Chemical Entities Mixtures and Reactions Ontological Framework
A molecule grouping class that groups the different ion forms of the base of an acid
Example(value='citrate', description=None)
Example(value='pimelate', description=None)
A molecule grouping class that can groups an acid together with all its conjugate bases. physiological
Example(value='citrate/citric acid', description=None)
A monoatomic ion that is positive, e.g Cu(2+)
Example(value='Helium(2+)', description='1S/He/q+2')
A grouping class that refines a charge-neutral entity
Example(value='copper cation', description=None)
A grouping class for a chemical salt named by anion
Example(value='chloride salt', description=None)
A grouping class for a chemical salt named by cation
Example(value='sodium salt', description=None)
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.
a polymer with a more than one type of repeating unit
Example(value='styrene-butadiene rubber', description='The repeat units based on styrene and 1,3-butadiene form two repeating units, which can alternate in any order in the macromolecule, making the polymer thus a random copolymer.')
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)
A mixin for an entity where the charge is explicitly specified (corresponding to the /q layer in InChI)
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)
A mixin for an entity where the stereochemistry is explicitly specified (corresponding to the /t, m/, and /s layers in InChI)
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
Example(value='butyl ethanoate', description='has parent alcohol butanol and has parent acid acetic acid')
An atom type that has atomic number, charge, and neutron number stated (equivalently: protons + mass + charge)
{'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'}
Example(value='Helium-4(2+)', description='The atom that is equivalent to an alpha particle 1S/He/q+2/i1+0')
Example(value='tricarboxylic acid/tricarboxylic acid anion', description=None)
A macromolecule consisting of a large number of monosaccharides linked glycosidically
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
Example(value='https://www.glycoepitope.jp/epitopes/EP0311', description='GalNAc(b1-4)[Neu5Ac(a2-3)]Gal(b1)')
a polymer with a single type of repeating unit
Example(value='polystyrene', description='composed only of styrene-based repeat units')
Isobars are atoms (nuclides) of different chemical elements that have the same number of nucleons.
Example(value='isobar-40', description='Any nuclide with a mass number of 40: 40S, 40Cl, 40Ar, 40K, and 40Ca')
A reaction that converts a molecule from one isomer to another.
A grouping class that classifies materials
Example(value='MREO', description='mixed rare earth oxides')
a named part of a molecule. In some instances moieties may be composed of yet smaller moieties and functional groups
A grouping class defined as a derivative of another molecule or molecular grouping class
Example(value='D-ornithine derivative', description=None)
Example(value='oxoacid derivative', description=None)
A molecule in which the units are identical. Example: methyl
molecule grouping class defined by addition of a group
A grouping class defined in terms of a derivative of a molecule and the addition of a group
Example(value='acetyl xylan', description=None)
molecule grouping class defined by components
A grouping class defined as an exhaustive list of components
Example(value='nucleoside', description='A nucleoside consists of a nucleobase and a five-carbon sugar (ribose or 2-deoxyribose)')
Example(value='nucleotide', description='a nucleotide is composed of a nucleobase, a five-carbon sugar, and one or more phosphate groups')
Example(value='polynucleotide', description='A polynucleotide molecule is a biopolymer composed of 13 or more nucleotide monomers covalently bonded in a chain')
A nanostructure is a structure of intermediate size between microscopic and molecular structures. Nanostructural detail is microstructure at nanoscale.
Example(value='Zinc oxide (ZnO) nanorod', description='A nanostructure that has rod morphology and is composed of zinc oxide')
Example(value='platinum copper nanoparticle', description='A nanostructure that is made from platinum and copper atoms')
A molecule in which the units are not identical. TODO: move this higher
a chemical compound that has equal amounts of left- and right-handed enantiomers of a chiral molecule. An example is Thalidomide
an atom that has excess nuclear energy, making it unstable
Example(value='radioactive isotope', description=None)
A molecule characterized by availability in small-molecule databases
polymeric arrays of monomeric units that are connected by reversible and highly directional secondary interactions–that is, non-covalent bonds
the measure of bond strength in a chemical bond.
the average distance between nuclei of two bonded atoms in a molecule
A deterministic SMILES string. Note there is no unique system for canonical smiles strings
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.
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
A chemical formula where numbers denote relative proportion of atoms. E.g. CH2O for glucose
a stereoisomer relationship where the two forms are mirror images of one another
A diastereoisomer of relationship in which the isomers differ at only one stereocenter
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.
A variant of an empirical formula where numbers are replaced by generic ns; e.g. CnH2n+2 for alkane
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.
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).
true if the molecule possesses a cycle in the atom connectivity graph
Location of a MolFile representing a chemical structure
Relation between a polymer and all instances of a repeated polymeric unit
Auxhiliary information on top of a RInChi
A half-reaction, such as a RInChI with starting materials and no identified products, is a valid RInChI
A hashed representation of an InChi string
A SMILES string that distinguishes between isomeric forms. E.g. [13C] for carbon-13
relationship that holds between two isotones, always holds if the isotones have a different atomic number and the same neutron number.
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.
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.
A chemical formula where numbers denote atom count. E.g. C6H12O6 for glucose
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)
relationship that holds between two nuclear isomers, always holds if the isomers have the same nucleon number but different energy states
a functional group or other substituent changes position on a parent structure.
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).
structural isomers (constitutional isomers) of chemical compounds that readily interconvert. Examples: a neutral amino acid and its zwitterion
molecular electronic absorption spectroscopy
a chemical compound consisting of an ionic assembly of cations and anions.
in SIO falls under molecular complex? Also in biolink
Example(value='sodium carbonate CHEBI:29377', description=None)
All pairs of atoms in this entity are transitively connected via covalent bonds
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
Example(value='monosaccharide', description=None)
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
although the stoichiometry is not known rough percentage parts can be provided
Example(value='toothpaste (sodium fluoride 0.243 w/v%[active] + H2O[inactive] + ... )', description=None)
A representation of an InChI string as an object, composed of distinct sublayers
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 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.
In bioptop, molecule complex is a sibling of structured biological entity under poly molecular composite entity
A grouping class that classifies molecular components. Example: inorganic anion group
An abstract part of a polymer that is all instances of a repeated monomer of a single type
A grouping class for reactions, for example, dehalogenase; breaking of covalent bond
A relationship between two or more entities that is quantified based on their similarity
A chemical entity below the granularity of an atom.
relationship that holds between two allotropes, where both allotropes are allotropes of the same element
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.
the number of electron pairs (bonds) between a pair of atoms
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
Example(value=None, description='glucose classified by monosaccharide')
The number of atoms bonded to the atom of interest. [https://doi.org/10.1021%2Fed083p791]
A stereoisomer non-mirror image non-identical stereoisomers
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
One of l->r, r->l, bidirectional, neutral
Example: R-thalidomide is the enantiomer form of 2-(2,6-dioxopiperidin-3-yl)-1H-isoindole-1,3(2H)-dione
The charge remaining on an atom when all ligands are removed homolytically. [https://doi.org/10.1021%2Fed083p791]
connects a base to the acid form. E.g. citrate(3-) has acid form citric acid
Relation between a molecule and the atoms it contains. Note that this is a shortcut relation: for granular representations go via atom occurrences
The pattern in which the atoms are bonded; e.g. hexagonal lattice, sheets, etc
Relation between a molecule and the groups it contains
Location of a MixFile representing a chemical mixture
connects an acid to the base that is stable at physiological pH. E.g. citric acid has physiological base citrate(3-)
connects an element to the equivalent form that is physiologically stable at pH 7.3
Relationship between a complex mixture and its parts
Example(value='RInChI=1.00.1S /layer2<>layer3<>layer4/d+/u2-0-1', description=None)
An organic molecule is a molecule composed of organic atoms (at least carbon, hydrogen, and optionally oxygen, phosphorus, nitrogen, sulfur) [SIO]
relationship that holds between two isotopes, always holds if the isotopes have the same atomic number and a different neutron number.
number of nucleons in an atom. proton number plus neutron number.
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]
the number of electrons that an atom uses in bonding [https://doi.org/10.1021%2Fed083p791]
example: In in ammonia, nitrogen has a valence of 3, each each hydrogen has a valency of 1
example: In methane, carbon has a valence of 4, and each hydrogen has a valency of 1
forumla: number of bonds + formal charge
forumla: number of electrons in valence shell of free atom – number of non-bonding electrons on atom in molecule
todo: determine if this is in CHEBI and how to map
A molecule consisting of atoms of the same element
Example(value='diamond', description=None)
Example(value='dioxygen', description=None)
atom grouping by periodic table placement
A grouping class that classifies atoms. For example, metal atom
an atom type in which only charge state is specified, designated by the element followed by charge
Example(value='chloride Cl-', description=None)
Applies to entities that have a charge state, which may be positive, negative, or neutral
A polyatomic entity that consists of two or more parts that are weakly bound, may be of known or unknown stoichiometry
A characteristic of a chemical entity that is realized under particular conditions
Example(value='sodium chloride', description=None)
this is mass-number neutral, so there can be no mass associated with a monatomic ion instance
A macromolecule composed of repeating subunits. Examples: cellulose
A molecule that has a charge. For example, nitrate is a molecular and ionic species; its formula is (NO3-).
A part of a complex mixture that is of uniform composition
a chain of connected monomers in a linear polymer - for example, a sub-region of an amino acid or nucleotide sequence.
- includes an interval corresponding to the whole molecule as an edge case
Applies to entities that are uncharged, i.e. have an elemental charge of zero
connects an acid to any of the the base anions. E.g. citric acid acid form of citrate(1-),citrate(2-),citrate(3-)
a relationship that holds between two forms of a parent molecule with identical chemical formulas but distinct arrangements of atoms in space
Describes how many hydrogen atoms are connected to each of the other atoms.
inchi stereochemical double bond sublayer
inchi tetrahedral stereochemical sublayer
A hashed representation of a RInChi string
a relationship that holds between two forms of the 'same' molecule with identical chemical formulas but different bonds
This mixin is applied on an entity (atom or molecule) that is negatively charged
This mixin is applied on an entity (atom or molecule) that is positively charged
Abstract grouping for slots that related chemical entities via a connectivity relationships
an atomic species characterized by the specific constitution of its nucleus
Example(value='https://en.wikipedia.org/wiki/Isotopes_of_tantalum#Tantalum-180m', description=None)
An atom type that only has a subset of properties (has atomic number, charge, and neutron number) stated
A block of the periodic table is a set of elements unified by the orbitals their valence electrons or vacancies lie in
A polyatomic entity that consists of two or more parts that are weakly bound, and of known stoichiometry
a particular instance of a stereogenic element that is geometrically a point, bearing different substituents, such that interchanging any two substituents leads to a stereoisomer
Relation between a molecule and the molecules it is made from.
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.
The main layer consists of chemical formula, atom connections, and hydrogen atoms. Example: CH3O/c1-2/h1H3/q-1
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.
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.
short symbol for chemical entity, e.g. K, C-16
Applies to entities that are charged, either positive or negative
one of two stereoisomers of a chiral molecule that are mirror images. Example: R-thalidomide
key= (enantiomer form of, absolute configuration)
key= (enantiomer form of, inchi tetrahedral stereochemical sublayer)
A substance composed of one or more chemical entities
Any chemical entity consisting of more than one atom.
Instances of this link a reaction to a chemical entity participant
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)
sometimes chebi hops over a state skipping an intermediate
a relationship that holds between two forms of the 'same' molecule with identical chemical formulas but different bonding patterns
A conugate base of an acid with charge specified. Example: citrate(3-)
An occurrence of an atom in the context of a particular molecule. For example, one of two occurrences of oxygen in nitrate
A connection between two atoms. Note this is the reified form of 'atomically connected to'.
generic form of an atom, with unspecified neutron or charge
Example(value='carbon', description=None)
Example(value='nickel', description=None)
A molecule capable of donating a hydron to an acceptor. Example: citric acid
A non-specific entity. For example "amino acid" is a grouping for "serine", "leucine" etc; ester is a grouping for nitroglycerin; alkane is a grouping for pentane, butane, methane, etc
A proper part of a molecule that is larger than an atom
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
name of chemical entity. E.g. nickel, carbon-16
A grouping class that classifies molecules. Example: carbohydrate, monosaccharide, amino acid, polyacrylamide
Molecular grouping classes are typically defined by elemental composition and structure as well as chemical properties
Unlike an actual molecule, a molecule grouping class will not have an inchi or properties such as mass
Example(value='nucleobase', description=None)
A relationship between two entities of the same type
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)
A large molecule, such as a polymer, lipid, or macrocycle
A generic grouping for miolecular formulae and empirical formulae
number of protons minus number of electrons
A chemical entity consisting of exactly one atomic nucleus and the electron(s) orbiting it.
A specific subtype of an atom with a specified neutron number
Wikidata has isotope as a subclass of nuclide, but nuclide has no instances that are not isotope instances.
Example(value='1H (protium)', description=None)
Example(value='2H (deuterium)', description=None)
Example(value='https://en.wikipedia.org/wiki/Carbon-12', description=None)
instances of this class mixin are OWL Classes
A chemical entity that consists of two or more atoms where all atoms are connected via covalent bonds.
Example(value='cysteine', description=None)
Example(value='phosphene', description=None)
An entity that can be described using using chemical properties.
Does not encompass chemical grouping classes, such as "amino acid". Use the class ChemicalGrouping for this.
Encompasses subatomic particles through to macromolecular structures.
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]