Class: chemical element (ChemicalElement)

generic form of an atom, with unspecified neutron or charge

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

      ChemicalElement : atomic_number

      ChemicalElement : empirical_formula

      ChemicalElement : has_chemical_role




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


      ChemicalElement : has_nuclear_parts




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


      ChemicalElement : has_physiologically_stable_form




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


      ChemicalElement : id

      ChemicalElement : inchi_chemical_sublayer

      ChemicalElement : inchi_string

      ChemicalElement : is_radical

      ChemicalElement : IUPAC_name

      ChemicalElement : name

      ChemicalElement : owl_subclass_of




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


      ChemicalElement : smiles_string

      ChemicalElement : symbol

      ChemicalElement : type

Inheritance

DomainEntity
- PhysicochemicalEntity
  - ChemicalEntity [ OwlClass]
    - Atom
      - PartiallySpecifiedAtom
        
        ChemicalElement

Slots

Name	Cardinality and Range	Description	Inheritance
atomic_number	0..1 Count	number of protons in an atom	Atom
symbol	0..1 String	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 element to the equivalent form that is physiologically stable at ...	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	has_element	range	ChemicalElement
Isobar	has_element	range	ChemicalElement
MonoatomicIon	has_element	range	ChemicalElement
AtomAnion	has_element	range	ChemicalElement
AtomCation	has_element	range	ChemicalElement

Aliases

element
generic atom

Examples

Value
carbon
nickel

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	chemrof:ChemicalElement
native	chemrof:ChemicalElement
exact	wd:Q11344, gc:Element

LinkML Source

Direct

name: ChemicalElement
description: generic form of an atom, with unspecified neutron or charge
title: chemical element
examples:
- value: carbon
- value: nickel
from_schema: https://w3id.org/chemrof
see_also:
- https://en.wikipedia.org/wiki/Chemical_element
aliases:
- element
- generic atom
exact_mappings:
- wd:Q11344
- gc:Element
is_a: PartiallySpecifiedAtom
slot_usage:
  symbol:
    name: symbol
    description: E.g. O, K, Ge
    aliases:
    - atomic symbol
    exact_mappings:
    - wd:P246
    domain_of:
    - Atom
    pattern: ^[A-Z][a-z]*
  in_periodic_table_group:
    name: in_periodic_table_group
    description: which number in periodic table column
    exact_mappings:
    - bo:group
    range: PeriodicTableGroup
  in_periodic_table_block:
    name: in_periodic_table_block
    description: block of periodic table unified by the orbitals their valence electrons
      or vacancies lie in
    exact_mappings:
    - bo:block
    range: PeriodicTableBlockEnum
  boiling_point_in_celcius:
    name: boiling_point_in_celcius
    range: float
  melting_point_in_celcius:
    name: melting_point_in_celcius
    range: float
  standard_atomic_weight:
    name: standard_atomic_weight
    range: float
  mass:
    name: mass
    range: float
  monoisotopic_mass:
    name: monoisotopic_mass
    range: float
  electron_configuration:
    name: electron_configuration
    range: string
  has_stereocenter:
    name: has_stereocenter
    range: Stereocenter
    multivalued: true
  has_physiologically_stable_form:
    name: has_physiologically_stable_form
    description: connects an element to the equivalent form that is physiologically
      stable at pH 7.3
    see_also:
    - https://ftp.expasy.org/databases/rhea/tsv/chebi_pH7_3_mapping.tsv
    aliases:
    - has Ph 7.3 mapping
    domain_of:
    - ChemicalEntity
defining_slots:
- atomic_number
unique_keys:
  main:
    unique_key_name: main
    unique_key_slots:
    - atomic_number
  mass:
    unique_key_name: mass
    unique_key_slots:
    - atomic_number
  periodic_table_position:
    unique_key_name: periodic_table_position
    unique_key_slots:
    - in_periodic_table_group
    - in_periodic_table_block

Induced

name: ChemicalElement
description: generic form of an atom, with unspecified neutron or charge
title: chemical element
examples:
- value: carbon
- value: nickel
from_schema: https://w3id.org/chemrof
see_also:
- https://en.wikipedia.org/wiki/Chemical_element
aliases:
- element
- generic atom
exact_mappings:
- wd:Q11344
- gc:Element
is_a: PartiallySpecifiedAtom
slot_usage:
  symbol:
    name: symbol
    description: E.g. O, K, Ge
    aliases:
    - atomic symbol
    exact_mappings:
    - wd:P246
    domain_of:
    - Atom
    pattern: ^[A-Z][a-z]*
  in_periodic_table_group:
    name: in_periodic_table_group
    description: which number in periodic table column
    exact_mappings:
    - bo:group
    range: PeriodicTableGroup
  in_periodic_table_block:
    name: in_periodic_table_block
    description: block of periodic table unified by the orbitals their valence electrons
      or vacancies lie in
    exact_mappings:
    - bo:block
    range: PeriodicTableBlockEnum
  boiling_point_in_celcius:
    name: boiling_point_in_celcius
    range: float
  melting_point_in_celcius:
    name: melting_point_in_celcius
    range: float
  standard_atomic_weight:
    name: standard_atomic_weight
    range: float
  mass:
    name: mass
    range: float
  monoisotopic_mass:
    name: monoisotopic_mass
    range: float
  electron_configuration:
    name: electron_configuration
    range: string
  has_stereocenter:
    name: has_stereocenter
    range: Stereocenter
    multivalued: true
  has_physiologically_stable_form:
    name: has_physiologically_stable_form
    description: connects an element to the equivalent form that is physiologically
      stable at pH 7.3
    see_also:
    - https://ftp.expasy.org/databases/rhea/tsv/chebi_pH7_3_mapping.tsv
    aliases:
    - has Ph 7.3 mapping
    domain_of:
    - ChemicalEntity
attributes:
  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: ChemicalElement
    domain_of:
    - Atom
    range: Count
  symbol:
    name: symbol
    description: E.g. O, K, Ge
    title: symbol
    from_schema: https://w3id.org/chemrof
    aliases:
    - atomic symbol
    exact_mappings:
    - wd:P246
    rank: 1000
    is_a: information_property
    slot_uri: bo:symbol
    alias: symbol
    owner: ChemicalElement
    domain_of:
    - Atom
    range: string
    pattern: ^[A-Z][a-z]*
  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: ChemicalElement
    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: ChemicalElement
    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: ChemicalElement
    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: ChemicalElement
    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: ChemicalElement
    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: ChemicalElement
    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: ChemicalElement
    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: ChemicalElement
    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: ChemicalElement
    domain_of:
    - ChemicalEntity
    range: ChemicalEncoding
  has_physiologically_stable_form:
    name: has_physiologically_stable_form
    description: connects an element to the equivalent form that is physiologically
      stable at pH 7.3
    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:
    - has Ph 7.3 mapping
    rank: 1000
    is_a: acid_form_of
    domain: MoleculeByChargeState
    alias: has_physiologically_stable_form
    owner: ChemicalElement
    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: ChemicalElement
    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: ChemicalElement
    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: ChemicalElement
    domain_of:
    - DomainEntity
    range: uriorcurie
defining_slots:
- atomic_number
unique_keys:
  main:
    unique_key_name: main
    unique_key_slots:
    - atomic_number
  mass:
    unique_key_name: mass
    unique_key_slots:
    - atomic_number
  periodic_table_position:
    unique_key_name: periodic_table_position
    unique_key_slots:
    - in_periodic_table_group
    - in_periodic_table_block

Class: chemical element (ChemicalElement)

Inheritance

Slots

Usages

Aliases

Examples

See Also

Identifier and Mapping Information

Schema Source

Mappings

LinkML Source

Direct

Induced