Class: atom occurrence (AtomOccurrence)
An occurrence of an atom in the context of a particular molecule. For example, one of two occurrences of oxygen in nitrate
classDiagram
class AtomOccurrence
click AtomOccurrence href "../AtomOccurrence"
OwlClass <|-- AtomOccurrence
click OwlClass href "../OwlClass"
ChemicalRelationship <|-- AtomOccurrence
click ChemicalRelationship href "../ChemicalRelationship"
AtomOccurrence : coordination_number
AtomOccurrence : formal_charge
AtomOccurrence : name
AtomOccurrence : occurrence_of
AtomOccurrence --> "1" Atom : occurrence_of
click Atom href "../Atom"
AtomOccurrence : owl_subclass_of
AtomOccurrence --> "0..1" OwlClass : owl_subclass_of
click OwlClass href "../OwlClass"
AtomOccurrence : oxidation_number
AtomOccurrence : valence
Inheritance
- ChemicalRelationship [ OwlClass]
- AtomOccurrence [ OwlClass]
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| name | 1 String |
direct | |
| occurrence_of | 1 Atom |
direct | |
| valence | 0..1 Integer |
the number of electrons that an atom uses in bonding [https://doi | direct |
| oxidation_number | 0..1 Integer |
The charge remaining on an atom when all ligands are removed heterolytically ... | direct |
| formal_charge | 0..1 Integer |
The charge remaining on an atom when all ligands are removed homolytically | direct |
| coordination_number | 0..1 Integer |
The number of atoms bonded to the atom of interest | direct |
| owl_subclass_of | 0..1 OwlClass |
Holds between C and P if C owl:subClassOf P | OwlClass |
Usages
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/chemrof
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | chemrof:AtomOccurrence |
| native | chemrof:AtomOccurrence |
LinkML Source
Direct
name: AtomOccurrence
description: An occurrence of an atom in the context of a particular molecule. For
example, one of two occurrences of oxygen in nitrate
title: atom occurrence
from_schema: https://w3id.org/chemrof
is_a: ChemicalRelationship
mixins:
- OwlClass
attributes:
name:
name: name
from_schema: https://w3id.org/chemrof
identifier: true
domain_of:
- DomainEntity
- GroupingClass
- Atom
- AtomOccurrence
required: true
occurrence_of:
name: occurrence_of
from_schema: https://w3id.org/chemrof
domain_of:
- SubatomicParticleOccurrence
- AtomOccurrence
range: Atom
required: true
valence:
name: valence
description: the number of electrons that an atom uses in bonding [https://doi.org/10.1021%2Fed083p791]
comments:
- 'forumla: number of electrons in valence shell of free atom – number of non-bonding
electrons on atom in molecule'
- 'forumla: number of bonds + formal charge'
- 'example: In methane, carbon has a valence of 4, and each hydrogen has a valency
of 1'
- 'example: In in ammonia, nitrogen has a valence of 3, each each hydrogen has
a valency of 1'
- 'todo: determine if this is in CHEBI and how to map'
from_schema: https://w3id.org/chemrof
aliases:
- atom valency
- valency
domain_of:
- AtomOccurrence
range: integer
oxidation_number:
name: oxidation_number
description: The charge remaining on an atom when all ligands are removed heterolytically
in their closed form, with the electrons being transferred to the more electronegative
partner; homonuclear bonds do not contribute to the oxidation number. [https://doi.org/10.1021%2Fed083p791]
from_schema: https://w3id.org/chemrof
aliases:
- oxidation
- oxidation state
exact_mappings:
- goldbook:O04363
domain_of:
- AtomOccurrence
range: integer
formal_charge:
name: formal_charge
description: The charge remaining on an atom when all ligands are removed homolytically.
[https://doi.org/10.1021%2Fed083p791]
from_schema: https://w3id.org/chemrof
aliases:
- charge
domain_of:
- AtomOccurrence
range: integer
coordination_number:
name: coordination_number
description: The number of atoms bonded to the atom of interest. [https://doi.org/10.1021%2Fed083p791]
from_schema: https://w3id.org/chemrof
aliases:
- coordination
domain_of:
- AtomOccurrence
range: integer
Induced
name: AtomOccurrence
description: An occurrence of an atom in the context of a particular molecule. For
example, one of two occurrences of oxygen in nitrate
title: atom occurrence
from_schema: https://w3id.org/chemrof
is_a: ChemicalRelationship
mixins:
- OwlClass
attributes:
name:
name: name
from_schema: https://w3id.org/chemrof
identifier: true
alias: name
owner: AtomOccurrence
domain_of:
- DomainEntity
- GroupingClass
- Atom
- AtomOccurrence
range: string
required: true
occurrence_of:
name: occurrence_of
from_schema: https://w3id.org/chemrof
alias: occurrence_of
owner: AtomOccurrence
domain_of:
- SubatomicParticleOccurrence
- AtomOccurrence
range: Atom
required: true
valence:
name: valence
description: the number of electrons that an atom uses in bonding [https://doi.org/10.1021%2Fed083p791]
comments:
- 'forumla: number of electrons in valence shell of free atom – number of non-bonding
electrons on atom in molecule'
- 'forumla: number of bonds + formal charge'
- 'example: In methane, carbon has a valence of 4, and each hydrogen has a valency
of 1'
- 'example: In in ammonia, nitrogen has a valence of 3, each each hydrogen has
a valency of 1'
- 'todo: determine if this is in CHEBI and how to map'
from_schema: https://w3id.org/chemrof
aliases:
- atom valency
- valency
alias: valence
owner: AtomOccurrence
domain_of:
- AtomOccurrence
range: integer
oxidation_number:
name: oxidation_number
description: The charge remaining on an atom when all ligands are removed heterolytically
in their closed form, with the electrons being transferred to the more electronegative
partner; homonuclear bonds do not contribute to the oxidation number. [https://doi.org/10.1021%2Fed083p791]
from_schema: https://w3id.org/chemrof
aliases:
- oxidation
- oxidation state
exact_mappings:
- goldbook:O04363
alias: oxidation_number
owner: AtomOccurrence
domain_of:
- AtomOccurrence
range: integer
formal_charge:
name: formal_charge
description: The charge remaining on an atom when all ligands are removed homolytically.
[https://doi.org/10.1021%2Fed083p791]
from_schema: https://w3id.org/chemrof
aliases:
- charge
alias: formal_charge
owner: AtomOccurrence
domain_of:
- AtomOccurrence
range: integer
coordination_number:
name: coordination_number
description: The number of atoms bonded to the atom of interest. [https://doi.org/10.1021%2Fed083p791]
from_schema: https://w3id.org/chemrof
aliases:
- coordination
alias: coordination_number
owner: AtomOccurrence
domain_of:
- AtomOccurrence
range: integer
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: AtomOccurrence
domain_of:
- OwlClass
range: OwlClass