Class: acid base conflation class (AcidBaseConflationClass)

A molecule grouping class that can groups an acid together with all its conjugate bases. physiological

 classDiagram
    class AcidBaseConflationClass
    click AcidBaseConflationClass href "../AcidBaseConflationClass"
      GroupingClassForAcidsOrBases <|-- AcidBaseConflationClass
        click GroupingClassForAcidsOrBases href "../GroupingClassForAcidsOrBases"

      AcidBaseConflationClass : conjugate_acid_of




    AcidBaseConflationClass --> "0..1" ChemicalEntity : conjugate_acid_of
    click ChemicalEntity href "../ChemicalEntity"


      AcidBaseConflationClass : conjugate_base_of




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


      AcidBaseConflationClass : id

      AcidBaseConflationClass : name

      AcidBaseConflationClass : owl_subclass_of




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


      AcidBaseConflationClass : subtype_of




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

Inheritance

GroupingClass [ OwlClass]
- PhysicochemicalEntityGroupingClass
  - ChemicalGroupingClass [ OwlClass]
    - MoleculeGroupingClass
      - GroupingClassForAcidsOrBases
        
        AcidBaseConflationClass

Slots

Name	Cardinality and Range	Description	Inheritance
conjugate_base_of	0..1 ChemicalEntity	connects the base form of an acid to an acid	GroupingClassForAcidsOrBases
conjugate_acid_of	0..1 ChemicalEntity		GroupingClassForAcidsOrBases
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

Examples

Value
citrate/citric acid

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/chemrof

Mappings

Mapping Type	Mapped Value
self	chemrof:AcidBaseConflationClass
native	chemrof:AcidBaseConflationClass

LinkML Source

Direct

name: AcidBaseConflationClass
description: A molecule grouping class that can groups an acid together with all its
  conjugate bases. physiological
title: acid base conflation class
examples:
- value: citrate/citric acid
from_schema: https://w3id.org/chemrof
is_a: GroupingClassForAcidsOrBases
slot_usage:
  has_physiological_form:
    name: has_physiological_form
    description: The base which defs this conflation class

Induced

name: AcidBaseConflationClass
description: A molecule grouping class that can groups an acid together with all its
  conjugate bases. physiological
title: acid base conflation class
examples:
- value: citrate/citric acid
from_schema: https://w3id.org/chemrof
is_a: GroupingClassForAcidsOrBases
slot_usage:
  has_physiological_form:
    name: has_physiological_form
    description: The base which defs this conflation class
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: AcidBaseConflationClass
    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: AcidBaseConflationClass
    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: AcidBaseConflationClass
    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: AcidBaseConflationClass
    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: AcidBaseConflationClass
    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: AcidBaseConflationClass
    domain_of:
    - GroupingClass
    range: MoleculeGroupingClass
    required: false
    multivalued: true