Class: grouping by SMARTS (GroupingBySmarts)

name: GroupingBySmarts
annotations:
  owl.template:
    tag: owl.template
    value: SubClassOf({{id}} {{genus}})
description: A grouping meta-pattern whose members are the individuals of a genus
  class that additionally match a SMARTS substructure pattern. SMARTS matching is
  a computational (non-DL) criterion, so the OWL rendering asserts only the genus
  as a necessary superclass (SubClassOf) and carries the SMARTS as an annotation for
  external cheminformatics classification. Concrete groupings are supplied as data
  instances (genus + smarts_string), not as schema subclasses.
title: grouping by SMARTS
examples:
- value: fatty acyl-CoA (genus acyl-CoA + CoA-thioester SMARTS)
from_schema: https://w3id.org/chemrof
is_a: MoleculeGroupingClass
slots:
- genus
slot_usage:
  classifies:
    name: classifies
    range: Molecule
defining_slots:
- genus
- smarts_string

name: GroupingBySmarts
annotations:
  owl.template:
    tag: owl.template
    value: SubClassOf({{id}} {{genus}})
description: A grouping meta-pattern whose members are the individuals of a genus
  class that additionally match a SMARTS substructure pattern. SMARTS matching is
  a computational (non-DL) criterion, so the OWL rendering asserts only the genus
  as a necessary superclass (SubClassOf) and carries the SMARTS as an annotation for
  external cheminformatics classification. Concrete groupings are supplied as data
  instances (genus + smarts_string), not as schema subclasses.
title: grouping by SMARTS
examples:
- value: fatty acyl-CoA (genus acyl-CoA + CoA-thioester SMARTS)
from_schema: https://w3id.org/chemrof
is_a: MoleculeGroupingClass
slot_usage:
  classifies:
    name: classifies
    range: Molecule
attributes:
  genus:
    name: genus
    description: The genus (parent class) of a genus-differentia grouping definition.
      Members of the grouping are asserted to be members of this class; rendered as
      the first conjunct of the OWL class expression.
    title: genus
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: genus
    owner: GroupingBySmarts
    domain_of:
    - GroupingBySmarts
    - GroupingByGenusAndRangeRestriction
    - GroupingByGenusAndPropertyValue
    range: uriorcurie
  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: GroupingBySmarts
    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: GroupingBySmarts
    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: GroupingBySmarts
    domain_of:
    - ChemicalGroupingClass
    range: ChemicalEncoding
  cxsmiles_string:
    name: cxsmiles_string
    description: A ChemAxon Extended SMILES string that appends a feature block to
      a SMILES string to capture annotations such as atom labels, R-groups, S-groups,
      coordinates, radicals, and enhanced stereochemistry.
    title: CXSMILES string
    examples:
    - value: '[H][C@@](COC([*])=O)(COP(O)(=O)O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@@H](OP(O)(O)=O)[C@H]1O)OC([*])=O
        |$;;;;;_R1;;;;;;;;;;;;;;;;;;;;;;;;;_R2$|'
      description: CXSMILES for 1-phosphatidyl-1D-myo-inositol 3-phosphate (R1,R2)
    from_schema: https://w3id.org/chemrof
    see_also:
    - https://docs.chemaxon.com/latest/formats_chemaxon-extended-smiles-and-smarts-cxsmiles-and-cxsmarts.html
    aliases:
    - CXSMILES
    - ChemAxon extended SMILES
    - extended SMILES
    exact_mappings:
    - wd:P10718
    rank: 1000
    is_a: smiles_string
    domain: ChemicalEntity
    alias: cxsmiles_string
    owner: GroupingBySmarts
    domain_of:
    - ChemicalEntity
    - ChemicalGroupingClass
    range: ChemicalEncoding
  owl_subclass_of:
    name: owl_subclass_of
    annotations:
      owl:
        tag: owl
        value: SubClassOf
    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: GroupingBySmarts
    domain_of:
    - OwlClass
    range: OwlClass
  name:
    name: name
    annotations:
      owl:
        tag: owl
        value: AnnotationAssertion
    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: GroupingBySmarts
    domain_of:
    - DomainEntity
    - GroupingClass
    - Atom
    - AtomOccurrence
    range: string
  description:
    name: description
    description: A human-readable textual description of an entity.
    title: description
    from_schema: https://w3id.org/chemrof
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: GroupingBySmarts
    domain_of:
    - GroupingClass
    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
    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: GroupingBySmarts
    domain_of:
    - GroupingClass
    range: MoleculeGroupingClass
    required: false
    multivalued: true
defining_slots:
- genus
- smarts_string