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chemrof schema

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.

Classes

  • ChemicalEntity - An entity that can be described using using chemical properties.
    • 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
        • 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
      • Molecule - A chemical entity that consists of two or more atoms where all atoms are connected via covalent bonds.
        • BronstedAcid - A molecule capable of donating a hydron to an acceptor. Example: citric acid
        • 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
          • Lipid
          • MonomolecularPolymer - A macromolecule composed of repeating subunits. Examples: cellulose
            • Copolymer - a polymer derived from more than one species of monomer
          • Peptide
          • Protein
        • MolecularSpecies - A molecule in which the units are identical. Example: methyl
        • NaturalProduct
        • NonSpeciesMolecule - A molecule in which the units are not identical. TODO: move this higher
        • PolyatomicIon - A molecule that has a charge. For example, nitrate is a molecular and ionic species; its formula is (NO3-).
          • MolecularAnion - A polyatomic ion that is negative
            • AcidBase - A conugate base of an acid with charge specified. Example: citrate(3-)
          • MolecularCation - A polyatomic ion that is positive
        • SmallMolecule - A molecule characterized by availability in small-molecule databases
        • Stereoisomer
          • Enantiomer - one of two stereoisomers of a chiral molecule that are mirror images. Example: R-thalidomide
        • UnchargedMolecule - A molecule that has no charge
    • SubatomicParticle - A chemical entity below the granularity of an atom.
  • ChemicalRole - A characteristic of a chemical entity that is realized under particular conditions
  • GroupingClass - 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
  • InformationalChemicalEntity
  • Location
    • Stereocenter - 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
      • 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.
  • Material - A substance composed of one or more chemical entities
    • Nanostructure - A nanostructure is a structure of intermediate size between microscopic and molecular structures. Nanostructural detail is microstructure at nanoscale.
  • Reaction - reaction
    • IsomeraseReaction - A reaction that converts a molecule from one isomer to another.
  • RelationalChemicalEntity - A reified relationship

Mixins

  • 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
  • ChargeState - Applies to entities that have a charge state, which may be positive, negative, or neutral
    • Charged
      • 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
  • Charged
    • 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
  • ChemicalEntityOrGrouping
  • Connectivity
  • 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)
  • IsPartOrWhole
  • OwlClass - instances of this class mixin are OWL Classes
  • SpecificityMixin
    • 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
    • ChargeState - Applies to entities that have a charge state, which may be positive, negative, or neutral
      • Charged
        • 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
  • Uncharged

Slots

Enums

Subsets

Types

Built in

  • Bool
  • Decimal
  • ElementIdentifier
  • NCName
  • NodeIdentifier
  • URI
  • URIorCURIE
  • XSDDate
  • XSDDateTime
  • XSDTime
  • float
  • int
  • str

Defined