Class: atom cation (AtomCation)
A monoatomic ion that is positive, e.g Cu(2+)
URI: chemrof:AtomCation
classDiagram
class AtomCation
CationState <|-- AtomCation
MonoatomicIon <|-- AtomCation
AtomCation : atomic_number
AtomCation : elemental_charge
AtomCation : empirical_formula
AtomCation : has_chemical_role
AtomCation --> ChemicalRole : has_chemical_role
AtomCation : has_element
AtomCation --> ChemicalElement : has_element
AtomCation : has_nuclear_parts
AtomCation --> SubatomicParticleOccurrence : has_nuclear_parts
AtomCation : has_physiologically_stable_form
AtomCation --> MoleculeByChargeState : has_physiologically_stable_form
AtomCation : id
AtomCation : inchi_chemical_sublayer
AtomCation : inchi_string
AtomCation : is_radical
AtomCation : IUPAC_name
AtomCation : name
AtomCation : owl_subclass_of
AtomCation --> OwlClass : owl_subclass_of
AtomCation : smiles_string
AtomCation : symbol
AtomCation : type
Inheritance
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| has_element | 0..1 ChemicalElement |
MonoatomicIon | |
| elemental_charge | 0..1 Integer |
number of protons minus number of electrons | AtomIonicForm, ChargeState |
| 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 |
|---|
| Helium(2+) |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/chemrof
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | chemrof:AtomCation |
| native | chemrof:AtomCation |
LinkML Source
Direct
name: AtomCation
description: A monoatomic ion that is positive, e.g Cu(2+)
title: atom cation
examples:
- value: Helium(2+)
description: 1S/He/q+2
from_schema: https://w3id.org/chemrof
is_a: MonoatomicIon
mixins:
- CationState
slot_usage:
elemental_charge:
name: elemental_charge
domain_of:
- ChargeState
- AtomIonicForm
- FullySpecifiedAtom
minimum_value: 1
defining_slots:
- elemental_charge
Induced
name: AtomCation
description: A monoatomic ion that is positive, e.g Cu(2+)
title: atom cation
examples:
- value: Helium(2+)
description: 1S/He/q+2
from_schema: https://w3id.org/chemrof
is_a: MonoatomicIon
mixins:
- CationState
slot_usage:
elemental_charge:
name: elemental_charge
domain_of:
- ChargeState
- AtomIonicForm
- FullySpecifiedAtom
minimum_value: 1
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: AtomCation
domain_of:
- Isotope
- Isobar
- MonoatomicIon
range: ChemicalElement
elemental_charge:
name: elemental_charge
description: number of protons minus number of electrons
title: elemental charge
from_schema: https://w3id.org/chemrof
rank: 1000
is_a: property_of_atom
domain: ChemicalEntity
alias: elemental_charge
owner: AtomCation
domain_of:
- ChargeState
- AtomIonicForm
- FullySpecifiedAtom
range: integer
minimum_value: 1
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: AtomCation
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: AtomCation
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: AtomCation
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: AtomCation
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: AtomCation
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: AtomCation
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: AtomCation
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: AtomCation
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: AtomCation
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: AtomCation
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: AtomCation
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: AtomCation
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: AtomCation
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: AtomCation
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: AtomCation
domain_of:
- DomainEntity
range: uriorcurie
defining_slots:
- elemental_charge