Class: molecular complex (MolecularComplex)

A molecular complex is a chemical complex composed of at least one weakly interacting molecule.[SIO] Examples: chromosome, double-standed DNA, protein-containing macromolecular complex

URI: chemrof:MolecularComplex

 classDiagram
    class MolecularComplex
      PreciseChemicalMixture <|-- MolecularComplex


      MolecularComplex <|-- SupramolecularPolymer


      MolecularComplex : empirical_formula

      MolecularComplex : has_chemical_role

          MolecularComplex --> ChemicalRole : has_chemical_role

      MolecularComplex : has_physiologically_stable_form

          MolecularComplex --> MoleculeByChargeState : has_physiologically_stable_form

      MolecularComplex : id

      MolecularComplex : inchi_atom_connections_sublayer

      MolecularComplex : inchi_chemical_sublayer

      MolecularComplex : inchi_string

      MolecularComplex : is_radical

      MolecularComplex : IUPAC_name

      MolecularComplex : name

      MolecularComplex : owl_subclass_of

          MolecularComplex --> OwlClass : owl_subclass_of

      MolecularComplex : smiles_string

      MolecularComplex : type

Inheritance

• DomainEntity
  • PhysicochemicalEntity
    • ChemicalEntity [ OwlClass]
      • PolyatomicEntity
        • ChemicalMixture
          • PreciseChemicalMixture [ WeaklyBonded]
            • MolecularComplex
              • SupramolecularPolymer

Slots

Name	Cardinality and Range	Description	Inheritance
inchi_atom_connections_sublayer	0..1 recommended String	The atoms in the chemical formula (except for hydrogens) are numbered in sequ...	PolyatomicEntity
IUPAC_name	0..1 String		ChemicalEntity
is_radical	0..1 Boolean		ChemicalEntity
has_chemical_role	0..1 ChemicalRole		ChemicalEntity
inchi_string	0..1 ChemicalEncoding		ChemicalEntity
inchi_chemical_sublayer	0..1 recommended String	The part of an InChI string that represents the chemical formula, occurring a...	ChemicalEntity
smiles_string	0..* ChemicalEncoding	A string encoding of a molecular graph, no chiral or isotopic information	ChemicalEntity
empirical_formula	0..1 ChemicalEncoding	A chemical formula where numbers denote relative proportion of atoms	ChemicalEntity
has_physiologically_stable_form	0..* MoleculeByChargeState	connects an acid to the form that is stable at physiological pH (7	ChemicalEntity
owl_subclass_of	0..1 OwlClass	Holds between C and P if C owl:subClassOf P	OwlClass
id	1..1 String		DomainEntity
name	0..1 String	name of chemical entity	DomainEntity
type	0..1 Uriorcurie		DomainEntity

Aliases

• poly molecular composite entity
• complex of molecular entities
• molecule complex

Comments

• In bioptop, molecule complex is a sibling of structured biological entity under poly molecular composite entity
• In SIO, molecular complex is an only child of chemical complex, which is under chemical substance. chemical complex is defined as A chemical complex is a chemical substance composed of a weakly connected molecules and ions in a known stoichiometry.

Identifier and Mapping Information

Schema Source

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

Mappings

Mapping Type	Mapped Value
self	chemrof:MolecularComplex
native	chemrof:MolecularComplex
exact	biotop:MoleculeComplex, SIO:010506, COB:0000080

LinkML Source

Direct

name: MolecularComplex
description: 'A molecular complex is a chemical complex composed of at least one weakly
  interacting molecule.[SIO] Examples: chromosome, double-standed DNA, protein-containing
  macromolecular complex'
title: molecular complex
comments:
- In bioptop, molecule complex is a sibling of structured biological entity under
  poly molecular composite entity
- In SIO, molecular complex is an only child of chemical complex, which is under chemical
  substance. chemical complex is defined as A chemical complex is a chemical substance
  composed of a weakly connected molecules and ions in a known stoichiometry.
from_schema: https://w3id.org/chemrof
aliases:
- poly molecular composite entity
- complex of molecular entities
- molecule complex
exact_mappings:
- biotop:MoleculeComplex
- SIO:010506
- COB:0000080
is_a: PreciseChemicalMixture

Induced

name: MolecularComplex
description: 'A molecular complex is a chemical complex composed of at least one weakly
  interacting molecule.[SIO] Examples: chromosome, double-standed DNA, protein-containing
  macromolecular complex'
title: molecular complex
comments:
- In bioptop, molecule complex is a sibling of structured biological entity under
  poly molecular composite entity
- In SIO, molecular complex is an only child of chemical complex, which is under chemical
  substance. chemical complex is defined as A chemical complex is a chemical substance
  composed of a weakly connected molecules and ions in a known stoichiometry.
from_schema: https://w3id.org/chemrof
aliases:
- poly molecular composite entity
- complex of molecular entities
- molecule complex
exact_mappings:
- biotop:MoleculeComplex
- SIO:010506
- COB:0000080
is_a: PreciseChemicalMixture
attributes:
  inchi_atom_connections_sublayer:
    name: inchi_atom_connections_sublayer
    description: The atoms in the chemical formula (except for hydrogens) are numbered
      in sequence; this sublayer describes which atoms are connected by bonds to which
      other ones.
    title: inchi atom connections sublayer
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: inchi_sublayer_in_main_layer
    alias: inchi_atom_connections_sublayer
    owner: MolecularComplex
    domain_of:
    - PolyatomicEntity
    - StandardInchiObject
    - EntityWithConnectivitySpecificied
    range: string
    required: false
    recommended: true
    pattern: ^c.*
  IUPAC_name:
    name: IUPAC_name
    title: IUPAC name
    from_schema: https://w3id.org/chemrof
    exact_mappings:
    - MI:2007
    rank: 1000
    is_a: information_property
    slot_uri: CHEMINF:000107
    alias: IUPAC_name
    owner: MolecularComplex
    domain_of:
    - ChemicalEntity
    range: string
  is_radical:
    name: is_radical
    title: is radical
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain: ChemicalEntity
    alias: is_radical
    owner: MolecularComplex
    domain_of:
    - ChemicalEntity
    range: boolean
  has_chemical_role:
    name: has_chemical_role
    title: has chemical role
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: has_chemical_role
    owner: MolecularComplex
    domain_of:
    - ChemicalEntity
    range: ChemicalRole
  inchi_string:
    name: inchi_string
    title: InChi
    todos:
    - declare this as a key once compound_key is introduced to linkml
    from_schema: https://w3id.org/chemrof
    see_also:
    - https://chemistry.stackexchange.com/questions/151072/can-cis-trans-isomers-have-same-inchi
    aliases:
    - InChi
    exact_mappings:
    - OntoRXN:hasInChi
    rank: 1000
    is_a: chemical_formula
    domain: ChemicalEntity
    alias: inchi_string
    owner: MolecularComplex
    domain_of:
    - ChemicalEntity
    range: ChemicalEncoding
  inchi_chemical_sublayer:
    name: inchi_chemical_sublayer
    description: The part of an InChI string that represents the chemical formula,
      occurring after the version string. E.g. C6H12O6 for glucose
    title: inchi chemical sublayer
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: inchi_sublayer_in_main_layer
    alias: inchi_chemical_sublayer
    owner: MolecularComplex
    domain_of:
    - ChemicalEntity
    - StandardInchiObject
    - EntityWithAtomsEnumerated
    range: string
    required: false
    recommended: true
    pattern: ^[A-Z0-9\.]+$
  smiles_string:
    name: smiles_string
    description: A string encoding of a molecular graph, no chiral or isotopic information.
      There are usually a large number of valid SMILES which represent a given structure.
      For example, CCO, OCC and C(O)C all specify the structure of ethanol.
    title: smiles string
    comments:
    - a problematic set of structures to describe using SMILES notation is those which
      cannot be easily described using molecular graphs (see “Limitations of molecular
      graph representations” section), such as organometallic compounds and ionic
      salts.
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: chemical_formula
    domain: ChemicalEntity
    multivalued: true
    alias: smiles_string
    owner: MolecularComplex
    domain_of:
    - ChemicalEntity
    range: ChemicalEncoding
  empirical_formula:
    name: empirical_formula
    description: A chemical formula where numbers denote relative proportion of atoms.
      E.g. CH2O for glucose
    title: empirical formula
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: chemical_formula
    domain: ChemicalEntity
    alias: empirical_formula
    owner: MolecularComplex
    domain_of:
    - ChemicalEntity
    range: ChemicalEncoding
  has_physiologically_stable_form:
    name: has_physiologically_stable_form
    description: connects an acid to the form that is stable at physiological pH (7.3).
      E.g. citric acid has physiological base citrate(3-)
    title: has physiologically stable form
    from_schema: https://w3id.org/chemrof
    see_also:
    - https://ftp.expasy.org/databases/rhea/tsv/chebi_pH7_3_mapping.tsv
    aliases:
    - protonation neutral form of
    - has Ph 7.3 mapping
    rank: 1000
    is_a: acid_form_of
    domain: MoleculeByChargeState
    multivalued: true
    alias: has_physiologically_stable_form
    owner: MolecularComplex
    domain_of:
    - ChemicalEntity
    range: MoleculeByChargeState
  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: MolecularComplex
    domain_of:
    - OwlClass
    range: OwlClass
  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: MolecularComplex
    domain_of:
    - DomainEntity
    - GroupingClass
    - ChemicalGroupingClass
    range: string
    required: true
  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: MolecularComplex
    domain_of:
    - DomainEntity
    - GroupingClass
    - Atom
    - AtomOccurrence
    range: string
  type:
    name: type
    title: type
    from_schema: https://w3id.org/chemrof
    rank: 1000
    designates_type: true
    alias: type
    owner: MolecularComplex
    domain_of:
    - DomainEntity
    range: uriorcurie