Class: atom (Atom)
A chemical entity consisting of exactly one atomic nucleus and the electron(s) orbiting it.
- NOTE: this is an abstract class and should not be instantiated directly
URI: chemrof:Atom
classDiagram
class Atom
click Atom href "../Atom"
ChemicalEntity <|-- Atom
click ChemicalEntity href "../ChemicalEntity"
Atom <|-- PartiallySpecifiedAtom
click PartiallySpecifiedAtom href "../PartiallySpecifiedAtom"
Atom <|-- FullySpecifiedAtom
click FullySpecifiedAtom href "../FullySpecifiedAtom"
Atom : atomic_number
Atom : empirical_formula
Atom : has_chemical_role
Atom --> "0..1" ChemicalRole : has_chemical_role
click ChemicalRole href "../ChemicalRole"
Atom : has_nuclear_parts
Atom --> "0..1" SubatomicParticleOccurrence : has_nuclear_parts
click SubatomicParticleOccurrence href "../SubatomicParticleOccurrence"
Atom : has_physiologically_stable_form
Atom --> "*" MoleculeByChargeState : has_physiologically_stable_form
click MoleculeByChargeState href "../MoleculeByChargeState"
Atom : id
Atom : inchi_chemical_sublayer
Atom : inchi_string
Atom : is_radical
Atom : IUPAC_name
Atom : name
Atom : owl_subclass_of
Atom --> "0..1" OwlClass : owl_subclass_of
click OwlClass href "../OwlClass"
Atom : smiles_string
Atom : symbol
Atom : type
Inheritance
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| atomic_number | 0..1 Count |
number of protons in an atom | direct |
| symbol | 0..1 String |
short symbol for chemical entity, e | direct |
| name | 0..1 String |
name of chemical entity | direct |
| has_nuclear_parts | 0..1 SubatomicParticleOccurrence |
direct | |
| 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
Aliases
- atomic species
- chemical species of an element
Comments
- {'chemical species of an element': 'Specific form of an element defined as to isotopic composition, electronic or oxidation state, and/or complex or molecular structure https://goldbook.iupac.org/terms/view/CT06859'}
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/chemrof
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | chemrof:Atom |
| native | chemrof:Atom |
| undefined | COB:0000011, SIO:010044 |
LinkML Source
Direct
name: Atom
description: A chemical entity consisting of exactly one atomic nucleus and the electron(s)
orbiting it.
title: atom
comments:
- '{''chemical species of an element'': ''Specific form of an element defined as to
isotopic composition, electronic or oxidation state, and/or complex or molecular
structure https://goldbook.iupac.org/terms/view/CT06859''}'
from_schema: https://w3id.org/chemrof
aliases:
- atomic species
- chemical species of an element
mappings:
- COB:0000011
- SIO:010044
is_a: ChemicalEntity
abstract: true
slots:
- atomic_number
- symbol
- name
- has_nuclear_parts
slot_usage:
has_part:
name: has_part
range: SubatomicParticle
Induced
name: Atom
description: A chemical entity consisting of exactly one atomic nucleus and the electron(s)
orbiting it.
title: atom
comments:
- '{''chemical species of an element'': ''Specific form of an element defined as to
isotopic composition, electronic or oxidation state, and/or complex or molecular
structure https://goldbook.iupac.org/terms/view/CT06859''}'
from_schema: https://w3id.org/chemrof
aliases:
- atomic species
- chemical species of an element
mappings:
- COB:0000011
- SIO:010044
is_a: ChemicalEntity
abstract: true
slot_usage:
has_part:
name: has_part
range: SubatomicParticle
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: Atom
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: Atom
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: Atom
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: Atom
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: Atom
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: Atom
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: Atom
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: Atom
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: Atom
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: Atom
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: Atom
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: Atom
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: Atom
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: Atom
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: Atom
domain_of:
- DomainEntity
range: uriorcurie