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Class: polyatomic ion (PolyatomicIon)

A molecule that has a net charge. For example, nitrate is a molecular and ionic species; its formula is (NO3-).

URI: chemrof:PolyatomicIon

 classDiagram
    class PolyatomicIon
    click PolyatomicIon href "../PolyatomicIon"
      Charged <|-- PolyatomicIon
        click Charged href "../Charged"
      MoleculeByChargeState <|-- PolyatomicIon
        click MoleculeByChargeState href "../MoleculeByChargeState"


      PolyatomicIon <|-- MolecularCation
        click MolecularCation href "../MolecularCation"
      PolyatomicIon <|-- MolecularAnion
        click MolecularAnion href "../MolecularAnion"


      PolyatomicIon : bronsted_acid_base_role




    PolyatomicIon --> "0..1" BronstedAcidBaseRoleEnum : bronsted_acid_base_role
    click BronstedAcidBaseRoleEnum href "../BronstedAcidBaseRoleEnum"


      PolyatomicIon : conjugate_acid_of




    PolyatomicIon --> "0..1" ChemicalEntity : conjugate_acid_of
    click ChemicalEntity href "../ChemicalEntity"


      PolyatomicIon : conjugate_base_of




    PolyatomicIon --> "0..1" ChemicalEntity : conjugate_base_of
    click ChemicalEntity href "../ChemicalEntity"


      PolyatomicIon : elemental_charge

      PolyatomicIon : empirical_formula

      PolyatomicIon : has_atom_occurrences




    PolyatomicIon --> "2..*" AtomOccurrence : has_atom_occurrences
    click AtomOccurrence href "../AtomOccurrence"


      PolyatomicIon : has_atoms




    PolyatomicIon --> "*" Atom : has_atoms
    click Atom href "../Atom"


      PolyatomicIon : has_bonds




    PolyatomicIon --> "*" AtomicBond : has_bonds
    click AtomicBond href "../AtomicBond"


      PolyatomicIon : has_chemical_role




    PolyatomicIon --> "0..1" ChemicalRole : has_chemical_role
    click ChemicalRole href "../ChemicalRole"


      PolyatomicIon : has_physiologically_stable_form




    PolyatomicIon --> "*" MoleculeByChargeState : has_physiologically_stable_form
    click MoleculeByChargeState href "../MoleculeByChargeState"


      PolyatomicIon : has_submolecules




    PolyatomicIon --> "*" Molecule : has_submolecules
    click Molecule href "../Molecule"


      PolyatomicIon : id

      PolyatomicIon : inchi_atom_connections_sublayer

      PolyatomicIon : inchi_chemical_sublayer

      PolyatomicIon : inchi_string

      PolyatomicIon : is_organic

      PolyatomicIon : is_radical

      PolyatomicIon : IUPAC_name

      PolyatomicIon : name

      PolyatomicIon : owl_subclass_of




    PolyatomicIon --> "0..1" OwlClass : owl_subclass_of
    click OwlClass href "../OwlClass"


      PolyatomicIon : smiles_string

      PolyatomicIon : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
conjugate_base_of 0..1
ChemicalEntity		 connects the base form of an acid to an acid direct
conjugate_acid_of 0..1
ChemicalEntity		 direct
bronsted_acid_base_role 0..1
BronstedAcidBaseRoleEnum		 MoleculeByChargeState
has_atom_occurrences 2..*
AtomOccurrence		 An individuated atom in the context of a chemical structure Molecule
has_bonds *
AtomicBond		 The set of all bonds connecting atoms in a molecule Molecule
has_submolecules *
Molecule		 Relation between a molecule and the molecules it is made from Molecule
has_atoms *
Atom		 Relation between a molecule and the atoms it contains Molecule
is_organic 0..1
Boolean		 An organic molecule is a molecule composed of organic atoms (at least carbon,... Molecule
inchi_atom_connections_sublayer 0..1 recommended
String		 The atoms in the chemical formula (except for hydrogens) are numbered in sequ... PolyatomicEntity
IUPAC_name 0..1
String		 ChemicalEntity
is_radical 0..1
Boolean		 ChemicalEntity
has_chemical_role 0..1
ChemicalRole		 ChemicalEntity
inchi_string 0..1
ChemicalEncoding		 ChemicalEntity
inchi_chemical_sublayer 0..1 recommended
String		 The part of an InChI string that represents the chemical formula, occurring a... ChemicalEntity
smiles_string *
ChemicalEncoding		 A string encoding of a molecular graph, no chiral or isotopic information ChemicalEntity
empirical_formula 0..1
ChemicalEncoding		 A chemical formula where numbers denote relative proportion of atoms ChemicalEntity
has_physiologically_stable_form *
MoleculeByChargeState		 connects an acid to the form that is stable at physiological pH (7 ChemicalEntity
owl_subclass_of 0..1
OwlClass		 Holds between C and P if C owl:subClassOf P OwlClass
id 1
String		 DomainEntity
name 0..1
String		 name of chemical entity DomainEntity
type 0..1
Uriorcurie		 DomainEntity
elemental_charge 0..1
Integer		 number of protons minus number of electrons ChargeState

Aliases

  • polyatomic ion species

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/chemrof

Mappings

Mapping Type Mapped Value
self chemrof:PolyatomicIon
native chemrof:PolyatomicIon

LinkML Source

Direct

name: PolyatomicIon
description: A molecule that has a net charge. For example, nitrate is a molecular
  and ionic species; its formula is (NO3-).
title: polyatomic ion
from_schema: https://w3id.org/chemrof
aliases:
- polyatomic ion species
is_a: MoleculeByChargeState
mixins:
- Charged
slots:
- conjugate_base_of
- conjugate_acid_of

Induced

name: PolyatomicIon
description: A molecule that has a net charge. For example, nitrate is a molecular
  and ionic species; its formula is (NO3-).
title: polyatomic ion
from_schema: https://w3id.org/chemrof
aliases:
- polyatomic ion species
is_a: MoleculeByChargeState
mixins:
- Charged
attributes:
  conjugate_base_of:
    name: conjugate_base_of
    description: '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)'
    title: conjugate base of
    notes:
    - sometimes chebi hops over a state skipping an intermediate
    from_schema: https://w3id.org/chemrof
    see_also:
    - https://academic.oup.com/nar/article/36/suppl_1/D344/2506390
    aliases:
    - is conjugate base of (chebi)
    rank: 1000
    is_a: direct_conjugatated_form_of
    mixins:
    - has_lower_charge_from
    domain: ChemicalEntity
    alias: conjugate_base_of
    owner: PolyatomicIon
    domain_of:
    - GroupingClassForAcidsOrBases
    - PolyatomicIon
    range: ChemicalEntity
  conjugate_acid_of:
    name: conjugate_acid_of
    title: conjugate acid of
    todos:
    - decide on domain/range. in chebi, daidzein monosulfate is conjugate acid of
      daidzein monosulfate(1-), yet it is an acid derivative, not an acid
    from_schema: https://w3id.org/chemrof
    see_also:
    - https://academic.oup.com/nar/article/36/suppl_1/D344/2506390
    aliases:
    - is conjugate acid of (chebi)
    rank: 1000
    is_a: direct_conjugatated_form_of
    mixins:
    - has_higher_charge_from
    domain: ChemicalEntity
    alias: conjugate_acid_of
    owner: PolyatomicIon
    domain_of:
    - GroupingClassForAcidsOrBases
    - PolyatomicIon
    inverse: conjugate_base_of
    range: ChemicalEntity
  bronsted_acid_base_role:
    name: bronsted_acid_base_role
    title: bronsted acid base role
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: bronsted_acid_base_role
    owner: PolyatomicIon
    domain_of:
    - MoleculeByChargeState
    range: BronstedAcidBaseRoleEnum
  has_atom_occurrences:
    name: has_atom_occurrences
    description: An individuated atom in the context of a chemical structure.
    title: has atom occurrences
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: has_atom_occurrences
    owner: PolyatomicIon
    domain_of:
    - Molecule
    range: AtomOccurrence
    multivalued: true
    inlined: true
    inlined_as_list: true
    minimum_cardinality: 2
  has_bonds:
    name: has_bonds
    description: The set of all bonds connecting atoms in a molecule
    title: has bonds
    from_schema: https://w3id.org/chemrof
    aliases:
    - adjacency matrix
    rank: 1000
    domain: Molecule
    alias: has_bonds
    owner: PolyatomicIon
    domain_of:
    - Molecule
    range: AtomicBond
    multivalued: true
  has_submolecules:
    name: has_submolecules
    description: Relation between a molecule and the molecules it is made from.
    title: has submolecules
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: has_part
    domain: Molecule
    alias: has_submolecules
    owner: PolyatomicIon
    domain_of:
    - Molecule
    range: Molecule
    multivalued: true
  has_atoms:
    name: has_atoms
    description: 'Relation between a molecule and the atoms it contains. Note that
      this is a shortcut relation: for granular representations go via atom occurrences'
    title: has atoms
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: has_part
    domain: Molecule
    alias: has_atoms
    owner: PolyatomicIon
    domain_of:
    - Molecule
    range: Atom
    multivalued: true
  is_organic:
    name: is_organic
    description: An organic molecule is a molecule composed of organic atoms (at least
      carbon, hydrogen, and optionally oxygen, phosphorus, nitrogen, sulfur) [SIO]
    title: is organic
    from_schema: https://w3id.org/chemrof
    close_mappings:
    - SIO:010072
    rank: 1000
    domain: ChemicalEntity
    alias: is_organic
    owner: PolyatomicIon
    domain_of:
    - Molecule
    range: boolean
  inchi_atom_connections_sublayer:
    name: inchi_atom_connections_sublayer
    description: 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.
    title: inchi atom connections sublayer
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: inchi_sublayer_in_main_layer
    alias: inchi_atom_connections_sublayer
    owner: PolyatomicIon
    domain_of:
    - PolyatomicEntity
    - StandardInchiObject
    - EntityWithConnectivitySpecificied
    range: string
    required: false
    recommended: true
    pattern: ^c.*
  IUPAC_name:
    name: IUPAC_name
    title: IUPAC name
    from_schema: https://w3id.org/chemrof
    exact_mappings:
    - MI:2007
    rank: 1000
    is_a: information_property
    slot_uri: CHEMINF:000107
    alias: IUPAC_name
    owner: PolyatomicIon
    domain_of:
    - ChemicalEntity
    range: string
  is_radical:
    name: is_radical
    title: is radical
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain: ChemicalEntity
    alias: is_radical
    owner: PolyatomicIon
    domain_of:
    - ChemicalEntity
    range: boolean
  has_chemical_role:
    name: has_chemical_role
    title: has chemical role
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: has_chemical_role
    owner: PolyatomicIon
    domain_of:
    - ChemicalEntity
    range: ChemicalRole
  inchi_string:
    name: inchi_string
    title: InChi
    todos:
    - declare this as a key once compound_key is introduced to linkml
    from_schema: https://w3id.org/chemrof
    see_also:
    - https://chemistry.stackexchange.com/questions/151072/can-cis-trans-isomers-have-same-inchi
    aliases:
    - InChi
    exact_mappings:
    - OntoRXN:hasInChi
    rank: 1000
    is_a: chemical_formula
    domain: ChemicalEntity
    alias: inchi_string
    owner: PolyatomicIon
    domain_of:
    - ChemicalEntity
    range: ChemicalEncoding
  inchi_chemical_sublayer:
    name: inchi_chemical_sublayer
    description: The part of an InChI string that represents the chemical formula,
      occurring after the version string. E.g. C6H12O6 for glucose
    title: inchi chemical sublayer
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: inchi_sublayer_in_main_layer
    alias: inchi_chemical_sublayer
    owner: PolyatomicIon
    domain_of:
    - ChemicalEntity
    - StandardInchiObject
    - EntityWithAtomsEnumerated
    range: string
    required: false
    recommended: true
    pattern: ^[A-Z0-9\.]+$
  smiles_string:
    name: smiles_string
    description: 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.
    title: smiles string
    comments:
    - 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.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: chemical_formula
    domain: ChemicalEntity
    alias: smiles_string
    owner: PolyatomicIon
    domain_of:
    - ChemicalEntity
    range: ChemicalEncoding
    multivalued: true
  empirical_formula:
    name: empirical_formula
    description: A chemical formula where numbers denote relative proportion of atoms.
      E.g. CH2O for glucose
    title: empirical formula
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: chemical_formula
    domain: ChemicalEntity
    alias: empirical_formula
    owner: PolyatomicIon
    domain_of:
    - ChemicalEntity
    range: ChemicalEncoding
  has_physiologically_stable_form:
    name: has_physiologically_stable_form
    description: connects an acid to the form that is stable at physiological pH (7.3).
      E.g. citric acid has physiological base citrate(3-)
    title: has physiologically stable form
    from_schema: https://w3id.org/chemrof
    see_also:
    - https://ftp.expasy.org/databases/rhea/tsv/chebi_pH7_3_mapping.tsv
    aliases:
    - protonation neutral form of
    - has Ph 7.3 mapping
    rank: 1000
    is_a: acid_form_of
    domain: MoleculeByChargeState
    alias: has_physiologically_stable_form
    owner: PolyatomicIon
    domain_of:
    - ChemicalEntity
    range: MoleculeByChargeState
    multivalued: true
  owl_subclass_of:
    name: owl_subclass_of
    description: '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)'
    title: owl subclass of
    from_schema: https://w3id.org/chemrof
    aliases:
    - is a
    exact_mappings:
    - rdfs:subClassOf
    narrow_mappings:
    - bo:family
    rank: 1000
    is_a: classification_relationship
    mixin: true
    domain: OwlClass
    alias: owl_subclass_of
    owner: PolyatomicIon
    domain_of:
    - OwlClass
    range: OwlClass
  id:
    name: id
    title: id
    from_schema: https://w3id.org/chemrof
    mappings:
    - schema:identifier
    rank: 1000
    is_a: information_property
    identifier: true
    alias: id
    owner: PolyatomicIon
    domain_of:
    - DomainEntity
    - GroupingClass
    - ChemicalGroupingClass
    range: string
    required: true
  name:
    name: name
    description: name of chemical entity. E.g. nickel, carbon-16
    title: name
    from_schema: https://w3id.org/chemrof
    close_mappings:
    - bo:symbol
    rank: 1000
    is_a: information_property
    slot_uri: rdfs:label
    alias: name
    owner: PolyatomicIon
    domain_of:
    - DomainEntity
    - GroupingClass
    - Atom
    - AtomOccurrence
    range: string
  type:
    name: type
    title: type
    from_schema: https://w3id.org/chemrof
    rank: 1000
    designates_type: true
    alias: type
    owner: PolyatomicIon
    domain_of:
    - DomainEntity
    range: uriorcurie
  elemental_charge:
    name: elemental_charge
    description: number of protons minus number of electrons
    title: elemental charge
    from_schema: https://w3id.org/chemrof
    mappings:
    - CHEMINF:000120
    rank: 1000
    is_a: property_of_atom
    domain: ChemicalEntity
    alias: elemental_charge
    owner: PolyatomicIon
    domain_of:
    - ChargeState
    - AtomIonicForm
    - FullySpecifiedAtom
    range: integer