Chemical Entities Mixtures and Reactions Ontological Framework
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.
URI: https://w3id.org/chemrof
Name: chemrof
Classes
| Class | Description |
|---|---|
| ChemicalEntityOrGrouping | None |
| ChemicalInformation | None |
| InchiObject | A representation of an InChI string as an object, composed of distinct sublayers |
| StandardInchiObject | None |
| PeriodicTablePlacement | None |
| ChemicalRelationship | A reified relationship |
| AtomicBond | A connection between two atoms. Note this is the reified form of 'atomically connected to'. |
| AtomOccurrence | An occurrence of an atom in the context of a particular molecule. For example, one of two occurrences of oxygen in nitrate |
| ChemicalSimilarity | A relationship between two or more chemical entities where there is some degree of similarity between these entities on their similarity |
| MoleculePairwiseSimilarity | None |
| TanimotoSimilarity | None |
| PolymerRepeatUnit | An abstract part of a polymer that is all instances of a repeated monomer of a single type |
| ProportionalPart | A part of a complex mixture that is of uniform composition |
| ReactionParticipant | Instances of this link a reaction to a chemical entity participant |
| SubatomicParticleOccurrence | None |
| ChemicalRole | A characteristic of a chemical entity that is realized under particular conditions |
| Collection | None |
| Connectivity | Abstract grouping for slots that related chemical entities via a connectivity relationships |
| FullyCovalentlyBonded | All pairs of atoms in this entity are transitively connected via covalent bonds |
| WeaklyBonded | Not covalently bonded |
| DomainEntity | A discrete, specific named entity in the domain of chemistry. |
| PhysicochemicalEntity | A discrete chemical structure, material structure, or subatomic particle type |
| ChemicalEntity | A discrete structure that is one or more atoms that can be described by a chemical formula. |
| Atom | A chemical entity consisting of exactly one atomic nucleus and the electron(s) orbiting it. |
| FullySpecifiedAtom | An atom type that has atomic number, charge, and neutron number stated (equivalently: protons + mass + charge) |
| PartiallySpecifiedAtom | An atom type that only has a subset of properties (has atomic number, charge, and neutron number) stated |
| AtomIonicForm | an atom type in which only charge state is specified, designated by the element followed by charge |
| MonoatomicIon | An atom type that has a charge |
| AtomAnion | A monoatomic ion that is negative |
| AtomCation | A monoatomic ion that is positive, e.g Cu(2+) |
| UnchargedAtom | An atom type that has no charge |
| ChemicalElement | generic form of an atom, with unspecified neutron or charge |
| Nuclide | an atomic species characterized by the specific constitution of its nucleus |
| Isobar | Isobars are atoms (nuclides) of different chemical elements that have the same number of nucleons. |
| Isotope | A specific subtype of an atom with a specified neutron number |
| Radionuclide | an atom that has excess nuclear energy, making it unstable |
| PolyatomicEntity | Any chemical entity consisting of more than one atom. |
| ChemicalMixture | A polyatomic entity that consists of two or more parts that are weakly bound, may be of known or unknown stoichiometry |
| ImpreciseChemicalMixture | 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 |
| PreciseChemicalMixture | A polyatomic entity that consists of two or more parts that are weakly bound, and of known stoichiometry |
| ChemicalSalt | a chemical compound consisting of an ionic assembly of cations and anions. |
| MolecularComplex | 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 |
| SupramolecularPolymer | polymeric arrays of monomeric units that are connected by reversible and highly directional secondary interactions–that is, non-covalent bonds |
| RacemicMixture | a chemical compound that has equal amounts of left- and right-handed enantiomers of a chiral molecule. An example is Thalidomide |
| MolecularComponent | A proper part of a molecule that is larger than an atom |
| ChemicalGroup | None |
| FunctionalGroup | None |
| Moiety | a named part of a molecule. In some instances moieties may be composed of yet smaller moieties and functional groups |
| PolymerPart | None |
| MolecularSubsequence | None |
| Monomer | None |
| SequenceInterval | a chain of connected monomers in a linear polymer - for example, a sub-region of an amino acid or nucleotide sequence. |
| AminoAcidSequenceInterval | None |
| NucleotideSequenceInterval | None |
| DNASequenceInterval | None |
| RNASequenceInterval | None |
| Molecule | A chemical entity that consists of two or more atoms where all atoms are connected via covalent bonds. |
| Allotrope | A molecule consisting of atoms of the same element |
| Ester | 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 |
| Macromolecule | A large molecule, such as a polymer, lipid, or macrocycle |
| Glycan | A macromolecule consisting of a large number of monosaccharides linked glycosidically |
| MonomolecularPolymer | A macromolecule composed of repeating subunits. Examples: cellulose |
| Copolymer | a polymer with a more than one type of repeating unit |
| Homopolymer | a polymer with a single type of repeating unit |
| Peptide | None |
| Protein | None |
| MolecularSpecies | A molecule in which the units are identical. Example: methyl |
| MoleculeByChargeState | A molecule that has a charge state specified |
| NetUnchargedMolecule | A molecule that has no net charge |
| NeutralMolecule | A molecule that has no net charge and is not a zwitterion |
| Zwitterion | A molecule that has both a positive and negative charges but is net neutral |
| PolyatomicIon | A molecule that has a net charge. For example, nitrate is a molecular and ionic species; its formula is (NO3-). |
| MolecularAnion | A polyatomic ion that is negative |
| MolecularCation | A polyatomic ion that is positive |
| NaturalProduct | None |
| NonSpeciesMolecule | A molecule in which the units are not identical. TODO: move this higher |
| SmallMolecule | A molecule characterized by availability in small-molecule databases |
| Stereoisomer | None |
| Enantiomer | one of two stereoisomers of a chiral molecule that are mirror images. Example: R-thalidomide |
| Material | A substance composed of repeated chemical units that has a specific arrangement of atoms or molecules. |
| Mineral | None |
| Nanomaterial | A material of which a single unit is sized (in at least one dimension) between 1 and 100 nm |
| SubatomicParticle | A chemical entity below the granularity of an atom. |
| Reaction | Reaction |
| IsomeraseReaction | A reaction that converts a molecule from one isomer to another. |
| GroupingClass | Instances of this class represent generic concepts that can be used to group more specific concepts, or to classify entities |
| PhysicochemicalEntityGroupingClass | None |
| ChemicalGroupingClass | 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 |
| AtomGroupingClass | A grouping class that classifies atoms. For example, metal atom |
| AtomGroupingByPeriodicTablePlacement | None |
| AtomGroupingByPeriodicTableBlock | Example: group 13 atom |
| AtomGroupingByPeriodicTableGroup | Example: p-block atom |
| AtomGroupingByProperty | Example: metal atom |
| ChemicalGroupingByCharge | A grouping class that refines a charge-neutral entity |
| MolecularComponentGroupingClass | A grouping class that classifies molecular components. Example: inorganic anion group |
| MoleculeGroupingClass | A grouping class that classifies molecules. Example: carbohydrate, monosaccharide, amino acid, polyacrylamide |
| ChemicalSaltGroupingClass | A grouping class for a chemical salt |
| ChemicalSaltByAnion | A grouping class for a chemical salt named by anion |
| ChemicalSaltByCation | A grouping class for a chemical salt named by cation |
| GeneralizedMolecularStructureClass | 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 |
| MonomericPolymericGroupingClass | None |
| GroupingClassForAcidsOrBases | None |
| AcidAnionGroupingClass | A molecule grouping class that groups the different ion forms of the base of an acid |
| AcidBaseConflationClass | A molecule grouping class that can groups an acid together with all its conjugate bases. physiological |
| GeneralAcidBaseGroupingClass | A molecule grouping class that can groups an acid together with all its conjugate bases. physiological |
| MolecularDerivativeGroupingClass | A grouping class defined as a derivative of another molecule or molecular grouping class |
| MoleculeGroupingClassDefinedByAdditionOfAGroup | A grouping class defined in terms of a derivative of a molecule and the addition of a group |
| MoleculeGroupingClassDefinedByComponents | A grouping class defined as an exhaustive list of components |
| MaterialGroupingClass | A grouping class that classifies materials |
| ReactionGroupingClass | A grouping class for reactions, for example, dehalogenase; breaking of covalent bond |
| Location | Abstract grouping for entities that represent abstract or concrete locations of chemical entities or their parts. |
| Stereocenter | a geometric point in a molecule in which the interchanging of two substituents creates a stereoisomer. |
| ChiralityCenter | 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. |
| OwlClass | instances of this class mixin are OWL Classes |
| SpecificityMixin | None |
| EntityWithAtomsEnumerated | 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) |
| EntityWithChargeSpecified | A mixin for an entity where the charge is explicitly specified (corresponding to the /q layer in InChI) |
| EntityWithConnectivitySpecificied | 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) |
| EntityWithIsotopeSpecified | A mixin for an entity where the charge is explicitly specified (corresponding to the /q layer in InChI) |
| EntityWithStereochemistrySpecified | A mixin for an entity where the stereochemistry is explicitly specified (corresponding to the /t, m/, and /s layers in InChI) |
| State | None |
| ChargeState | Applies to entities that have a charge state, which may be positive, negative, or neutral |
| Charged | Applies to entities that are charged, either positive or negative |
| AnionState | This mixin is applied on an entity (atom or molecule) that is negatively charged |
| CationState | This mixin is applied on an entity (atom or molecule) that is positively charged |
| Uncharged | Applies to entities that are uncharged, i.e. have an elemental charge of zero |
Slots
| Slot | Description |
|---|---|
| absolute_configuration | |
| acid_form_of | connects an acid to any of the the base anions |
| acidity | |
| allotropic_analog_of | relationship that holds between two allotropes, where both allotropes are all... |
| alternate_form_of | A relationship between two entities of the same type |
| atomic_number | number of protons in an atom |
| atomically_connected_to | |
| AZE_notation_html | E |
| boiling_point_in_celcius | |
| bond_angle | |
| bond_energy | the measure of bond strength in a chemical bond |
| bond_length | the average distance between nuclei of two bonded atoms in a molecule |
| bond_length_in_angstroms | the average distance between nuclei of two bonded atoms in a molecule |
| bond_order | the number of electron pairs (bonds) between a pair of atoms |
| bond_type | |
| bronsted_acid_base_role | |
| canonical_smiles_string | A deterministic SMILES string |
| carbbank_representation | The carbohydrate structure format used by the Complex Carbohydrate Structure ... |
| carboydrate_representation | |
| charge | |
| charge_agnostic_entity | |
| chebi_formula | A CHEBI formular combines aspects of molecular and generalized molecular form... |
| chemical_formula | A generic grouping for molecular formulae and empirical formulae |
| chemical_isomer_of | a relationship that holds between two forms of a parent molecule with identic... |
| chemical_property | |
| chemical_representation | |
| chemical_to_chemical_relationship | |
| chirality_agnostic_form | |
| classification_relationship | |
| classified_by | A subtype_of relationship holds between I and C if I is a specific entity of ... |
| classifies | |
| composed_of | |
| conjugate_acid_of | |
| conjugate_base_of | connects the base form of an acid to an acid |
| coordination_number | The number of atoms bonded to the atom of interest |
| Count | |
| curly_smiles_string | CurlySMILES is a chemical line notation which extends SMILES with annotations... |
| decay_energy | |
| decay_mode | |
| decay_product | |
| degree_of_polymerization | |
| derivative_of | |
| derived_from_organisms | |
| description | |
| diastereoisomers_of | A stereoisomer non-mirror image non-identical stereoisomers |
| direct_conjugatated_form_of | |
| direction | One of l->r, r->l, bidirectional, neutral |
| electron_configuration | |
| elemental_charge | number of protons minus number of electrons |
| empirical_formula | A chemical formula where numbers denote relative proportion of atoms |
| enantiomer_form_of | Example: R-thalidomide is the enantiomer form of 2-(2,6-dioxopiperidin-3-yl)... |
| enantiomer_of | a stereoisomer relationship where the two forms are mirror images of one anot... |
| energy_level | e |
| entities | |
| epimer_of | A diastereoisomer of relationship in which the isomers differ at only one ste... |
| extended_smiles_string | |
| formal_charge | The charge remaining on an atom when all ligands are removed homolytically |
| functional_isomer_of | structural isomers that have the same molecular formula (that is, the same nu... |
| generalized_empirical_formula | A variant of an empirical formula where numbers are replaced by generic ns; e |
| glycoct_condensed | This is a multiline format used by GlycomeDB, among others, and uses a graph ... |
| glycominds_linearcode_representation | A linear notation proposed by GlycoMinds, Ltd |
| half_life | |
| hard_or_soft | |
| has_acid_form | connects a base to the acid form |
| has_anionic_component | |
| has_atom_occurrences | An individuated atom in the context of a chemical structure |
| has_atoms | Relation between a molecule and the atoms it contains |
| has_bonding_structure | The pattern in which the atoms are bonded; e |
| has_bonds | |
| has_cationic_component | |
| has_charge_state | |
| has_chemical_role | |
| has_cyclic_structure | true if the molecule possesses a cycle in the atom connectivity graph |
| has_derivative | |
| has_different_charge_state_from | |
| has_element | |
| has_group | Relation between a molecule and the groups it contains |
| has_higher_charge_from | |
| has_ionic_component | |
| has_left_enantiomer | |
| has_lower_charge_from | |
| has_minchi_representation | Proposed new Mixtures InChI |
| has_mixfile_location | Location of a MixFile representing a chemical mixture |
| has_molfile_location | Location of a MolFile representing a chemical structure |
| has_morphological_category | e |
| has_nuclear_parts | |
| has_parent_acid | |
| has_parent_alcohol | |
| has_part | basic parthood relations |
| has_physiologically_stable_form | connects an acid to the form that is stable at physiological pH (7 |
| has_polymer_repeat_units | Relation between a polymer and all instances of a repeated polymeric unit |
| has_proportional_parts | Relationship between a complex mixture and its parts |
| has_rauxinfo_representation | Auxhiliary information on top of a RInChi |
| has_reaction_smiles_representation | |
| has_repeat_unit | |
| has_right_enantiomer | |
| has_rinchi_representation | Proposed Reactions InChI |
| has_role | |
| has_sequence_representation | |
| has_stereocenter | |
| has_submolecules | Relation between a molecule and the molecules it is made from |
| has_subtype | |
| hashed_chemical_formula | A hashed version of a chemical formula |
| id | |
| in_periodic_table_block | A block of the periodic table is a set of elements unified by the orbitals th... |
| in_periodic_table_group | |
| inchi2d_key_string | A hashed representation of an InChi2D string |
| inchi2d_string | |
| inchi_atom_connections_sublayer | The atoms in the chemical formula (except for hydrogens) are numbered in sequ... |
| inchi_charge_sublayer | |
| inchi_chemical_sublayer | The part of an InChI string that represents the chemical formula, occurring a... |
| inchi_component | A part of an InChI object |
| inchi_fixed_H_layer | |
| inchi_hydrogen_connections_sublayer | Describes how many hydrogen atoms are connected to each of the other atoms |
| inchi_isotopic_layer | |
| inchi_key_string | A hashed representation of an InChi string |
| inchi_proton_sublayer | |
| inchi_reconnected_layer | |
| inchi_stereochemical_double_bond_sublayer | |
| inchi_stereochemical_type_sublayer | |
| inchi_string | |
| inchi_sublayer | |
| inchi_sublayer_in_main_layer | The main layer consists of chemical formula, atom connections, and hydrogen a... |
| inchi_tetrahedral_stereochemical_sublayer | |
| inchi_version_string | The first part of the inchi_string, after 'InChI=' |
| information_property | |
| is_balanced | |
| is_branched | |
| is_diastereoselective | |
| is_fully_characterized | False if includes R-groups |
| is_organic | An organic molecule is a molecule composed of organic atoms (at least carbon,... |
| is_radical | |
| is_stereo | |
| is_substitutent_group_from | |
| is_transport | |
| isobar_of | equal mass number (Z1 + N1 = Z2 + N2) |
| isomeric_smiles_string | A SMILES string that distinguishes between isomeric forms |
| isotone_of | relationship that holds between two isotones, always holds if the isotones ha... |
| isotope_of | relationship that holds between two isotopes, always holds if the isotopes ha... |
| isotopologue_of | a relationship that holds between two forms of a parent molecule with identic... |
| IUPAC_name | |
| kegg_chemical_function_representation | A multiline format used by the KEGG GLYCAN database and represents glycans as... |
| left_molecule | |
| left_participants | |
| linucs_representation | A unique linear notation proposed and used by GLYCOSCIENCES |
| logP6_partition_coefficient | logP partition coefficient calculated from 2D structure using contributions f... |
| long_rinchi_key_string | |
| lychi_string | |
| mass | |
| maximum_percentage | |
| melting_point_in_celcius | |
| minimal_percentage | |
| mode_of_formation | |
| molar_cohesive_energy | |
| molar_refractivity | Molar refractivity calculated from 2D structure using contributions from pre-... |
| molar_value | |
| molecular_charge | |
| molecular_electronic_absorption_spectroscopy | |
| molecular_electronic_spectroscopy | |
| molecular_formula | A chemical formula where numbers denote atom count |
| molecular_heat_capacity | |
| molecular_hydration | |
| molecular_mass | |
| molecular_property | |
| molecular_replacement | |
| molecular_shape | |
| molecular_size | |
| molecular_spectroscopy | |
| molecular_spectroscopy_by_energy_state | |
| molecular_structure | |
| monoisotopic_mass | |
| name | name of chemical entity |
| neutron_number | number of neutrons in an atom |
| next_in_homologous_series_from | Next in a sequence of compounds with the same functional group and similar ch... |
| nuclear_isomer_of | relationship that holds between two nuclear isomers, always holds if the isom... |
| nucleon_number | number of nucleons in an atom |
| number_of_aromatic_rings | |
| number_of_heavy_atoms | number of of non-hydrogen atoms |
| number_of_hydrogen_bond_acceptors | number of hydrogen bond acceptors corresponding to sum of nitrogen atoms with... |
| number_of_hydrogen_bond_donors | number of hydrogen bond donors corresponding to sum of nitrogen and oxygen at... |
| number_of_rings | |
| number_of_rotatable_bonds | number of rotatable bonds corresponds to single bonds excluding following typ... |
| object | |
| object_atom_occurrence | |
| occurrence_of | |
| optical_configuration | |
| owl_subclass_of | Holds between C and P if C owl:subClassOf P |
| oxidation_number | The charge remaining on an atom when all ligands are removed heterolytically ... |
| participant | |
| polymer_architecture_type | morphological structure of a polymer |
| polymer_of | |
| position_isomer_of | a functional group or other substituent changes position on a parent structur... |
| property_of_atom | |
| reaction_center | |
| reaction_has_bidirectional_form | |
| reaction_rate | |
| reaction_rate_coefficient | |
| relative_configuration | |
| repetition_of | the macromolecule that is repeated |
| right_molecule | |
| right_participants | |
| rinchi_key_string | A hashed representation of a RInChi string |
| score | |
| selfies_string | |
| short_rinchi_key_string | |
| skeletal_isomer_of | components of the (usually carbon) skeleton are distinctly re-ordered to crea... |
| smarts_string | |
| smiles_string | A string encoding of a molecular graph, no chiral or isotopic information |
| standard_atomic_weight | |
| stereoisomer_of | a relationship that holds between two forms of the 'same' molecule with ident... |
| stoichiometry | |
| structural_isomer_of | a relationship that holds between two forms of the 'same' molecule with ident... |
| subatomic_particle_count | |
| subatomic_particle_type | |
| subject | |
| subject_atom_occurrence | |
| subtype_of | A subtype_of relationship holds between C and P if C is a more specialized fo... |
| symbol | short symbol for chemical entity, e |
| tautomer_of | structural isomers (constitutional isomers) of chemical compounds that readil... |
| thermophysical_property | |
| topological_polar_surface_area | Topological Polar Surface Area corresponding to nitrogen and oxygen atoms cal... |
| torsional_angle | |
| transitive_conjugatated_form_of | |
| tucan_string | |
| type | |
| valence | the number of electrons that an atom uses in bonding [https://doi |
| van_der_waals_molecular_volume | van der Waals molecular volume calculated from 2D structure using atomic radi... |
| variant_reaction_of | |
| wurcs_representation |
Enumerations
Types
| Type | Description |
|---|---|
| AminoAcidSequenceString | |
| Boolean | A binary (true or false) value |
| ChemicalEncoding | |
| Count | |
| Curie | a compact URI |
| Date | a date (year, month and day) in an idealized calendar |
| DateOrDatetime | Either a date or a datetime |
| Datetime | The combination of a date and time |
| Decimal | A real number with arbitrary precision that conforms to the xsd:decimal speci... |
| DNASequenceString | |
| Double | A real number that conforms to the xsd:double specification |
| FileLocation | |
| Float | A real number that conforms to the xsd:float specification |
| Integer | An integer |
| Jsonpath | A string encoding a JSON Path |
| Jsonpointer | A string encoding a JSON Pointer |
| Ncname | Prefix part of CURIE |
| Nodeidentifier | A URI, CURIE or BNODE that represents a node in a model |
| NumberOfYears | |
| Objectidentifier | A URI or CURIE that represents an object in the model |
| PeriodicTableGroup | |
| SequenceString | |
| Sparqlpath | A string encoding a SPARQL Property Path |
| String | A character string |
| Time | A time object represents a (local) time of day, independent of any particular... |
| Uri | a complete URI |
| Uriorcurie | a URI or a CURIE |
Subsets
| Subset | Description |
|---|---|