Class: molecule grouping class (MoleculeGroupingClass)

A grouping class that classifies molecules. Example: carbohydrate, monosaccharide, amino acid, polyacrylamide

URI: chemrof:MoleculeGroupingClass

 classDiagram
    class MoleculeGroupingClass
      ChemicalGroupingClass <|-- MoleculeGroupingClass


      MoleculeGroupingClass <|-- MolecularDerivativeGroupingClass
      MoleculeGroupingClass <|-- MoleculeGroupingClassDefinedByComponents
      MoleculeGroupingClass <|-- MoleculeGroupingClassDefinedByAdditionOfAGroup
      MoleculeGroupingClass <|-- ChemicalSaltGroupingClass
      MoleculeGroupingClass <|-- GeneralizedMolecularStructureClass
      MoleculeGroupingClass <|-- GroupingClassForAcidsOrBases


      MoleculeGroupingClass : id

      MoleculeGroupingClass : name

      MoleculeGroupingClass : owl_subclass_of

          MoleculeGroupingClass --> OwlClass : owl_subclass_of

      MoleculeGroupingClass : subtype_of

          MoleculeGroupingClass --> MoleculeGroupingClass : subtype_of

Inheritance

• GroupingClass [ OwlClass]
  • PhysicochemicalEntityGroupingClass
    • ChemicalGroupingClass [ OwlClass]
      • MoleculeGroupingClass
        • MolecularDerivativeGroupingClass
        • MoleculeGroupingClassDefinedByComponents
        • MoleculeGroupingClassDefinedByAdditionOfAGroup
        • ChemicalSaltGroupingClass
        • GeneralizedMolecularStructureClass
        • GroupingClassForAcidsOrBases

Slots

Name	Cardinality and Range	Description	Inheritance
id	1..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	0..* MoleculeGroupingClass	grouping classes can be arranged in hierarchies arbitrarily deep	GroupingClass

Usages

used by	used in	type	used
ChemicalGroupingByCharge	subtype_of	range	MoleculeGroupingClass
MoleculeGroupingClass	subtype_of	range	MoleculeGroupingClass
MolecularDerivativeGroupingClass	subtype_of	range	MoleculeGroupingClass
MoleculeGroupingClassDefinedByComponents	subtype_of	range	MoleculeGroupingClass
MoleculeGroupingClassDefinedByAdditionOfAGroup	subtype_of	range	MoleculeGroupingClass
ChemicalSaltGroupingClass	subtype_of	range	MoleculeGroupingClass
ChemicalSaltByCation	subtype_of	range	MoleculeGroupingClass
ChemicalSaltByAnion	subtype_of	range	MoleculeGroupingClass
GeneralizedMolecularStructureClass	subtype_of	range	MoleculeGroupingClass
MonomericPolymericGroupingClass	subtype_of	range	MoleculeGroupingClass
GroupingClassForAcidsOrBases	subtype_of	range	MoleculeGroupingClass
AcidAnionGroupingClass	subtype_of	range	MoleculeGroupingClass
GeneralAcidBaseGroupingClass	subtype_of	range	MoleculeGroupingClass
AcidBaseConflationClass	subtype_of	range	MoleculeGroupingClass
AtomGroupingClass	subtype_of	range	MoleculeGroupingClass
AtomGroupingByPeriodicTablePlacement	subtype_of	range	MoleculeGroupingClass
AtomGroupingByPeriodicTableGroup	subtype_of	range	MoleculeGroupingClass
AtomGroupingByPeriodicTableBlock	subtype_of	range	MoleculeGroupingClass
AtomGroupingByProperty	subtype_of	range	MoleculeGroupingClass

Examples

Value
nucleobase

Comments

• Unlike an actual molecule, a molecule grouping class will not have an inchi or properties such as mass
• Molecular grouping classes are typically defined by elemental composition and structure as well as chemical properties

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: MoleculeGroupingClass
description: 'A grouping class that classifies molecules. Example: carbohydrate, monosaccharide,
  amino acid, polyacrylamide'
title: molecule grouping class
comments:
- Unlike an actual molecule, a molecule grouping class will not have an inchi or properties
  such as mass
- Molecular grouping classes are typically defined by elemental composition and structure
  as well as chemical properties
examples:
- value: nucleobase
from_schema: https://w3id.org/chemrof
is_a: ChemicalGroupingClass
slot_usage:
  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
    domain_of:
    - GroupingClass
    range: MoleculeGroupingClass
  classifies:
    name: classifies
    range: Molecule

Induced

name: MoleculeGroupingClass
description: 'A grouping class that classifies molecules. Example: carbohydrate, monosaccharide,
  amino acid, polyacrylamide'
title: molecule grouping class
comments:
- Unlike an actual molecule, a molecule grouping class will not have an inchi or properties
  such as mass
- Molecular grouping classes are typically defined by elemental composition and structure
  as well as chemical properties
examples:
- value: nucleobase
from_schema: https://w3id.org/chemrof
is_a: ChemicalGroupingClass
slot_usage:
  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
    domain_of:
    - GroupingClass
    range: MoleculeGroupingClass
  classifies:
    name: classifies
    range: Molecule
attributes:
  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: MoleculeGroupingClass
    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: MoleculeGroupingClass
    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: MoleculeGroupingClass
    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
    multivalued: true
    alias: subtype_of
    owner: MoleculeGroupingClass
    domain_of:
    - GroupingClass
    range: MoleculeGroupingClass
    required: false