Class: fully specified atom (FullySpecifiedAtom)

An atom type that has atomic number, charge, and neutron number stated (equivalently: protons + mass + charge)

URI: chemrof:FullySpecifiedAtom

 classDiagram
    class FullySpecifiedAtom
    click FullySpecifiedAtom href "../FullySpecifiedAtom"
      Atom <|-- FullySpecifiedAtom
        click Atom href "../Atom"

      FullySpecifiedAtom : atomic_number

      FullySpecifiedAtom : elemental_charge

      FullySpecifiedAtom : empirical_formula

      FullySpecifiedAtom : has_chemical_role




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


      FullySpecifiedAtom : has_nuclear_parts




    FullySpecifiedAtom --> "0..1" SubatomicParticleOccurrence : has_nuclear_parts
    click SubatomicParticleOccurrence href "../SubatomicParticleOccurrence"


      FullySpecifiedAtom : has_physiologically_stable_form




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


      FullySpecifiedAtom : id

      FullySpecifiedAtom : inchi_chemical_sublayer

      FullySpecifiedAtom : inchi_string

      FullySpecifiedAtom : is_radical

      FullySpecifiedAtom : IUPAC_name

      FullySpecifiedAtom : name

      FullySpecifiedAtom : neutron_number

      FullySpecifiedAtom : owl_subclass_of




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


      FullySpecifiedAtom : smiles_string

      FullySpecifiedAtom : symbol

      FullySpecifiedAtom : type

Inheritance

• DomainEntity
  • PhysicochemicalEntity
    • ChemicalEntity [ OwlClass]
      • Atom
        • FullySpecifiedAtom

Slots

Name	Cardinality and Range	Description	Inheritance
elemental_charge	0..1 Integer	number of protons minus number of electrons	direct
neutron_number	0..1 Count	number of neutrons in an atom	direct
atomic_number	0..1 Count	number of protons in an atom	Atom
symbol	0..1 String	short symbol for chemical entity, e	Atom
name	0..1 String	name of chemical entity	Atom, DomainEntity
has_nuclear_parts	0..1 SubatomicParticleOccurrence		Atom
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
type	0..1 Uriorcurie		DomainEntity

Aliases

• atomic species
• chemical species of an element

Examples

Value
Helium-4(2+)

Comments

• 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

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: FullySpecifiedAtom
description: 'An atom type that has atomic number, charge, and neutron number stated
  (equivalently: protons + mass + charge)'
title: fully specified atom
comments:
- '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'
examples:
- value: Helium-4(2+)
  description: The atom that is equivalent to an alpha particle 1S/He/q+2/i1+0
from_schema: https://w3id.org/chemrof
aliases:
- atomic species
- chemical species of an element
is_a: Atom
slots:
- elemental_charge
- neutron_number

Induced

name: FullySpecifiedAtom
description: 'An atom type that has atomic number, charge, and neutron number stated
  (equivalently: protons + mass + charge)'
title: fully specified atom
comments:
- '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'
examples:
- value: Helium-4(2+)
  description: The atom that is equivalent to an alpha particle 1S/He/q+2/i1+0
from_schema: https://w3id.org/chemrof
aliases:
- atomic species
- chemical species of an element
is_a: Atom
attributes:
  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: FullySpecifiedAtom
    domain_of:
    - ChargeState
    - AtomIonicForm
    - FullySpecifiedAtom
    range: integer
  neutron_number:
    name: neutron_number
    description: number of neutrons in an atom
    title: neutron number
    from_schema: https://w3id.org/chemrof
    aliases:
    - N
    mappings:
    - CHEMINF:000078
    rank: 1000
    is_a: subatomic_particle_count
    domain: Atom
    alias: neutron_number
    owner: FullySpecifiedAtom
    domain_of:
    - Isotope
    - FullySpecifiedAtom
    range: Count
  atomic_number:
    name: atomic_number
    description: number of protons in an atom
    title: atomic number
    from_schema: https://w3id.org/chemrof
    aliases:
    - proton number
    - Z
    mappings:
    - CHEMINF:000079
    exact_mappings:
    - wd:P1086
    rank: 1000
    is_a: subatomic_particle_count
    domain: Atom
    slot_uri: bo:atomicNumber
    alias: atomic_number
    owner: FullySpecifiedAtom
    domain_of:
    - Atom
    range: Count
  symbol:
    name: symbol
    description: short symbol for chemical entity, e.g. K, C-16
    title: symbol
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: information_property
    slot_uri: bo:symbol
    alias: symbol
    owner: FullySpecifiedAtom
    domain_of:
    - Atom
    range: string
  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: FullySpecifiedAtom
    domain_of:
    - DomainEntity
    - GroupingClass
    - Atom
    - AtomOccurrence
    range: string
  has_nuclear_parts:
    name: has_nuclear_parts
    title: has nuclear parts
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: property_of_atom
    domain: Atom
    alias: has_nuclear_parts
    owner: FullySpecifiedAtom
    domain_of:
    - Atom
    range: SubatomicParticleOccurrence
  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: FullySpecifiedAtom
    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: FullySpecifiedAtom
    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: FullySpecifiedAtom
    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: FullySpecifiedAtom
    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: FullySpecifiedAtom
    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: FullySpecifiedAtom
    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: FullySpecifiedAtom
    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: FullySpecifiedAtom
    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: FullySpecifiedAtom
    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: FullySpecifiedAtom
    domain_of:
    - DomainEntity
    - GroupingClass
    - ChemicalGroupingClass
    range: string
    required: true
  type:
    name: type
    title: type
    from_schema: https://w3id.org/chemrof
    rank: 1000
    designates_type: true
    alias: type
    owner: FullySpecifiedAtom
    domain_of:
    - DomainEntity
    range: uriorcurie