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Class: isobar (Isobar)

Isobars are atoms (nuclides) of different chemical elements that have the same number of nucleons.

URI: chemrof:Isobar

 classDiagram
    class Isobar
      Nuclide <|-- Isobar

      Isobar : atomic_number

      Isobar : decay_energy

      Isobar : decay_mode

      Isobar : decay_product

          Isobar --> Isotope : decay_product

      Isobar : empirical_formula

      Isobar : energy_level

      Isobar : half_life

      Isobar : has_chemical_role

          Isobar --> ChemicalRole : has_chemical_role

      Isobar : has_element

          Isobar --> ChemicalElement : has_element

      Isobar : has_nuclear_parts

          Isobar --> SubatomicParticleOccurrence : has_nuclear_parts

      Isobar : has_physiologically_stable_form

          Isobar --> MoleculeByChargeState : has_physiologically_stable_form

      Isobar : id

      Isobar : inchi_chemical_sublayer

      Isobar : inchi_string

      Isobar : is_radical

      Isobar : isobar_of

          Isobar --> ChemicalEntity : isobar_of

      Isobar : IUPAC_name

      Isobar : mode_of_formation

      Isobar : name

      Isobar : nucleon_number

      Isobar : owl_subclass_of

          Isobar --> OwlClass : owl_subclass_of

      Isobar : smiles_string

      Isobar : symbol

      Isobar : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
has_element 0..1
ChemicalElement		 direct
nucleon_number 0..1
Count		 number of nucleons in an atom direct
isobar_of 0..1
ChemicalEntity		 equal mass number (Z1 + N1 = Z2 + N2) 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 0..*
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 0..*
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..1
String		 DomainEntity
type 0..1
Uriorcurie		 DomainEntity

Examples

Value
isobar-40

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: Isobar
description: Isobars are atoms (nuclides) of different chemical elements that have
  the same number of nucleons.
title: isobar
examples:
- value: isobar-40
  description: 'Any nuclide with a mass number of 40:  40S, 40Cl, 40Ar, 40K, and 40Ca'
from_schema: https://w3id.org/chemrof
is_a: Nuclide
slots:
- has_element
- nucleon_number
- isobar_of
- half_life
- decay_product
- decay_mode
- decay_energy
- mode_of_formation
defining_slots:
- has_element
- nucleon_number

Induced

name: Isobar
description: Isobars are atoms (nuclides) of different chemical elements that have
  the same number of nucleons.
title: isobar
examples:
- value: isobar-40
  description: 'Any nuclide with a mass number of 40:  40S, 40Cl, 40Ar, 40K, and 40Ca'
from_schema: https://w3id.org/chemrof
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: Isobar
    domain_of:
    - Isotope
    - Isobar
    - MonoatomicIon
    range: ChemicalElement
  nucleon_number:
    name: nucleon_number
    description: number of nucleons in an atom. proton number plus neutron number.
    title: nucleon number
    from_schema: https://w3id.org/chemrof
    aliases:
    - mass number
    rank: 1000
    is_a: subatomic_particle_count
    domain: Atom
    alias: nucleon_number
    owner: Isobar
    domain_of:
    - Isobar
    range: Count
    equals_expression: '{atomic_number}+{neutron_number}'
  isobar_of:
    name: isobar_of
    description: equal mass number (Z1 + N1 = Z2 + N2)
    title: isobar of
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: alternate_form_of
    domain: ChemicalEntity
    alias: isobar_of
    owner: Isobar
    domain_of:
    - Isobar
    range: ChemicalEntity
  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: Isobar
    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: Isobar
    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: Isobar
    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: Isobar
    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: Isobar
    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: Isobar
    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: Isobar
    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: Isobar
    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: Isobar
    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: Isobar
    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: Isobar
    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: Isobar
    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: Isobar
    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: Isobar
    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: Isobar
    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
    multivalued: true
    alias: smiles_string
    owner: Isobar
    domain_of:
    - ChemicalEntity
    range: ChemicalEncoding
  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: Isobar
    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
    multivalued: true
    alias: has_physiologically_stable_form
    owner: Isobar
    domain_of:
    - ChemicalEntity
    range: MoleculeByChargeState
  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: Isobar
    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: Isobar
    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: Isobar
    domain_of:
    - DomainEntity
    range: uriorcurie
defining_slots:
- has_element
- nucleon_number