Class: molecule grouping class (MoleculeGroupingClass)

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

 classDiagram
    class MoleculeGroupingClass
    click MoleculeGroupingClass href "../MoleculeGroupingClass"
      ChemicalGroupingClass <|-- MoleculeGroupingClass
        click ChemicalGroupingClass href "../ChemicalGroupingClass"


      MoleculeGroupingClass <|-- MolecularDerivativeGroupingClass
        click MolecularDerivativeGroupingClass href "../MolecularDerivativeGroupingClass"
      MoleculeGroupingClass <|-- MoleculeGroupingClassDefinedByComponents
        click MoleculeGroupingClassDefinedByComponents href "../MoleculeGroupingClassDefinedByComponents"
      MoleculeGroupingClass <|-- MoleculeGroupingClassDefinedByAdditionOfAGroup
        click MoleculeGroupingClassDefinedByAdditionOfAGroup href "../MoleculeGroupingClassDefinedByAdditionOfAGroup"
      MoleculeGroupingClass <|-- ChemicalSaltGroupingClass
        click ChemicalSaltGroupingClass href "../ChemicalSaltGroupingClass"
      MoleculeGroupingClass <|-- GeneralizedMolecularStructureClass
        click GeneralizedMolecularStructureClass href "../GeneralizedMolecularStructureClass"
      MoleculeGroupingClass <|-- GroupingClassForAcidsOrBases
        click GroupingClassForAcidsOrBases href "../GroupingClassForAcidsOrBases"


      MoleculeGroupingClass : id

      MoleculeGroupingClass : name

      MoleculeGroupingClass : owl_subclass_of




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


      MoleculeGroupingClass : subtype_of




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

Inheritance

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

Slots

Name	Cardinality and Range	Description	Inheritance
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

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
    alias: subtype_of
    owner: MoleculeGroupingClass
    domain_of:
    - GroupingClass
    range: MoleculeGroupingClass
    required: false
    multivalued: true