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
in scheme: chemrof

thermophysical_property
type: DatatypeProperty
title: thermophysical property
sub property of: chemical_property
in scheme: chemrof

SubatomicParticle
type: Class
subclass of: SubatomicParticleEnum
subclass of: PermissibleValue
definition: A particle smaller than an atom.

ChargeState
type: Class
title: charge state
subclass of: State
definition: Applies to entities that have a charge state, which may be positive, negative, or neutral
in scheme: chemrof
mapping relation: CHEMINF_000120

ChemicalGroup
type: Class
title: chemical group
subclass of: MolecularComponent
alternative label: FunctionalGroup
alternative label: chemical functional group
alternative label: group
in scheme: chemrof

ChemicalSalt
type: Class
title: chemical salt
subclass of: Restriction
  max cardinality: 1
  on property: elemental_charge
subclass of: Restriction
  all values from: CationState
  on property: has_cationic_component
subclass of: Restriction
  max cardinality: 1
  on property: has_anionic_component
subclass of: Restriction
  max cardinality: 1
  on property: has_cationic_component
subclass of: Restriction
  all values from: Datatype
    intersection of: Datatype
      on datatype: integer
      with restrictions:
        min inclusive: 0
    intersection of: Datatype
      on datatype: integer
      with restrictions:
        max inclusive: 0
  on property: elemental_charge
subclass of: Restriction
  min cardinality: 0
  on property: elemental_charge
subclass of: Restriction
  all values from: AnionState
  on property: has_anionic_component
subclass of: Restriction
  min cardinality: 0
  on property: has_anionic_component
subclass of: Restriction
  min cardinality: 0
  on property: has_cationic_component
subclass of: PreciseChemicalMixture
definition: a chemical compound consisting of an ionic assembly of cations and anions.
in scheme: chemrof
note: in SIO falls under molecular complex? Also in biolink

Connectivity
type: Class
title: connectivity
subclass of: Mixin
definition: Abstract grouping for slots that related chemical entities via a connectivity relationships
in scheme: chemrof

Count
type: DatatypeProperty
in scheme: chemrof

ElementMetallicClassification
type: Class
title: element_metallic_classification
subclass of: EnumDefinition
union of: Metallic
union of: Non-Metallic
union of: Semi-Metallic
in scheme: chemrof
permissible values: Metallic
permissible values: Non-Metallic
permissible values: Semi-Metallic

GroupingClass
type: Class
title: grouping class
subclass of: Restriction
  min cardinality: 0
  on property: name
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  min cardinality: 0
  on property: subtype_of
subclass of: Restriction
  all values from: GroupingClass
  on property: subtype_of
subclass of: Restriction
  on property: mixins
  some values from: OwlClass
subclass of: Restriction
  min cardinality: 1
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: id
subclass of: Restriction
  all values from: string
  on property: name
subclass of: Restriction
  all values from: string
  on property: id
subclass of: ClassDefinition
definition: Instances of this class represent generic concepts that can be used to group more specific concepts, or to classify entities
in scheme: chemrof

GroupingClassForAcidsOrBases
type: Class
title: grouping class for acids or bases
subclass of: Restriction
  min cardinality: 0
  on property: conjugate_base_of
subclass of: Restriction
  all values from: Thing
  on property: conjugate_acid_of
subclass of: Restriction
  min cardinality: 0
  on property: conjugate_acid_of
subclass of: Restriction
  max cardinality: 1
  on property: conjugate_base_of
subclass of: Restriction
  max cardinality: 1
  on property: conjugate_acid_of
subclass of: Restriction
  all values from: Thing
  on property: conjugate_base_of
subclass of: MoleculeGroupingClass
in scheme: chemrof

ImpreciseChemicalMixture
type: Class
title: imprecise chemical mixture
subclass of: Restriction
  min cardinality: 0
  on property: has_mixfile_location
subclass of: Restriction
  all values from: anyURI
  on property: has_mixfile_location
subclass of: Restriction
  all values from: ProportionalPart
  on property: has_proportional_parts
subclass of: Restriction
  all values from: string
  on property: has_minchi_representation
subclass of: Restriction
  min cardinality: 0
  on property: has_minchi_representation
subclass of: Restriction
  max cardinality: 1
  on property: has_mixfile_location
subclass of: Restriction
  max cardinality: 1
  on property: has_minchi_representation
subclass of: Restriction
  min cardinality: 0
  on property: has_proportional_parts
subclass of: ChemicalMixture
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
in scheme: chemrof
note: although the stoichiometry is not known rough percentage parts can be provided

MolecularComplex
type: Class
title: molecular complex
subclass of: PreciseChemicalMixture
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
in scheme: chemrof
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

PhysicochemicalEntityGroupingClass
type: Class
title: physicochemical entity grouping class
subclass of: Restriction
  min cardinality: 0
  on property: classifies
subclass of: Restriction
  min cardinality: 0
  on property: subtype_of
subclass of: Restriction
  max cardinality: 1
  on property: classifies
subclass of: Restriction
  all values from: PhysicochemicalEntityGroupingClass
  on property: subtype_of
subclass of: Restriction
  all values from: PhysicochemicalEntity
  on property: classifies
subclass of: GroupingClass
in scheme: chemrof

Stereocenter
type: Class
source: Stereocenter
title: stereocenter
subclass of: Location
alternative label: stereogenic center
definition: a geometric point in a molecule in which the interchanging of two substituents creates a stereoisomer.
in scheme: chemrof

Stereoisomer
type: Class
title: stereoisomer
subclass of: Restriction
  all values from: string
  on property: isomeric_smiles_string
subclass of: Restriction
  min cardinality: 0
  on property: isomeric_smiles_string
subclass of: Restriction
  max cardinality: 1
  on property: isomeric_smiles_string
subclass of: Molecule
in scheme: chemrof

Uncharged
type: Class
title: uncharged
subclass of: ChargeState
alternative label: neutral charge
definition: Applies to entities that are uncharged, i.e. have an elemental charge of zero
in scheme: chemrof
mapping relation: CHEMINF_000401

absolute_configuration
type: DatatypeProperty
title: absolute configuration
range: string
in scheme: chemrof

acidity
type: DatatypeProperty
range: float
in scheme: chemrof

allotropic_analog_of
type: ObjectProperty
title: allotropic analog of
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
in scheme: chemrof

boiling_point_in_celcius
type: DatatypeProperty
title: boiling point in celcius
range: float
in scheme: chemrof

bond_angle
type: DatatypeProperty
title: bond angle
range: float
in scheme: chemrof

bond_energy
type: DatatypeProperty
alternative label: average bond enthalpy
alternative label: mean bond enthalpy
definition: the measure of bond strength in a chemical bond.
in scheme: chemrof

bond_length
type: DatatypeProperty
definition: the average distance between nuclei of two bonded atoms in a molecule
in scheme: chemrof

bond_length_in_angstroms
type: DatatypeProperty
title: bond length in angstroms
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.
in scheme: chemrof

bond_order
type: DatatypeProperty
definition: the number of electron pairs (bonds) between a pair of atoms
in scheme: chemrof

bond_type
type: ObjectProperty
title: bond type
range: BondTypeEnum
in scheme: chemrof

bronsted_acid_base_role
type: ObjectProperty
title: bronsted acid base role
range: BronstedAcidBaseRoleEnum
in scheme: chemrof

charge_agnostic_entity
type: ObjectProperty
title: charge agnostic entity
range: ChemicalEntity
in scheme: chemrof

chemical_isomer_of
type: ObjectProperty
title: chemical isomer of
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
in scheme: chemrof

chirality_agnostic_form
type: ObjectProperty
title: chirality agnostic form
range: Molecule
in scheme: chemrof

composed_of
type: ObjectProperty
title: composed of
range: ChemicalEntity
in scheme: chemrof

coordination_number
type: DatatypeProperty
title: coordination number
range: integer
alternative label: coordination
definition: The number of atoms bonded to the atom of interest. [https://doi.org/10.1021%2Fed083p791]
in scheme: chemrof

degree_of_polymerization
type: DatatypeProperty
title: degree of polymerization
range: int
in scheme: chemrof

description
type: DatatypeProperty
in scheme: chemrof

direction
type: DatatypeProperty
definition: One of l->r, r->l, bidirectional, neutral
in scheme: chemrof

electron_configuration
type: DatatypeProperty
title: electron configuration
range: string
in scheme: chemrof

empirical_formula
type: DatatypeProperty
title: empirical formula
sub property of: chemical_formula
definition: A chemical formula where numbers denote relative proportion of atoms. E.g. CH2O for glucose
in scheme: chemrof

enantiomer_form_of
type: ObjectProperty
title: enantiomer form of
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
in scheme: chemrof

energy_level
type: DatatypeProperty
title: energy level
alternative label: energy state
definition: e.g. ground, stable
in scheme: chemrof

formal_charge
type: DatatypeProperty
title: formal charge
range: integer
alternative label: charge
definition: The charge remaining on an atom when all ligands are removed homolytically. [https://doi.org/10.1021%2Fed083p791]
in scheme: chemrof

hard_or_soft
type: ObjectProperty
title: hard or soft
range: HardOrSoftEnum
in scheme: chemrof

has_bonding_structure
type: DatatypeProperty
title: has bonding structure
definition: The pattern in which the atoms are bonded; e.g. hexagonal lattice, sheets, etc
in scheme: chemrof

has_charge_state
type: DatatypeProperty
title: has charge state
range: anyURI
in scheme: chemrof

has_chemical_role
type: ObjectProperty
title: has chemical role
range: ChemicalRole
in scheme: chemrof

has_group
type: DatatypeProperty
title: has group
domain: Atom
sub property of: has_submolecules
definition: Relation between a molecule and the groups it contains
in scheme: chemrof

has_left_enantiomer
type: ObjectProperty
title: has left enantiomer
range: Enantiomer
in scheme: chemrof

has_minchi_representation
type: DatatypeProperty
title: has minchi representation
sub property of: chemical_representation
alternative label: MInChi
definition: Proposed new Mixtures InChI
in scheme: chemrof

has_mixfile_location
type: DatatypeProperty
title: has mixfile location
range: anyURI
sub property of: information_property
definition: Location of a MixFile representing a chemical mixture
in scheme: chemrof

has_morphological_category
type: ObjectProperty
title: has morphological category
range: NanostructureMorphologyEnum
definition: e.g. rod, sheet
in scheme: chemrof

has_nuclear_parts
type: ObjectProperty
title: has nuclear parts
range: SubatomicParticleOccurrence
sub property of: property_of_atom
in scheme: chemrof

has_parent_acid
type: ObjectProperty
title: has parent acid
range: MoleculeByChargeState
in scheme: chemrof

has_parent_alcohol
type: ObjectProperty
title: has parent alcohol
range: ChemicalEntity
in scheme: chemrof

has_reaction_representation
type: DatatypeProperty
sub property of: chemical_representation
in scheme: chemrof

has_reaction_smiles_representation
type: DatatypeProperty
title: has reaction SMILES representation
sub property of: has_reaction_representation
alternative label: reaction SMILES
in scheme: chemrof

has_right_enantiomer
type: ObjectProperty
title: has right enantiomer
range: Enantiomer
in scheme: chemrof

has_rinchi_representation
type: DatatypeProperty
title: has rinchi representation
sub property of: chemical_representation
alternative label: RInChi
definition: Proposed Reactions InChI
in scheme: chemrof
note: A half-reaction, such as a RInChI with starting materials and no identified products, is a valid RInChI

has_role
type: ObjectProperty
title: has role
range: IngredientRoleEnum
in scheme: chemrof

hashed_chemical_formula
type: DatatypeProperty
title: hashed chemical formula
domain: ChemicalEntity
range: string
sub property of: chemical_representation
definition: A hashed version of a chemical formula
in scheme: chemrof

inchi_string
type: DatatypeProperty
title: InChi
sub property of: chemical_formula
in scheme: chemrof

inchi_sublayer_in_main_layer
type: DatatypeProperty
title: inchi sublayer in main layer
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
in scheme: chemrof

inchi_version_string
type: DatatypeProperty
title: inchi version string
range: Datatype
  on datatype: string
  with restrictions:
    pattern: ^1[S]
sub property of: inchi_component
alternative label: inchi version prefix
definition: The first part of the inchi_string, after 'InChI='
in scheme: chemrof
inchi.index: 1

is_balanced
type: DatatypeProperty
title: is balanced
range: boolean
in scheme: chemrof

is_branched
type: DatatypeProperty
title: is branched
range: boolean
in scheme: chemrof

is_diastereoselective
type: DatatypeProperty
title: is diastereoselective
range: boolean
in scheme: chemrof

is_fully_characterized
type: DatatypeProperty
title: is fully characterized
range: boolean
definition: False if includes R-groups
in scheme: chemrof

is_organic
type: DatatypeProperty
title: is organic
domain: ChemicalEntity
range: boolean
definition: An organic molecule is a molecule composed of organic atoms (at least carbon, hydrogen, and optionally oxygen, phosphorus, nitrogen, sulfur) [SIO]
in scheme: chemrof

is_radical
type: DatatypeProperty
title: is radical
domain: ChemicalEntity
range: boolean
in scheme: chemrof

is_stereo
type: DatatypeProperty
title: is stereo
range: boolean
in scheme: chemrof

is_substitutent_group_from
type: ObjectProperty
title: is substitutent group from
range: Molecule
in scheme: chemrof

is_transport
type: DatatypeProperty
title: is transport
range: boolean
in scheme: chemrof

isobar_of
type: DatatypeProperty
title: isobar of
sub property of: alternate_form_of
definition: equal mass number (Z1 + N1 = Z2 + N2)
in scheme: chemrof

isomeric_smiles_string
type: DatatypeProperty
title: isomeric smiles string
sub property of: smiles_string
alternative label: iso-SMILES
definition: A SMILES string that distinguishes between isomeric forms. E.g. [13C] for carbon-13
in scheme: chemrof

isotope_of
type: ObjectProperty
title: isotope of
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.
in scheme: chemrof

left_molecule
type: ObjectProperty
title: left molecule
range: Molecule
in scheme: chemrof

markush_string
type: DatatypeProperty
sub property of: chemical_formula
in scheme: chemrof

maximum_percentage
type: DatatypeProperty
title: maximum percentage
range: float
in scheme: chemrof

melting_point_in_celcius
type: DatatypeProperty
title: melting point in celcius
range: float
in scheme: chemrof

minimal_percentage
type: DatatypeProperty
title: minimal percentage
range: float
in scheme: chemrof

molecular_mass
type: DatatypeProperty
title: molecular mass
range: float
sub property of: molecular_property
definition: The sum of the relative atomic masses of the constituent atoms of a molecule.
in scheme: chemrof

monoisotopic_mass
type: DatatypeProperty
title: monoisotopic mass
range: float
in scheme: chemrof

nucleon_number
type: DatatypeProperty
title: nucleon number
domain: Atom
range: int
sub property of: subatomic_particle_count
alternative label: mass number
definition: number of nucleons in an atom. proton number plus neutron number.
in scheme: chemrof

object
type: ObjectProperty
in scheme: chemrof

optical_configuration
type: DatatypeProperty
title: optical configuration
range: string
in scheme: chemrof

oxidation_number
type: DatatypeProperty
title: oxidation number
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]
in scheme: chemrof

participant
type: ObjectProperty
range: ChemicalEntity
in scheme: chemrof

pka_ionic_strength
type: DatatypeProperty
title: pKa ionic strength
range: float
sub property of: molecular_property
definition: Ionic strength of solution in mol/L at which pKa was measured. Default is 0.0 M if not specified.
in scheme: chemrof
note: Salt concentration affects pKa through electrostatic shielding of charges
note: Standard ionic strength is 0.0 M (zero ionic strength corresponding to distilled water)

pka_pressure
type: DatatypeProperty
title: pKa pressure
range: float
sub property of: molecular_property
definition: Pressure in atmospheres at which pKa was measured. Default is 1 atm if not specified.
in scheme: chemrof
note: Generally minor effect under standard laboratory conditions
note: Standard pressure is 1 atm

pka_solvent
type: DatatypeProperty
title: pKa solvent
range: string
sub property of: molecular_property
definition: Solvent system for pKa measurement. Default is water (H₂O) if not specified.
in scheme: chemrof
note: Standard solvent is water (H₂O)
note: pKa values in non-aqueous solvents can be dramatically different due to polarity effects

pka_temperature
type: DatatypeProperty
title: pKa temperature
range: float
sub property of: molecular_property
definition: Temperature in Celsius at which pKa was measured. Default is 25°C if not specified.
in scheme: chemrof
note: Standard temperature is 25°C (298.15 K)
note: pKa values can shift significantly with temperature following the van't Hoff equation

polymer_architecture_type
type: DatatypeProperty
title: polymer architecture type
definition: morphological structure of a polymer
in scheme: chemrof

property_of_atom
type: DatatypeProperty
title: property of atom
domain: Atom
sub property of: chemical_property
in scheme: chemrof

reaction_center
type: DatatypeProperty
title: reaction center
in scheme: chemrof

reaction_rate
type: DatatypeProperty
title: reaction rate
range: float
alternative label: v
definition: the overall speed of a reaction, typically measured in concentration change per unit time
in scheme: chemrof

reaction_rate_coefficient
type: DatatypeProperty
title: reaction rate coefficient
range: float
alternative label: reaction rate constant
definition: a proportionality constant that relates the reaction rate to reactant concentrations.
in scheme: chemrof

reaction_type
type: ObjectProperty
title: reaction type
range: ReactionTypeEnum
definition: Classification of the chemical reaction based on mechanistic and functional categories
in scheme: chemrof

relative_configuration
type: DatatypeProperty
title: relative configuration
range: string
in scheme: chemrof

repetition_of
type: ObjectProperty
title: repetition of
range: Molecule
definition: the macromolecule that is repeated
in scheme: chemrof

right_molecule
type: ObjectProperty
title: right molecule
range: Molecule
in scheme: chemrof

smarts_string
type: DatatypeProperty
title: smarts string
sub property of: chemical_formula
definition: a molecular pattern matching language, related to the popular SMILES molecular language, that can be used to specify sub-structural patterns in molecules.
in scheme: chemrof

standard_atomic_weight
type: DatatypeProperty
title: standard atomic weight
range: float
in scheme: chemrof

stoichiometry
type: DatatypeProperty
range: integer
in scheme: chemrof

subatomic_particle_count
type: DatatypeProperty
title: subatomic particle count
sub property of: property_of_atom
in scheme: chemrof

subatomic_particle_type
type: ObjectProperty
title: subatomic particle type
range: SubatomicParticleEnum
in scheme: chemrof

subject
type: ObjectProperty
in scheme: chemrof

torsional_angle
type: DatatypeProperty
title: torsional angle
range: float
in scheme: chemrof

valence
type: DatatypeProperty
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]
in scheme: chemrof
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

water_solubility
type: DatatypeProperty
title: water solubility
range: float
sub property of: molecular_property
definition: The maximum amount of a substance that can dissolve in water at 25°C, expressed in grams per liter (g/L).
in scheme: chemrof
note: Standard temperature is 25°C (298.15 K)
note: This property represents the maximum equilibrium solubility in pure water

functional_group_interconversion
type: Class
subclass of: ReactionTypeEnum
subclass of: PermissibleValue
definition: Conversion of one functional group to another without changing the carbon skeleton

Allotrope
type: Class
title: allotrope
subclass of: Restriction
  max cardinality: 1
  on property: has_bonding_structure
subclass of: Restriction
  min cardinality: 1
  on property: allotropic_analog_of
subclass of: Restriction
  max cardinality: 1
  on property: allotropic_analog_of
subclass of: Restriction
  min cardinality: 1
  on property: has_bonding_structure
subclass of: Restriction
  all values from: ChemicalElement
  on property: allotropic_analog_of
subclass of: Restriction
  all values from: string
  on property: has_bonding_structure
subclass of: Molecule
definition: A molecule consisting of atoms of the same element
in scheme: chemrof

AnionState
type: Class
title: anion state
subclass of: Charged
alternative label: negatively charged state
definition: This mixin is applied on an entity (atom or molecule) that is negatively charged
in scheme: chemrof
mapping relation: CHEMINF_000403

AtomIonicForm
type: Class
title: atom ionic form
subclass of: Restriction
  min cardinality: 0
  on property: elemental_charge
subclass of: Restriction
  all values from: integer
  on property: elemental_charge
subclass of: Restriction
  max cardinality: 1
  on property: elemental_charge
subclass of: PartiallySpecifiedAtom
alternative label: atom ionic species
definition: an atom type in which only charge state is specified, designated by the element followed by charge
in scheme: chemrof

BronstedAcidBaseRoleEnum
type: Class
title: bronsted_acid_base_role_enum
subclass of: EnumDefinition
union of: acid
union of: base
in scheme: chemrof
permissible values: acid
permissible values: base

CationState
type: Class
title: cation state
subclass of: Charged
alternative label: positively charged state
definition: This mixin is applied on an entity (atom or molecule) that is positively charged
in scheme: chemrof
mapping relation: CHEMINF_000402

ChemicalMixture
type: Class
title: chemical mixture
subclass of: PolyatomicEntity
definition: A polyatomic entity that consists of two or more parts that are weakly bound, may be of known or unknown stoichiometry
in scheme: chemrof

MonoatomicIon
type: Class
title: monoatomic ion
subclass of: Restriction
  all values from: ChemicalElement
  on property: has_element
subclass of: Restriction
  max cardinality: 1
  on property: has_element
subclass of: Restriction
  min cardinality: 0
  on property: has_element
subclass of: Restriction
  on property: mixins
  some values from: Charged
subclass of: AtomIonicForm
alternative label: charged atom
definition: An atom type that has a charge
in scheme: chemrof
mapping relation: CHEBI_24867
mapping relation: COB_0000042
note: this is mass-number neutral, so there can be no mass associated with a monatomic ion instance

MonomolecularPolymer
type: Class
title: monomolecular polymer
subclass of: Restriction
  max cardinality: 1
  on property: polymer_architecture_type
subclass of: Restriction
  all values from: ChemicalEntity
  on property: has_repeat_unit
subclass of: Restriction
  min cardinality: 0
  on property: is_branched
subclass of: Restriction
  max cardinality: 1
  on property: has_repeat_unit
subclass of: Restriction
  min cardinality: 0
  on property: has_repeat_unit
subclass of: Restriction
  all values from: string
  on property: polymer_architecture_type
subclass of: Restriction
  min cardinality: 0
  on property: polymer_of
subclass of: Restriction
  min cardinality: 0
  on property: polymer_architecture_type
subclass of: Restriction
  max cardinality: 1
  on property: polymer_of
subclass of: Restriction
  max cardinality: 1
  on property: is_branched
subclass of: Restriction
  all values from: boolean
  on property: is_branched
subclass of: Restriction
  all values from: 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
in scheme: chemrof

NetUnchargedMolecule
type: Class
title: uncharged molecule
subclass of: Restriction
  on property: mixins
  some values from: Uncharged
subclass of: MoleculeByChargeState
definition: A molecule that has no net charge
in scheme: chemrof

NucleotideSequenceInterval
type: Class
title: nucleotide sequence interval
subclass of: Restriction
  all values from: string
  on property: has_sequence_representation
subclass of: Restriction
  min cardinality: 0
  on property: has_sequence_representation
subclass of: Restriction
  max cardinality: 1
  on property: has_sequence_representation
subclass of: SequenceInterval
in scheme: chemrof

PolyatomicIon
type: Class
title: polyatomic ion
subclass of: Restriction
  min cardinality: 0
  on property: conjugate_base_of
subclass of: Restriction
  all values from: Thing
  on property: conjugate_base_of
subclass of: Restriction
  on property: mixins
  some values from: Charged
subclass of: Restriction
  max cardinality: 1
  on property: conjugate_acid_of
subclass of: Restriction
  all values from: Thing
  on property: conjugate_acid_of
subclass of: Restriction
  min cardinality: 0
  on property: conjugate_acid_of
subclass of: Restriction
  max cardinality: 1
  on property: conjugate_base_of
subclass of: MoleculeByChargeState
alternative label: polyatomic ion species
definition: A molecule that has a net charge. For example, nitrate is a molecular and ionic species; its formula is (NO3-).
in scheme: chemrof

PolymerPart
type: Class
title: polymer part
subclass of: MolecularComponent
in scheme: chemrof

ReactionParticipant
type: Class
title: reaction participant
subclass of: Restriction
  min cardinality: 0
  on property: stoichiometry
subclass of: Restriction
  all values from: integer
  on property: stoichiometry
subclass of: Restriction
  all values from: ChemicalEntity
  on property: participant
subclass of: Restriction
  max cardinality: 1
  on property: participant
subclass of: Restriction
  max cardinality: 1
  on property: stoichiometry
subclass of: Restriction
  min cardinality: 0
  on property: participant
subclass of: ChemicalRelationship
definition: Instances of this link a reaction to a chemical entity participant
in scheme: chemrof

SequenceInterval
type: Class
title: sequence interval
subclass of: Restriction
  all values from: string
  on property: has_sequence_representation
subclass of: Restriction
  max cardinality: 1
  on property: has_sequence_representation
subclass of: Restriction
  min cardinality: 0
  on property: has_sequence_representation
subclass of: MolecularComponent
definition: a chain of connected monomers in a linear polymer - for example, a sub-region of an amino acid or nucleotide sequence.
in scheme: chemrof
note: - includes an interval corresponding to the whole molecule as an edge case

SubatomicParticle
type: Class
title: subatomic particle
subclass of: Restriction
  all values from: SubatomicParticleEnum
  on property: subatomic_particle_type
subclass of: Restriction
  min cardinality: 0
  on property: subatomic_particle_type
subclass of: Restriction
  max cardinality: 1
  on property: subatomic_particle_type
subclass of: PhysicochemicalEntity
definition: A chemical entity below the granularity of an atom.
in scheme: chemrof
mapping relation: SubatomicParticle
mapping relation: COB_0000007

acid_form_of
type: ObjectProperty
title: acid form of
domain: ChemicalEntity
range: ChemicalEntity
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-)
in scheme: chemrof

structural_isomer_of
type: DatatypeProperty
title: structural isomer of
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
in scheme: chemrof

Charged
type: Class
title: charged
subclass of: ChargeState
alternative label: ion
alternative label: ionic state
definition: Applies to entities that are charged, either positive or negative
in scheme: chemrof

ChemicalGroupingClass
type: Class
title: chemical grouping class
subclass of: Restriction
  all values from: ChemicalGroupingClass
  on property: subtype_of
subclass of: Restriction
  all values from: string
  on property: smarts_string
subclass of: Restriction
  all values from: ChemicalEntity
  on property: classifies
subclass of: Restriction
  max cardinality: 1
  on property: markush_string
subclass of: Restriction
  min cardinality: 0
  on property: markush_string
subclass of: Restriction
  all values from: string
  on property: markush_string
subclass of: Restriction
  min cardinality: 0
  on property: subtype_of
subclass of: Restriction
  max cardinality: 1
  on property: id
subclass of: Restriction
  on property: mixins
  some values from: OwlClass
subclass of: Restriction
  max cardinality: 1
  on property: classifies
subclass of: Restriction
  min cardinality: 0
  on property: smarts_string
subclass of: Restriction
  min cardinality: 1
  on property: id
subclass of: Restriction
  max cardinality: 1
  on property: smarts_string
subclass of: Restriction
  min cardinality: 0
  on property: classifies
subclass of: Restriction
  all values from: string
  on property: id
subclass of: PhysicochemicalEntityGroupingClass
definition: Instances of this class represent generic chemical concepts that can be used to group more specific concepts, or to classify entities. 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
in scheme: chemrof

Subspecies
type: Class
subclass of: ClassificationLevelEnum
subclass of: PermissibleValue

HardOrSoftEnum
type: Class
title: hard_or_soft_enum
subclass of: EnumDefinition
union of: hard
union of: soft
union of: borderline
in scheme: chemrof
permissible values: borderline
permissible values: hard
permissible values: soft

Material
type: Class
title: material
subclass of: Restriction
  max cardinality: 1
  on property: has_repeat_unit
subclass of: Restriction
  all values from: ChemicalEntity
  on property: has_part
subclass of: Restriction
  min cardinality: 0
  on property: has_repeat_unit
subclass of: Restriction
  all values from: ChemicalEntity
  on property: has_repeat_unit
subclass of: Restriction
  min cardinality: 0
  on property: has_part
subclass of: Restriction
  max cardinality: 1
  on property: has_part
subclass of: PhysicochemicalEntity
definition: A substance composed of repeated chemical units that has a specific arrangement of atoms or molecules.
editorial note: this is intentionally placed outside the chemical entity hierarchy as the concept encompasses more than the chemical structure.
in scheme: chemrof

Nuclide
type: Class
title: nuclide
subclass of: Restriction
  min cardinality: 0
  on property: energy_level
subclass of: Restriction
  max cardinality: 1
  on property: energy_level
subclass of: Restriction
  all values from: string
  on property: energy_level
subclass of: PartiallySpecifiedAtom
alternative label: nuclear species
alternative label: nucleide
definition: an atomic species characterized by the specific constitution of its nucleus
in scheme: chemrof

PartiallySpecifiedAtom
type: Class
title: partially specified atom
subclass of: Atom
definition: An atom type that only has a subset of properties (has atomic number, charge, and neutron number) stated
in scheme: chemrof

PreciseChemicalMixture
type: Class
title: precise chemical mixture
subclass of: Restriction
  on property: mixins
  some values from: WeaklyBonded
subclass of: ChemicalMixture
alternative label: chemical substance (SIO)
definition: A polyatomic entity that consists of two or more parts that are weakly bound, and of known stoichiometry
in scheme: chemrof

bond_breaking
type: Class
subclass of: ReactionTypeEnum
subclass of: PermissibleValue
definition: Reactions that break existing bonds to form fragments or rearrange structures

atomic_number
type: DatatypeProperty
title: atomic number
domain: Atom
range: int
sub property of: subatomic_particle_count
alternative label: Z
alternative label: proton number
definition: number of protons in an atom
in scheme: chemrof
mapping relation: CHEMINF_000079

has_submolecules
type: ObjectProperty
title: has submolecules
domain: Molecule
range: Molecule
sub property of: has_part
definition: Relation between a molecule and the molecules it is made from.
in scheme: chemrof

Enantiomer
type: Class
title: enantiomer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_tetrahedral_stereochemical_sublayer
subclass of: Restriction
  all values from: string
  on property: absolute_configuration
subclass of: Restriction
  max cardinality: 1
  on property: relative_configuration
subclass of: Restriction
  all values from: string
  on property: optical_configuration
subclass of: Restriction
  all values from: string
  on property: inchi_tetrahedral_stereochemical_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: optical_configuration
subclass of: Restriction
  min cardinality: 0
  on property: enantiomer_form_of
subclass of: Restriction
  max cardinality: 1
  on property: optical_configuration
subclass of: Restriction
  max cardinality: 1
  on property: enantiomer_form_of
subclass of: Restriction
  max cardinality: 1
  on property: absolute_configuration
subclass of: Restriction
  all values from: string
  on property: relative_configuration
subclass of: Restriction
  all values from: Molecule
  on property: enantiomer_form_of
subclass of: Restriction
  all values from: string
  on property: inchi_stereochemical_type_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_stereochemical_type_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: relative_configuration
subclass of: Restriction
  min cardinality: 0
  on property: absolute_configuration
subclass of: Restriction
  min cardinality: 1
  on property: inchi_stereochemical_type_sublayer
subclass of: Restriction
  min cardinality: 1
  on property: inchi_tetrahedral_stereochemical_sublayer
subclass of: Stereoisomer
definition: one of two stereoisomers of a chiral molecule that are mirror images. Example: R-thalidomide
in scheme: chemrof
note: key= (enantiomer form of, absolute configuration)
note: key= (enantiomer form of, inchi tetrahedral stereochemical sublayer)

IUPAC_name
type: DatatypeProperty
title: IUPAC name
range: string
sub property of: information_property
in scheme: chemrof

IngredientRoleEnum
type: Class
title: ingredient_role_enum
subclass of: EnumDefinition
union of: active ingredient
union of: inactive ingredient
union of: excipient
union of: solvent
in scheme: chemrof
permissible values: active ingredient
permissible values: excipient
permissible values: inactive ingredient
permissible values: solvent

PhysicochemicalEntity
type: Class
title: physicochemical entity
subclass of: DomainEntity
definition: A discrete chemical structure, material structure, or subatomic particle type
in scheme: chemrof

PolyatomicEntity
type: Class
title: polyatomic entity
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^c.*
  on property: inchi_atom_connections_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_atom_connections_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_atom_connections_sublayer
subclass of: ChemicalEntity
definition: Any chemical entity consisting of more than one atom.
in scheme: chemrof

Reaction
type: Class
title: reaction
subclass of: Restriction
  max cardinality: 1
  on property: reaction_rate_coefficient
subclass of: Restriction
  all values from: string
  on property: has_reaction_smiles_representation
subclass of: Restriction
  min cardinality: 0
  on property: description
subclass of: Restriction
  min cardinality: 0
  on property: reaction_rate_coefficient
subclass of: Restriction
  all values from: string
  on property: reaction_center
subclass of: Restriction
  min cardinality: 0
  on property: is_fully_characterized
subclass of: Restriction
  min cardinality: 0
  on property: direction
subclass of: Restriction
  min cardinality: 0
  on property: has_rinchi_representation
subclass of: Restriction
  max cardinality: 1
  on property: is_stereo
subclass of: Restriction
  max cardinality: 1
  on property: is_balanced
subclass of: Restriction
  all values from: string
  on property: has_rinchi_representation
subclass of: Restriction
  min cardinality: 0
  on property: reaction_type
subclass of: Restriction
  all values from: float
  on property: reaction_rate
subclass of: Restriction
  min cardinality: 0
  on property: reaction_rate
subclass of: Restriction
  all values from: boolean
  on property: is_diastereoselective
subclass of: Restriction
  max cardinality: 1
  on property: has_rinchi_representation
subclass of: Restriction
  min cardinality: 0
  on property: is_balanced
subclass of: Restriction
  max cardinality: 1
  on property: description
subclass of: Restriction
  max cardinality: 1
  on property: is_transport
subclass of: Restriction
  max cardinality: 1
  on property: direction
subclass of: Restriction
  min cardinality: 0
  on property: is_stereo
subclass of: Restriction
  all values from: boolean
  on property: is_fully_characterized
subclass of: Restriction
  max cardinality: 1
  on property: reaction_rate
subclass of: Restriction
  all values from: ReactionParticipant
  on property: left_participants
subclass of: Restriction
  all values from: float
  on property: reaction_rate_coefficient
subclass of: Restriction
  all values from: string
  on property: direction
subclass of: Restriction
  min cardinality: 0
  on property: has_reaction_smiles_representation
subclass of: Restriction
  min cardinality: 0
  on property: left_participants
subclass of: Restriction
  max cardinality: 1
  on property: reaction_center
subclass of: Restriction
  all values from: boolean
  on property: is_balanced
subclass of: Restriction
  max cardinality: 1
  on property: has_reaction_smiles_representation
subclass of: Restriction
  all values from: boolean
  on property: is_stereo
subclass of: Restriction
  max cardinality: 1
  on property: is_diastereoselective
subclass of: Restriction
  min cardinality: 0
  on property: reaction_center
subclass of: Restriction
  min cardinality: 0
  on property: is_transport
subclass of: Restriction
  min cardinality: 0
  on property: right_participants
subclass of: Restriction
  all values from: ReactionTypeEnum
  on property: reaction_type
subclass of: Restriction
  max cardinality: 1
  on property: is_fully_characterized
subclass of: Restriction
  min cardinality: 0
  on property: is_diastereoselective
subclass of: Restriction
  all values from: string
  on property: description
subclass of: Restriction
  max cardinality: 1
  on property: reaction_type
subclass of: Restriction
  all values from: ReactionParticipant
  on property: right_participants
subclass of: Restriction
  all values from: boolean
  on property: is_transport
subclass of: DomainEntity
definition: Reaction
in scheme: chemrof

SpecificityMixin
type: Class
title: specificity mixin
subclass of: Mixin
in scheme: chemrof

carboydrate_representation
type: DatatypeProperty
title: carboydrate representation
sub property of: chemical_representation
in scheme: chemrof

chemical_to_chemical_relationship
type: DatatypeProperty
title: chemical to chemical relationship
in scheme: chemrof

decay_energy
type: DatatypeProperty
title: decay energy
domain: Isotope
sub property of: chemical_property
in scheme: chemrof

decay_mode
type: DatatypeProperty
title: decay mode
domain: Isotope
range: string
sub property of: chemical_property
in scheme: chemrof

decay_product
type: ObjectProperty
title: decay product
domain: Isotope
range: Isotope
sub property of: chemical_property
in scheme: chemrof

half_life
type: DatatypeProperty
title: half life
domain: Isotope
range: int
sub property of: chemical_property
in scheme: chemrof

in_periodic_table_block
type: ObjectProperty
title: in periodic table block
range: PeriodicTableBlockEnum
definition: A block of the periodic table is a set of elements unified by the orbitals their valence electrons or vacancies lie in
in scheme: chemrof

in_periodic_table_group
type: DatatypeProperty
title: in periodic table group
range: int
in scheme: chemrof

inchi_proton_sublayer
type: DatatypeProperty
title: inchi proton sublayer
range: Datatype
  on datatype: string
  with restrictions:
    pattern: ^p[\-]\d+
sub property of: inchi_sublayer
in scheme: chemrof

mass
type: DatatypeProperty
range: float
in scheme: chemrof

mode_of_formation
type: DatatypeProperty
title: mode of formation
domain: Isotope
range: string
sub property of: chemical_property
in scheme: chemrof

neutron_number
type: DatatypeProperty
title: neutron number
domain: Atom
range: int
sub property of: subatomic_particle_count
alternative label: N
definition: number of neutrons in an atom
in scheme: chemrof
mapping relation: CHEMINF_000078

occurrence_of
type: ObjectProperty
title: occurrence of
range: Atom
in scheme: chemrof

owl_subclass_of
type: ObjectProperty
title: owl subclass of
domain: OwlClass
range: OwlClass
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)
in scheme: chemrof
narrow match: terminologyfamily

score
type: DatatypeProperty
range: float
in scheme: chemrof

symbol
type: DatatypeProperty
range: string
sub property of: information_property
definition: short symbol for chemical entity, e.g. K, C-16
in scheme: chemrof

ChemicalRelationship
type: Class
title: chemical relationship
subclass of: Restriction
  on property: mixins
  some values from: OwlClass
subclass of: ClassDefinition
definition: A reified relationship
in scheme: chemrof

DomainEntity
type: Class
title: domain entity
subclass of: Restriction
  all values from: string
  on property: name
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  min cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: type
subclass of: Restriction
  max cardinality: 1
  on property: id
subclass of: Restriction
  min cardinality: 0
  on property: name
subclass of: Restriction
  all values from: anyURI
  on property: type
subclass of: Restriction
  max cardinality: 1
  on property: type
subclass of: Restriction
  all values from: string
  on property: id
subclass of: ClassDefinition
definition: A discrete, specific named entity in the domain of chemistry.
in scheme: chemrof

conjugate_acid_of
type: DatatypeProperty
title: conjugate acid of
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)
in scheme: chemrof

has_major_microspecies_at_pH7_3
type: ObjectProperty
title: has physiologically stable form
range: ChemicalEntity
sub property of: acid_form_of
inverse of: major_microspecies_at_pH7_3_of
alternative label: has Ph 7.3 mapping
alternative label: protonation neutral form of
definition: Links different variants of the same chemical in different protonation states, where the target of this link is the (predicited) to be most common protonation state for this chemical at a pH of 7.3. This link may point to it's source. Connects an acid to the form that is stable at physiological pH (7.3). E.g. citric acid has physiological base citrate(3-)
in scheme: chemrof

smiles_string
type: DatatypeProperty
title: smiles string
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.
in scheme: chemrof
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.

AtomOccurrence
type: Class
title: atom occurrence
subclass of: Restriction
  all values from: integer
  on property: oxidation_number
subclass of: Restriction
  max cardinality: 1
  on property: formal_charge
subclass of: Restriction
  min cardinality: 0
  on property: coordination_number
subclass of: Restriction
  on property: mixins
  some values from: OwlClass
subclass of: Restriction
  max cardinality: 1
  on property: coordination_number
subclass of: Restriction
  min cardinality: 0
  on property: oxidation_number
subclass of: Restriction
  all values from: integer
  on property: coordination_number
subclass of: Restriction
  all values from: string
  on property: name
subclass of: Restriction
  all values from: integer
  on property: formal_charge
subclass of: Restriction
  max cardinality: 1
  on property: occurrence_of
subclass of: Restriction
  max cardinality: 1
  on property: oxidation_number
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  min cardinality: 1
  on property: name
subclass of: Restriction
  all values from: Atom
  on property: occurrence_of
subclass of: Restriction
  min cardinality: 0
  on property: valence
subclass of: Restriction
  min cardinality: 0
  on property: formal_charge
subclass of: Restriction
  all values from: integer
  on property: valence
subclass of: Restriction
  max cardinality: 1
  on property: valence
subclass of: Restriction
  min cardinality: 1
  on property: occurrence_of
subclass of: ChemicalRelationship
definition: An occurrence of an atom in the context of a particular molecule. For example, one of two occurrences of oxygen in nitrate
in scheme: chemrof

ChemicalElement
type: Class
title: chemical element
subclass of: Restriction
  max cardinality: 1
  on property: monoisotopic_mass
subclass of: Restriction
  max cardinality: 1
  on property: standard_atomic_weight
subclass of: Restriction
  all values from: PeriodicTableBlockEnum
  on property: in_periodic_table_block
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^[A-Z][a-z]*
  on property: symbol
subclass of: Restriction
  max cardinality: 1
  on property: symbol
subclass of: Restriction
  min cardinality: 0
  on property: melting_point_in_celcius
subclass of: Restriction
  min cardinality: 0
  on property: in_periodic_table_block
subclass of: Restriction
  min cardinality: 0
  on property: standard_atomic_weight
subclass of: Restriction
  max cardinality: 1
  on property: in_periodic_table_block
subclass of: Restriction
  all values from: ChemicalElement
  on property: has_major_microspecies_at_pH7_3
subclass of: Restriction
  all values from: float
  on property: boiling_point_in_celcius
subclass of: Restriction
  min cardinality: 0
  on property: boiling_point_in_celcius
subclass of: Restriction
  max cardinality: 1
  on property: boiling_point_in_celcius
subclass of: Restriction
  min cardinality: 0
  on property: in_periodic_table_group
subclass of: Restriction
  all values from: float
  on property: melting_point_in_celcius
subclass of: Restriction
  min cardinality: 0
  on property: symbol
subclass of: Restriction
  max cardinality: 1
  on property: melting_point_in_celcius
subclass of: Restriction
  all values from: float
  on property: standard_atomic_weight
subclass of: Restriction
  all values from: float
  on property: monoisotopic_mass
subclass of: Restriction
  max cardinality: 1
  on property: mass
subclass of: Restriction
  all values from: string
  on property: electron_configuration
subclass of: Restriction
  all values from: int
  on property: in_periodic_table_group
subclass of: Restriction
  min cardinality: 0
  on property: mass
subclass of: Restriction
  min cardinality: 0
  on property: monoisotopic_mass
subclass of: Restriction
  min cardinality: 0
  on property: has_stereocenter
subclass of: Restriction
  all values from: Stereocenter
  on property: has_stereocenter
subclass of: Restriction
  all values from: float
  on property: mass
subclass of: Restriction
  max cardinality: 1
  on property: has_major_microspecies_at_pH7_3
subclass of: Restriction
  max cardinality: 1
  on property: in_periodic_table_group
subclass of: Restriction
  min cardinality: 0
  on property: electron_configuration
subclass of: Restriction
  min cardinality: 0
  on property: has_major_microspecies_at_pH7_3
subclass of: Restriction
  max cardinality: 1
  on property: electron_configuration
subclass of: PartiallySpecifiedAtom
has key: atomic_number
alternative label: element
alternative label: generic atom
definition: generic form of an atom, with unspecified neutron or charge
in scheme: chemrof

ClassificationLevelEnum
type: Class
title: classification_level_enum
subclass of: EnumDefinition
union of: Uncategorized
union of: Class
union of: Species
union of: Category
union of: Subspecies
union of: StructuralSubspecies
union of: IsomericSubspecies
union of: MolecularSubspecies
in scheme: chemrof
permissible values: Category
permissible values: Class
permissible values: IsomericSubspecies
permissible values: MolecularSubspecies
permissible values: Species
permissible values: StructuralSubspecies
permissible values: Subspecies
permissible values: Uncategorized

MolecularComponent
type: Class
title: molecular component
subclass of: PolyatomicEntity
alternative label: molecular part
alternative label: submolecule
definition: A proper part of a molecule that is larger than an atom
in scheme: chemrof

PeriodicTableBlockEnum
type: Class
title: periodic_table_block_enum
subclass of: EnumDefinition
union of: s-block
union of: p-block
union of: d-block
union of: f-block
union of: g-block
in scheme: chemrof
permissible values: d-block
permissible values: f-block
permissible values: s-block
permissible values: p-block
permissible values: g-block

bond_formation
type: Class
subclass of: ReactionTypeEnum
subclass of: PermissibleValue
definition: Reactions that create new bonds between atoms or groups

conjugate_base_of
type: DatatypeProperty
title: conjugate base of
sub property of: direct_conjugatated_form_of
sub property of: has_lower_charge_from
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
in scheme: chemrof

information_property
type: DatatypeProperty
title: information property
in scheme: chemrof

ElementFamilyEnum
type: Class
title: element_family_enum
subclass of: 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
in scheme: chemrof
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

Macromolecule
type: Class
title: macromolecule
subclass of: Restriction
  min cardinality: 0
  on property: has_submolecules
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
in scheme: chemrof
note: check on classification of lipids

MoleculeByChargeState
type: Class
title: molecule by charge state
subclass of: Restriction
  min cardinality: 0
  on property: acidity
subclass of: Restriction
  max cardinality: 1
  on property: bronsted_acid_base_role
subclass of: Restriction
  min cardinality: 0
  on property: bronsted_acid_base_role
subclass of: Restriction
  max cardinality: 1
  on property: hard_or_soft
subclass of: Restriction
  max cardinality: 1
  on property: acidity
subclass of: Restriction
  all values from: float
  on property: acidity
subclass of: Restriction
  all values from: MoleculeByChargeState
  on property: acid_form_of
subclass of: Restriction
  min cardinality: 0
  on property: hard_or_soft
subclass of: Restriction
  all values from: BronstedAcidBaseRoleEnum
  on property: bronsted_acid_base_role
subclass of: Restriction
  all values from: HardOrSoftEnum
  on property: hard_or_soft
subclass of: Restriction
  min cardinality: 0
  on property: acid_form_of
subclass of: Molecule
alternative label: chargeomer
definition: A molecule that has a charge state specified
in scheme: chemrof

MoleculeGroupingClass
type: Class
title: molecule grouping class
subclass of: Restriction
  all values from: Molecule
  on property: classifies
subclass of: Restriction
  min cardinality: 0
  on property: subtype_of
subclass of: Restriction
  max cardinality: 1
  on property: classifies
subclass of: Restriction
  min cardinality: 0
  on property: classifies
subclass of: Restriction
  all values from: MoleculeGroupingClass
  on property: subtype_of
subclass of: ChemicalGroupingClass
definition: A grouping class that classifies molecules. Example: carbohydrate, monosaccharide, amino acid, polyacrylamide
in scheme: chemrof
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

chemical_representation
type: DatatypeProperty
title: chemical representation
domain: ChemicalEntity
range: string
sub property of: information_property
alternative label: has chemical encoding
in scheme: chemrof

derivative_of
type: ObjectProperty
title: derivative of
range: DomainEntity
sub property of: alternate_form_of
in scheme: chemrof

has_anionic_component
type: DatatypeProperty
title: has anionic component
sub property of: has_ionic_component
in scheme: chemrof

has_cationic_component
type: DatatypeProperty
title: has cationic component
sub property of: has_ionic_component
in scheme: chemrof

has_element
type: ObjectProperty
title: has element
range: ChemicalElement
sub property of: alternate_form_of
in scheme: chemrof

has_sequence_representation
type: DatatypeProperty
title: has sequence representation
range: string
sub property of: chemical_representation
in scheme: chemrof

id
type: DatatypeProperty
sub property of: information_property
in scheme: chemrof
mapping relation: identifier

inchi_charge_sublayer
type: DatatypeProperty
title: inchi charge sublayer
range: Datatype
  on datatype: string
  with restrictions:
    pattern: ^q.*
sub property of: inchi_sublayer
in scheme: chemrof

inchi_chemical_sublayer
type: DatatypeProperty
title: inchi chemical sublayer
range: Datatype
  on datatype: string
  with restrictions:
    pattern: ^[A-Z0-9\.]+$
sub property of: inchi_sublayer_in_main_layer
definition: The part of an InChI string that represents the chemical formula, occurring after the version string. E.g. C6H12O6 for glucose
in scheme: chemrof
note: Coordination Complexes: In coordination chemistry, dots can separate the metal complex from its counterions or ligands that are not directly bonded to the metal center. For example, "[Co(NH₃)₆]Cl₃" indicates a complex of cobalt with six ammonia ligands, and the three chloride ions are counterions. If written as "[Co(NH₃)₆]·3Cl", it would similarly denote the presence of three chloride ions associated with the complex, though this notation is less common
note: Molecular Assemblies: For certain supramolecular structures or assemblies, dots might be used to indicate a non-covalent association of components. This usage is less common and more context-dependent
note: Salt Formulations: Dots can also be used to denote the proportions in which different components are combined to form a salt. For instance, "CaCl₂·2AgNO₃" would suggest a complex formed from one unit of calcium chloride and two units of silver nitrate, though this particular example is more illustrative than practical.
note: in the case of hydrates, the dot separates the formula of the compound from the water molecules. For example, CuSO₄·5H₂O represents copper(II) sulfate pentahydrate, indicating that there are five water molecules associated with each copper(II) sulfate unit in the crystal.
inchi.index: 2

inchi_hydrogen_connections_sublayer
type: DatatypeProperty
title: inchi hydrogen connections sublayer
range: Datatype
  on datatype: string
  with restrictions:
    pattern: ^h.*
sub property of: inchi_sublayer_in_main_layer
definition: Describes how many hydrogen atoms are connected to each of the other atoms.
in scheme: chemrof

inchi_isotopic_layer
type: DatatypeProperty
title: inchi isotopic layer
range: Datatype
  on datatype: string
  with restrictions:
    pattern: ^[ih].*
sub property of: inchi_sublayer
in scheme: chemrof

inchi_stereochemical_double_bond_sublayer
type: DatatypeProperty
title: inchi stereochemical double bond sublayer
range: Datatype
  on datatype: string
  with restrictions:
    pattern: ^b.*
sub property of: inchi_sublayer
in scheme: chemrof

inchi_sublayer
type: DatatypeProperty
title: inchi sublayer
sub property of: inchi_component
in scheme: chemrof

alternate_form_of
type: ObjectProperty
title: alternate form of
domain: ChemicalEntity
range: ChemicalEntity
sub property of: chemical_to_chemical_relationship
definition: A relationship between two entities of the same type
in scheme: chemrof

polymer_of
type: ObjectProperty
title: polymer of
range: Macromolecule
sub property of: has_part
in scheme: chemrof

NanostructureMorphologyEnum
type: Class
title: nanostructure_morphology_enum
subclass of: 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
in scheme: chemrof
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

has_repeat_unit
type: ObjectProperty
title: has repeat unit
range: ChemicalEntity
in scheme: chemrof

inchi_atom_connections_sublayer
type: DatatypeProperty
title: inchi atom connections sublayer
range: Datatype
  on datatype: string
  with restrictions:
    pattern: ^c.*
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.
in scheme: chemrof

inchi_stereochemical_type_sublayer
type: DatatypeProperty
title: inchi stereochemical type sublayer
range: Datatype
  on datatype: string
  with restrictions:
    pattern: ^s.*
sub property of: inchi_sublayer
in scheme: chemrof

inchi_tetrahedral_stereochemical_sublayer
type: DatatypeProperty
title: inchi tetrahedral stereochemical sublayer
range: Datatype
  on datatype: string
  with restrictions:
    pattern: ^[tm].*
sub property of: inchi_sublayer
in scheme: chemrof

chemical_formula
type: DatatypeProperty
title: chemical formula
domain: ChemicalEntity
range: string
sub property of: chemical_representation
definition: A generic grouping for molecular formulae and empirical formulae
in scheme: chemrof
mapping relation: data_0846
mapping relation: hasRepresentation

Atom
type: Class
title: atom
subclass of: Restriction
  max cardinality: 1
  on property: atomic_number
subclass of: Restriction
  all values from: SubatomicParticleOccurrence
  on property: has_nuclear_parts
subclass of: Restriction
  max cardinality: 1
  on property: symbol
subclass of: Restriction
  min cardinality: 0
  on property: symbol
subclass of: Restriction
  max cardinality: 1
  on property: name
subclass of: Restriction
  all values from: string
  on property: symbol
subclass of: Restriction
  all values from: int
  on property: atomic_number
subclass of: Restriction
  min cardinality: 0
  on property: has_part
subclass of: Restriction
  max cardinality: 1
  on property: has_part
subclass of: Restriction
  min cardinality: 0
  on property: name
subclass of: Restriction
  max cardinality: 1
  on property: has_nuclear_parts
subclass of: Restriction
  min cardinality: 0
  on property: has_nuclear_parts
subclass of: Restriction
  min cardinality: 0
  on property: atomic_number
subclass of: Restriction
  all values from: string
  on property: name
subclass of: Restriction
  all values from: SubatomicParticle
  on property: has_part
subclass of: ChemicalEntity
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.
in scheme: chemrof
mapping relation: COB_0000011
mapping relation: SIO_010044
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'}

BondTypeEnum
type: Class
title: bond_type_enum
subclass of: 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
union of: polar covalent
union of: sigma
in scheme: chemrof
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: polar covalent
permissible values: polycentric
permissible values: salt bridge
permissible values: sigma

OwlClass
type: Class
title: owl class
subclass of: Mixin
alternative label: metaclass
alternative label: second order class
alternative label: species
definition: instances of this class mixin are OWL Classes
in scheme: chemrof

has_part
type: DatatypeProperty
title: has part
sub property of: chemical_to_chemical_relationship
definition: basic parthood relations
in scheme: chemrof
mapping relation: BFO_0000050
mapping relation: hasBioChemEntityPart

Isotope
type: Class
title: isotope
subclass of: Restriction
  max cardinality: 1
  on property: decay_product
subclass of: Restriction
  all values from: int
  on property: neutron_number
subclass of: Restriction
  max cardinality: 1
  on property: decay_mode
subclass of: Restriction
  min cardinality: 0
  on property: has_element
subclass of: Restriction
  min cardinality: 0
  on property: decay_mode
subclass of: Restriction
  min cardinality: 0
  on property: isotope_of
subclass of: Restriction
  all values from: string
  on property: decay_mode
subclass of: Restriction
  all values from: Isotope
  on property: isotope_of
subclass of: Restriction
  max cardinality: 1
  on property: has_element
subclass of: Restriction
  all values from: int
  on property: half_life
subclass of: Restriction
  max cardinality: 1
  on property: isotope_of
subclass of: Restriction
  all values from: ChemicalElement
  on property: has_element
subclass of: Restriction
  all values from: Isotope
  on property: decay_product
subclass of: Restriction
  all values from: string
  on property: mode_of_formation
subclass of: Restriction
  all values from: string
  on property: decay_energy
subclass of: Restriction
  min cardinality: 0
  on property: decay_energy
subclass of: Restriction
  min cardinality: 0
  on property: half_life
subclass of: Restriction
  min cardinality: 0
  on property: decay_product
subclass of: Restriction
  max cardinality: 1
  on property: half_life
subclass of: Restriction
  min cardinality: 0
  on property: mode_of_formation
subclass of: Restriction
  max cardinality: 1
  on property: mode_of_formation
subclass of: Restriction
  max cardinality: 1
  on property: neutron_number
subclass of: Restriction
  max cardinality: 1
  on property: decay_energy
subclass of: Restriction
  min cardinality: 0
  on property: neutron_number
subclass of: Nuclide
definition: A specific subtype of an atom with a specified neutron number
in scheme: chemrof
note: Wikidata has isotope as a subclass of nuclide, but nuclide has no instances that are not isotope instances.

molecular_property
type: DatatypeProperty
title: molecular property
sub property of: chemical_property
in scheme: chemrof

chemical_property
type: DatatypeProperty
title: chemical property
in scheme: chemrof

subtype_of
type: ObjectProperty
title: subtype of
domain: OwlClass
range: OwlClass
sub property of: chemical_to_chemical_relationship
sub property of: owl_subclass_of
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
in scheme: chemrof
narrow match: subClassOf

ReactionTypeEnum
type: Class
title: reaction_type_enum
subclass of: EnumDefinition
union of: functional_group_interconversion
union of: bond_formation
union of: bond_breaking
union of: oxidation
union of: reduction
union of: acylation
union of: carbon_carbon_bond_formation
union of: heteroatom_alkylation_arylation
union of: addition
union of: cyclization
union of: condensation
union of: elimination
union of: ring_opening
union of: hydrolysis
union of: substitution
union of: isomerization
union of: functional_group_addition
union of: aromatic_heterocycle_formation
union of: protection
union of: deprotection
union of: resolution
definition: Classification of chemical reactions based on mechanistic and functional categories
in scheme: chemrof
permissible values: condensation
permissible values: cyclization
permissible values: oxidation
permissible values: acylation
permissible values: carbon_carbon_bond_formation
permissible values: heteroatom_alkylation_arylation
permissible values: isomerization
permissible values: reduction
permissible values: addition
permissible values: functional_group_interconversion
permissible values: substitution
permissible values: hydrolysis
permissible values: elimination
permissible values: aromatic_heterocycle_formation
permissible values: bond_breaking
permissible values: bond_formation
permissible values: deprotection
permissible values: functional_group_addition
permissible values: protection
permissible values: resolution
permissible values: ring_opening

classifies
type: DatatypeProperty
sub property of: chemical_to_chemical_relationship
inverse of: classified_by
in scheme: chemrof

elemental_charge
type: DatatypeProperty
title: elemental charge
domain: ChemicalEntity
range: integer
sub property of: property_of_atom
definition: number of protons minus number of electrons
in scheme: chemrof
mapping relation: CHEMINF_000120

name
type: DatatypeProperty
range: string
sub property of: information_property
definition: name of chemical entity. E.g. nickel, carbon-16
in scheme: chemrof

ChemicalEntity
type: Class
title: chemical entity
subclass of: Restriction
  min cardinality: 0
  on property: inchi_charge_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: pka_ionic_strength
subclass of: Restriction
  max cardinality: 1
  on property: pka_solvent
subclass of: Restriction
  min cardinality: 0
  on property: smiles_string
subclass of: Restriction
  min cardinality: 0
  on property: water_solubility
subclass of: Restriction
  max cardinality: 1
  on property: inchi_stereochemical_double_bond_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: pka_ionization_constant
subclass of: Restriction
  all values from: float
  on property: pka_ionic_strength
subclass of: Restriction
  max cardinality: 1
  on property: water_solubility
subclass of: Restriction
  max cardinality: 1
  on property: inchi_hydrogen_connections_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: pka_temperature
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^c.*
  on property: inchi_atom_connections_sublayer
subclass of: Restriction
  all values from: string
  on property: IUPAC_name
subclass of: Restriction
  max cardinality: 1
  on property: smiles_string
subclass of: Restriction
  all values from: float
  on property: pka_ionization_constant
subclass of: Restriction
  all values from: float
  on property: water_solubility
subclass of: Restriction
  max cardinality: 1
  on property: inchi_charge_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: has_major_microspecies_at_pH7_3
subclass of: Restriction
  all values from: ChemicalRole
  on property: has_chemical_role
subclass of: Restriction
  min cardinality: 0
  on property: inchi_tetrahedral_stereochemical_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: IUPAC_name
subclass of: Restriction
  max cardinality: 1
  on property: pka_ionic_strength
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^s.*
  on property: inchi_stereochemical_type_sublayer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^h.*
  on property: inchi_hydrogen_connections_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_string
subclass of: Restriction
  min cardinality: 0
  on property: inchi_isotopic_layer
subclass of: Restriction
  max cardinality: 1
  on property: has_major_microspecies_at_pH7_3
subclass of: Restriction
  all values from: float
  on property: pka_temperature
subclass of: Restriction
  max cardinality: 1
  on property: is_radical
subclass of: Restriction
  max cardinality: 1
  on property: empirical_formula
subclass of: Restriction
  min cardinality: 0
  on property: inchi_string
subclass of: Restriction
  max cardinality: 1
  on property: inchi_stereochemical_type_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_hydrogen_connections_sublayer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^[A-Z0-9\.]+$
  on property: inchi_chemical_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: has_chemical_role
subclass of: Restriction
  all values from: string
  on property: inchi_string
subclass of: Restriction
  all values from: ChemicalEntity
  on property: has_major_microspecies_at_pH7_3
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^[tm].*
  on property: inchi_tetrahedral_stereochemical_sublayer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^q.*
  on property: inchi_charge_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_atom_connections_sublayer
subclass of: Restriction
  on property: mixins
  some values from: OwlClass
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^p[\-]\d+
  on property: inchi_proton_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_atom_connections_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_proton_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: IUPAC_name
subclass of: Restriction
  min cardinality: 0
  on property: pka_solvent
subclass of: Restriction
  min cardinality: 0
  on property: molecular_mass
subclass of: Restriction
  max cardinality: 1
  on property: has_chemical_role
subclass of: Restriction
  min cardinality: 0
  on property: is_radical
subclass of: Restriction
  all values from: boolean
  on property: is_radical
subclass of: Restriction
  max cardinality: 1
  on property: inchi_tetrahedral_stereochemical_sublayer
subclass of: Restriction
  all values from: string
  on property: pka_solvent
subclass of: Restriction
  max cardinality: 1
  on property: pka_pressure
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^b.*
  on property: inchi_stereochemical_double_bond_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: pka_temperature
subclass of: Restriction
  min cardinality: 0
  on property: inchi_chemical_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_stereochemical_double_bond_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: empirical_formula
subclass of: PhysicochemicalEntity
has key: smiles_string
alternative label: chemical
alternative label: chemical species
alternative label: specific chemical entity
definition: A discrete structure that is one or more atoms that can be described by a chemical formula.
in scheme: chemrof
mapping relation: CHEBI_24431
mapping relation: CHEMINF_000000
mapping relation: ChemSpecies
note: Does not encompass chemical grouping classes, such as "amino acid". Use the class ChemicalGrouping for this.
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]

Molecule
type: Class
title: molecule
subclass of: Restriction
  min cardinality: 0
  on property: has_part
subclass of: Restriction
  all values from: Molecule
  on property: has_submolecules
subclass of: Restriction
  min cardinality: 0
  on property: has_submolecules
subclass of: Restriction
  min cardinality: 0
  on property: is_organic
subclass of: Restriction
  all values from: AtomicBond
  on property: has_bonds
subclass of: Restriction
  all values from: boolean
  on property: is_organic
subclass of: Restriction
  on property: mixins
  some values from: FullyCovalentlyBonded
subclass of: Restriction
  max cardinality: 1
  on property: is_organic
subclass of: Restriction
  max cardinality: 1
  on property: has_part
subclass of: Restriction
  min cardinality: 0
  on property: has_atom_occurrences
subclass of: Restriction
  min cardinality: 0
  on property: has_atoms
subclass of: Restriction
  all values from: AtomOccurrence
  on property: has_atom_occurrences
subclass of: Restriction
  all values from: Datatype
    on datatype: integer
    with restrictions:
      min inclusive: 1
  on property: has_part
subclass of: Restriction
  min cardinality: 0
  on property: has_bonds
subclass of: Restriction
  all values from: Atom
  on property: has_atoms
subclass of: PolyatomicEntity
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.
in scheme: chemrof
mapping relation: COB_0000013

SubatomicParticleEnum
type: Class
title: subatomic_particle_enum
subclass of: 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: SubatomicParticle
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: electron
union of: neutron
union of: lepton
union of: helion
union of: charm quark
union of: down quark
union of: pi positive meson
in scheme: chemrof
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: nucleon
permissible values: lepton
permissible values: baryon
permissible values: fermion
permissible values: boson
permissible values: SubatomicParticle
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

type
type: DatatypeProperty
range: anyURI
in scheme: chemrof

chemrof
type: Ontology
license: https://creativecommons.org/publicdomain/zero/1.0/
title: Chemical Entities Mixtures and Reactions Ontological Framework
version: 0.0.1
definition: A data model for managing information about chemical entities, ranging from atoms through molecules to complex mixtures. Aspects of this have been cribbed from various sources including CHEBI, SIO, Wikipedia/Wikidata, the NCATS Translator Chemical Working Group, but all mistakes are my own. For full context/motivation see the [GitHub repo](https://github.com/chemkg/chemrof).

Restriction
subclass of: Restriction
  all values from: Datatype
    on datatype: integer
    with restrictions:
      min inclusive: 1
  on property: elemental_charge
subclass of: Restriction
  max cardinality: 1
  on property: elemental_charge
subclass of: Restriction
  min cardinality: 0
  on property: elemental_charge
on property: mixins
some values from: CationState

Restriction
subclass of: Restriction
  min cardinality: 0
  on property: inchi_hydrogen_connections_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_hydrogen_connections_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_atom_connections_sublayer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^c.*
  on property: inchi_atom_connections_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_atom_connections_sublayer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^h.*
  on property: inchi_hydrogen_connections_sublayer
on property: mixins
some values from: EntityWithConnectivitySpecificied

Restriction
subclass of: Restriction
  min cardinality: 0
  on property: owl_subclass_of
subclass of: Restriction
  all values from: OwlClass
  on property: owl_subclass_of
subclass of: Restriction
  max cardinality: 1
  on property: owl_subclass_of
on property: mixins
some values from: OwlClass

Restriction
subclass of: Restriction
  all values from: Datatype
    on datatype: integer
    with restrictions:
      max inclusive: -1
  on property: elemental_charge
subclass of: Restriction
  max cardinality: 1
  on property: elemental_charge
subclass of: Restriction
  min cardinality: 0
  on property: elemental_charge
on property: mixins
some values from: AnionState

Restriction
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^q.*
  on property: inchi_charge_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_charge_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_charge_sublayer
on property: mixins
some values from: EntityWithChargeSpecified

Restriction
subclass of: Restriction
  max cardinality: 1
  on property: inchi_tetrahedral_stereochemical_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_tetrahedral_stereochemical_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_stereochemical_double_bond_sublayer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^b.*
  on property: inchi_stereochemical_double_bond_sublayer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^s.*
  on property: inchi_stereochemical_type_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_stereochemical_type_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_stereochemical_type_sublayer
subclass of: Restriction
  max cardinality: 1
  on property: inchi_stereochemical_double_bond_sublayer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^[tm].*
  on property: inchi_tetrahedral_stereochemical_sublayer
on property: mixins
some values from: EntityWithStereochemistrySpecified

Restriction
subclass of: Restriction
  max cardinality: 1
  on property: inchi_isotopic_layer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^[ih].*
  on property: inchi_isotopic_layer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_isotopic_layer
on property: mixins
some values from: EntityWithIsotopeSpecified

Restriction
subclass of: Restriction
  all values from: integer
  on property: elemental_charge
subclass of: Restriction
  max cardinality: 1
  on property: elemental_charge
subclass of: Restriction
  min cardinality: 0
  on property: elemental_charge
on property: mixins
some values from: ChargeState

Restriction
subclass of: Restriction
  min cardinality: 0
  on property: elemental_charge
subclass of: Restriction
  all values from: Datatype
    intersection of: Datatype
      on datatype: integer
      with restrictions:
        min inclusive: 0
    intersection of: Datatype
      on datatype: integer
      with restrictions:
        max inclusive: 0
  on property: elemental_charge
subclass of: Restriction
  max cardinality: 1
  on property: elemental_charge
on property: mixins
some values from: Uncharged

Restriction
subclass of: Restriction
  max cardinality: 1
  on property: inchi_chemical_sublayer
subclass of: Restriction
  min cardinality: 0
  on property: inchi_chemical_sublayer
subclass of: Restriction
  all values from: Datatype
    on datatype: string
    with restrictions:
      pattern: ^[A-Z0-9\.]+$
  on property: inchi_chemical_sublayer
on property: mixins
some values from: EntityWithAtomsEnumerated

Restriction
all values from: Datatype
  on datatype: string
  with restrictions:
    pattern: ^[ih].*
on property: inchi_isotopic_layer

Restriction
max cardinality: 1
on property: inchi_chemical_sublayer

Restriction
min cardinality: 0
on property: inchi_proton_sublayer

Restriction
max cardinality: 1
on property: molecular_mass

Restriction
max cardinality: 1
on property: inchi_isotopic_layer

Restriction
min cardinality: 0
on property: inchi_stereochemical_type_sublayer

Restriction
min cardinality: 0
on property: pka_pressure