Class: isotope (Isotope)

A specific subtype of an atom with a specified neutron number

 classDiagram
    class Isotope
    click Isotope href "../Isotope"
      Nuclide <|-- Isotope
        click Nuclide href "../Nuclide"

      Isotope : atomic_number

      Isotope : decay_energy

      Isotope : decay_mode

      Isotope : decay_product




    Isotope --> "0..1" Isotope : decay_product
    click Isotope href "../Isotope"


      Isotope : empirical_formula

      Isotope : energy_level

      Isotope : half_life

      Isotope : has_chemical_role




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


      Isotope : has_element




    Isotope --> "0..1" ChemicalElement : has_element
    click ChemicalElement href "../ChemicalElement"


      Isotope : has_nuclear_parts




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


      Isotope : has_physiologically_stable_form




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


      Isotope : id

      Isotope : inchi_chemical_sublayer

      Isotope : inchi_string

      Isotope : is_radical

      Isotope : isotope_of




    Isotope --> "0..1" Isotope : isotope_of
    click Isotope href "../Isotope"


      Isotope : IUPAC_name

      Isotope : mode_of_formation

      Isotope : name

      Isotope : neutron_number

      Isotope : owl_subclass_of




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


      Isotope : smiles_string

      Isotope : symbol

      Isotope : type

Inheritance

DomainEntity
- PhysicochemicalEntity
  - ChemicalEntity [ OwlClass]
    - Atom
      - PartiallySpecifiedAtom
        
        Nuclide
        
        Isotope

Slots

Name	Cardinality and Range	Description	Inheritance
has_element	0..1 ChemicalElement		direct
neutron_number	0..1 Count	number of neutrons in an atom	direct
isotope_of	0..1 Isotope	relationship that holds between two isotopes, always holds if the isotopes ha...	direct
half_life	0..1 NumberOfYears		direct
decay_product	0..1 Isotope		direct
decay_mode	0..1 String		direct
decay_energy	0..1 String		direct
mode_of_formation	0..1 String		direct
energy_level	0..1 String	e	Nuclide
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

Usages

used by	used in	type	used
Isotope	isotope_of	domain	Isotope
Isotope	isotope_of	range	Isotope
Isotope	half_life	domain	Isotope
Isotope	decay_product	domain	Isotope
Isotope	decay_product	range	Isotope
Isotope	decay_mode	domain	Isotope
Isotope	decay_energy	domain	Isotope
Isotope	mode_of_formation	domain	Isotope
Isobar	half_life	domain	Isotope
Isobar	decay_product	domain	Isotope
Isobar	decay_product	range	Isotope
Isobar	decay_mode	domain	Isotope
Isobar	decay_energy	domain	Isotope
Isobar	mode_of_formation	domain	Isotope

Examples

Value
1H (protium)
2H (deuterium)
https://en.wikipedia.org/wiki/Carbon-12
https://en.wikipedia.org/wiki/Actinium-225

Comments

Wikidata has isotope as a subclass of nuclide, but nuclide has no instances that are not isotope instances.

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	chemrof:Isotope
native	chemrof:Isotope
exact	wd:Q25276

LinkML Source

Direct

name: Isotope
description: A specific subtype of an atom with a specified neutron number
title: isotope
comments:
- Wikidata has isotope as a subclass of nuclide, but nuclide has no instances that
  are not isotope instances.
examples:
- value: 1H (protium)
- value: 2H (deuterium)
- value: https://en.wikipedia.org/wiki/Carbon-12
- value: https://en.wikipedia.org/wiki/Actinium-225
from_schema: https://w3id.org/chemrof
exact_mappings:
- wd:Q25276
is_a: Nuclide
slots:
- has_element
- neutron_number
- isotope_of
- half_life
- decay_product
- decay_mode
- decay_energy
- mode_of_formation
defining_slots:
- has_element
- neutron_number

Induced

name: Isotope
description: A specific subtype of an atom with a specified neutron number
title: isotope
comments:
- Wikidata has isotope as a subclass of nuclide, but nuclide has no instances that
  are not isotope instances.
examples:
- value: 1H (protium)
- value: 2H (deuterium)
- value: https://en.wikipedia.org/wiki/Carbon-12
- value: https://en.wikipedia.org/wiki/Actinium-225
from_schema: https://w3id.org/chemrof
exact_mappings:
- wd:Q25276
is_a: Nuclide
attributes:
  has_element:
    name: has_element
    title: has element
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: alternate_form_of
    domain: ChemicalEntity
    alias: has_element
    owner: Isotope
    domain_of:
    - Isotope
    - Isobar
    - MonoatomicIon
    range: ChemicalElement
  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: Isotope
    domain_of:
    - Isotope
    - FullySpecifiedAtom
    range: Count
  isotope_of:
    name: isotope_of
    description: relationship that holds between two isotopes, always holds if the
      isotopes have the same atomic number and a different neutron number.
    title: isotope of
    examples:
    - description: deuterium (CHEBI:29237) isotope of protium (CHEBI:29236)
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: alternate_form_of
    domain: Isotope
    alias: isotope_of
    owner: Isotope
    domain_of:
    - Isotope
    range: Isotope
  half_life:
    name: half_life
    title: half life
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: chemical_property
    domain: Isotope
    alias: half_life
    owner: Isotope
    domain_of:
    - Isotope
    - Isobar
    range: NumberOfYears
  decay_product:
    name: decay_product
    title: decay product
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: chemical_property
    domain: Isotope
    alias: decay_product
    owner: Isotope
    domain_of:
    - Isotope
    - Isobar
    range: Isotope
  decay_mode:
    name: decay_mode
    title: decay mode
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: chemical_property
    domain: Isotope
    alias: decay_mode
    owner: Isotope
    domain_of:
    - Isotope
    - Isobar
    range: string
  decay_energy:
    name: decay_energy
    title: decay energy
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: chemical_property
    domain: Isotope
    alias: decay_energy
    owner: Isotope
    domain_of:
    - Isotope
    - Isobar
    range: string
  mode_of_formation:
    name: mode_of_formation
    title: mode of formation
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: chemical_property
    domain: Isotope
    alias: mode_of_formation
    owner: Isotope
    domain_of:
    - Isotope
    - Isobar
    range: string
  energy_level:
    name: energy_level
    description: e.g. ground, stable
    title: energy level
    from_schema: https://w3id.org/chemrof
    aliases:
    - energy state
    rank: 1000
    alias: energy_level
    owner: Isotope
    domain_of:
    - Nuclide
    range: string
  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: Isotope
    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: Isotope
    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: Isotope
    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: Isotope
    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: Isotope
    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: Isotope
    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: Isotope
    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: Isotope
    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: Isotope
    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: Isotope
    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: Isotope
    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: Isotope
    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: Isotope
    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: Isotope
    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: Isotope
    domain_of:
    - DomainEntity
    range: uriorcurie
defining_slots:
- has_element
- neutron_number