Class: chemical grouping class (ChemicalGroupingClass)

name: ChemicalGroupingClass
description: Instances of this class represent generic chemical concepts that can
  be used to group more specific concepts, or to classify entities. For example "amino
  acid" is a grouping for "serine", "leucine" etc; ester is a grouping for nitroglycerin;
  alkane is a grouping for pentane, butane, methane, etc
title: chemical grouping class
from_schema: https://w3id.org/chemrof
is_a: PhysicochemicalEntityGroupingClass
abstract: true
mixins:
- OwlClass
slots:
- id
- smarts_string
- markush_string
slot_usage:
  subtype_of:
    name: subtype_of
    range: ChemicalGroupingClass
  classifies:
    name: classifies
    range: ChemicalEntity

name: ChemicalGroupingClass
description: Instances of this class represent generic chemical concepts that can
  be used to group more specific concepts, or to classify entities. For example "amino
  acid" is a grouping for "serine", "leucine" etc; ester is a grouping for nitroglycerin;
  alkane is a grouping for pentane, butane, methane, etc
title: chemical grouping class
from_schema: https://w3id.org/chemrof
is_a: PhysicochemicalEntityGroupingClass
abstract: true
mixins:
- OwlClass
slot_usage:
  subtype_of:
    name: subtype_of
    range: ChemicalGroupingClass
  classifies:
    name: classifies
    range: ChemicalEntity
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: ChemicalGroupingClass
    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: ChemicalGroupingClass
    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: ChemicalGroupingClass
    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: ChemicalGroupingClass
    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: ChemicalGroupingClass
    domain_of:
    - DomainEntity
    - GroupingClass
    - Atom
    - AtomOccurrence
    range: string
  subtype_of:
    name: subtype_of
    description: A subtype_of relationship holds between C and P if C is a more specialized
      form of P. Here C and P denotes instances of OWL classes, where C and P both
      function as grouping class
    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: ChemicalGroupingClass
    domain_of:
    - GroupingClass
    range: ChemicalGroupingClass
    required: false
    multivalued: true