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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" ChemicalEntity : conjugate_acid_of
    click ChemicalEntity href "../ChemicalEntity"


      GroupingClassForAcidsOrBases : conjugate_base_of




    GroupingClassForAcidsOrBases --> "0..1" ChemicalEntity : conjugate_base_of
    click ChemicalEntity href "../ChemicalEntity"


      GroupingClassForAcidsOrBases : id

      GroupingClassForAcidsOrBases : name

      GroupingClassForAcidsOrBases : owl_subclass_of




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


      GroupingClassForAcidsOrBases : subtype_of




    GroupingClassForAcidsOrBases --> "*" MoleculeGroupingClass : subtype_of
    click MoleculeGroupingClass href "../MoleculeGroupingClass"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
conjugate_base_of 0..1
ChemicalEntity		 connects the base form of an acid to an acid direct
conjugate_acid_of 0..1
ChemicalEntity		 direct
id 1
String		 ChemicalGroupingClass, GroupingClass
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: ChemicalEntity
  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: ChemicalEntity
  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
  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
    rank: 1000
    is_a: chemical_to_chemical_relationship
    domain: OwlClass
    alias: subtype_of
    owner: GroupingClassForAcidsOrBases
    domain_of:
    - GroupingClass
    range: MoleculeGroupingClass
    required: false
    multivalued: true