Skip to content

Class: nuclide (Nuclide)

an atomic species characterized by the specific constitution of its nucleus

URI: chemrof:Nuclide

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


      Nuclide <|-- Radionuclide
        click Radionuclide href "../Radionuclide"
      Nuclide <|-- Isotope
        click Isotope href "../Isotope"
      Nuclide <|-- Isobar
        click Isobar href "../Isobar"


      Nuclide : atomic_number

      Nuclide : empirical_formula

      Nuclide : energy_level

      Nuclide : has_chemical_role




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


      Nuclide : has_nuclear_parts




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


      Nuclide : has_physiologically_stable_form




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


      Nuclide : id

      Nuclide : inchi_chemical_sublayer

      Nuclide : inchi_string

      Nuclide : is_radical

      Nuclide : IUPAC_name

      Nuclide : name

      Nuclide : owl_subclass_of




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


      Nuclide : smiles_string

      Nuclide : symbol

      Nuclide : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
energy_level 0..1
String
e 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

  • nucleide
  • nuclear species

Examples

Value
https://en.wikipedia.org/wiki/Isotopes_of_tantalum#Tantalum-180m

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Nuclide
description: an atomic species characterized by the specific constitution of its nucleus
title: nuclide
examples:
- value: https://en.wikipedia.org/wiki/Isotopes_of_tantalum#Tantalum-180m
from_schema: https://w3id.org/chemrof
aliases:
- nucleide
- nuclear species
is_a: PartiallySpecifiedAtom
slots:
- energy_level

Induced

name: Nuclide
description: an atomic species characterized by the specific constitution of its nucleus
title: nuclide
examples:
- value: https://en.wikipedia.org/wiki/Isotopes_of_tantalum#Tantalum-180m
from_schema: https://w3id.org/chemrof
aliases:
- nucleide
- nuclear species
is_a: PartiallySpecifiedAtom
attributes:
  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: Nuclide
    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: Nuclide
    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: Nuclide
    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: Nuclide
    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: Nuclide
    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: Nuclide
    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: Nuclide
    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: Nuclide
    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: Nuclide
    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: Nuclide
    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: Nuclide
    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: Nuclide
    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: Nuclide
    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: Nuclide
    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: Nuclide
    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: Nuclide
    domain_of:
    - DomainEntity
    range: uriorcurie