Class: grouping class for acids or bases (GroupingClassForAcidsOrBases)
- NOTE: this is an abstract class and should not be instantiated directly
URI: chemrof:GroupingClassForAcidsOrBases
classDiagram
class GroupingClassForAcidsOrBases
click GroupingClassForAcidsOrBases href "../GroupingClassForAcidsOrBases"
MoleculeGroupingClass <|-- GroupingClassForAcidsOrBases
click MoleculeGroupingClass href "../MoleculeGroupingClass"
GroupingClassForAcidsOrBases <|-- AcidAnionGroupingClass
click AcidAnionGroupingClass href "../AcidAnionGroupingClass"
GroupingClassForAcidsOrBases <|-- GeneralAcidBaseGroupingClass
click GeneralAcidBaseGroupingClass href "../GeneralAcidBaseGroupingClass"
GroupingClassForAcidsOrBases <|-- AcidBaseConflationClass
click AcidBaseConflationClass href "../AcidBaseConflationClass"
GroupingClassForAcidsOrBases : conjugate_acid_of
GroupingClassForAcidsOrBases --> "0..1" DomainEntity : conjugate_acid_of
click DomainEntity href "../DomainEntity"
GroupingClassForAcidsOrBases : conjugate_base_of
GroupingClassForAcidsOrBases --> "0..1" DomainEntity : conjugate_base_of
click DomainEntity href "../DomainEntity"
GroupingClassForAcidsOrBases : id
GroupingClassForAcidsOrBases : markush_string
GroupingClassForAcidsOrBases : name
GroupingClassForAcidsOrBases : owl_subclass_of
GroupingClassForAcidsOrBases --> "0..1" OwlClass : owl_subclass_of
click OwlClass href "../OwlClass"
GroupingClassForAcidsOrBases : smarts_string
GroupingClassForAcidsOrBases : subtype_of
GroupingClassForAcidsOrBases --> "*" MoleculeGroupingClass : subtype_of
click MoleculeGroupingClass href "../MoleculeGroupingClass"
Inheritance
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
conjugate_base_of | 0..1 DomainEntity |
connects the base form of an acid to an acid | direct |
conjugate_acid_of | 0..1 DomainEntity |
direct | |
id | 1 String |
ChemicalGroupingClass, GroupingClass | |
smarts_string | 0..1 ChemicalEncoding |
a molecular pattern matching language, related to the popular SMILES molecula... | ChemicalGroupingClass |
markush_string | 0..1 ChemicalEncoding |
ChemicalGroupingClass | |
owl_subclass_of | 0..1 OwlClass |
Holds between C and P if C owl:subClassOf P | OwlClass |
name | 0..1 String |
name of chemical entity | GroupingClass |
subtype_of | * MoleculeGroupingClass |
grouping classes can be arranged in hierarchies arbitrarily deep | GroupingClass |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/chemrof
Mappings
Mapping Type | Mapped Value |
---|---|
self | chemrof:GroupingClassForAcidsOrBases |
native | chemrof:GroupingClassForAcidsOrBases |
LinkML Source
Direct
name: GroupingClassForAcidsOrBases
title: grouping class for acids or bases
from_schema: https://w3id.org/chemrof
is_a: MoleculeGroupingClass
abstract: true
slots:
- conjugate_base_of
- conjugate_acid_of
Induced
name: GroupingClassForAcidsOrBases
title: grouping class for acids or bases
from_schema: https://w3id.org/chemrof
is_a: MoleculeGroupingClass
abstract: true
attributes:
conjugate_base_of:
name: conjugate_base_of
description: 'connects the base form of an acid to an acid. Also connects the
different charge states of the base. Example: the different charge states of
lactate (CHEBI:24996) conjugate base of lactic acid (CHEBI:28358)'
title: conjugate base of
notes:
- sometimes chebi hops over a state skipping an intermediate
from_schema: https://w3id.org/chemrof
see_also:
- https://academic.oup.com/nar/article/36/suppl_1/D344/2506390
aliases:
- is conjugate base of (chebi)
rank: 1000
is_a: direct_conjugatated_form_of
mixins:
- has_lower_charge_from
domain: ChemicalEntity
alias: conjugate_base_of
owner: GroupingClassForAcidsOrBases
domain_of:
- GroupingClassForAcidsOrBases
- PolyatomicIon
range: DomainEntity
conjugate_acid_of:
name: conjugate_acid_of
title: conjugate acid of
todos:
- decide on domain/range. in chebi, daidzein monosulfate is conjugate acid of
daidzein monosulfate(1-), yet it is an acid derivative, not an acid
from_schema: https://w3id.org/chemrof
see_also:
- https://academic.oup.com/nar/article/36/suppl_1/D344/2506390
aliases:
- is conjugate acid of (chebi)
rank: 1000
is_a: direct_conjugatated_form_of
mixins:
- has_higher_charge_from
domain: ChemicalEntity
alias: conjugate_acid_of
owner: GroupingClassForAcidsOrBases
domain_of:
- GroupingClassForAcidsOrBases
- PolyatomicIon
inverse: conjugate_base_of
range: DomainEntity
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: GroupingClassForAcidsOrBases
domain_of:
- DomainEntity
- GroupingClass
- ChemicalGroupingClass
range: string
required: true
smarts_string:
name: smarts_string
description: a molecular pattern matching language, related to the popular SMILES
molecular language, that can be used to specify sub-structural patterns in molecules.
title: smarts string
examples:
- value: '[#1,#6:60][C@@:6]12[CX4:7][CX4H2,CX4H0:8]([CX4H3,CX4H2,#1:80])([CX4H3,CX4H2,#1:81])[CX3:9](=[CX3H2:10])[C@@:11]1([C:1](=[O:2])[CX4,c:4][CX4,c:3][CX4,c,O,NX3!r3:5]2)[C:99]#[N:97]>>[C:10]#[C:9][*:8]([*:80])([*:81])[C:7][C@@:6]1([*:60])[*:5][*:3][*:4][C:1](=[O:2])[C:11]1[C:99]#[N:97]'
from_schema: https://w3id.org/chemrof
rank: 1000
is_a: chemical_formula
domain: ChemicalEntity
alias: smarts_string
owner: GroupingClassForAcidsOrBases
domain_of:
- ChemicalGroupingClass
range: ChemicalEncoding
markush_string:
name: markush_string
from_schema: https://w3id.org/chemrof
rank: 1000
is_a: chemical_formula
domain: ChemicalEntity
alias: markush_string
owner: GroupingClassForAcidsOrBases
domain_of:
- ChemicalGroupingClass
range: ChemicalEncoding
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: GroupingClassForAcidsOrBases
domain_of:
- OwlClass
range: OwlClass
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: GroupingClassForAcidsOrBases
domain_of:
- DomainEntity
- GroupingClass
- Atom
- AtomOccurrence
range: string
subtype_of:
name: subtype_of
description: grouping classes can be arranged in hierarchies arbitrarily deep.
Note that subtype_of should only connect two grouping classes
title: subtype of
from_schema: https://w3id.org/chemrof
aliases:
- metasubclass of
exact_mappings:
- wd:P2445
narrow_mappings:
- rdfs:subClassOf
rank: 1000
is_a: chemical_to_chemical_relationship
mixins:
- owl_subclass_of
domain: OwlClass
alias: subtype_of
owner: GroupingClassForAcidsOrBases
domain_of:
- GroupingClass
range: MoleculeGroupingClass
required: false
multivalued: true