Class: chemical entity (ChemicalEntity)

name: ChemicalEntity
id_prefixes:
- CHEBI
- CHEMBL.COMPOUND
- DRUGBANK
- PUBCHEM.COMPOUND
- MESH
- HMDB
- INCHI
- INCHIKEY
- UNII
- KEGG
- SEED
- MetaNetX.chemical
- bigg.metabolite
- npatlas
- comptox
description: A discrete structure that is one or more atoms that can be described
  by a chemical formula.
title: chemical entity
comments:
- Does not encompass chemical grouping classes, such as "amino acid". Use the class
  ChemicalGrouping for this.
- In common chemical usage generic and specific chemical names (such as radical or
  hydroxide ion) or chemical formulae refer either to a chemical species or to a molecular
  entity[https://goldbook.iupac.org/terms/view/CT01038]
from_schema: https://w3id.org/chemrof
aliases:
- specific chemical entity
- chemical
- chemical species
mappings:
- CHEBI:24431
- CHEMINF:000000
- OntoRxn:ChemSpecies
exact_mappings:
- SIO:010004
- wdeschema:E239
is_a: PhysicochemicalEntity
abstract: true
mixins:
- OwlClass
slots:
- IUPAC_name
- is_radical
- has_chemical_role
- inchi_string
- inchi_chemical_sublayer
- smiles_string
- empirical_formula
- has_major_microspecies_at_pH7_3
- molecular_mass
slot_usage:
  inchi_chemical_sublayer:
    name: inchi_chemical_sublayer
    required: false
    recommended: true
unique_keys:
  smiles_string:
    unique_key_name: smiles_string
    unique_key_slots:
    - smiles_string

name: ChemicalEntity
id_prefixes:
- CHEBI
- CHEMBL.COMPOUND
- DRUGBANK
- PUBCHEM.COMPOUND
- MESH
- HMDB
- INCHI
- INCHIKEY
- UNII
- KEGG
- SEED
- MetaNetX.chemical
- bigg.metabolite
- npatlas
- comptox
description: A discrete structure that is one or more atoms that can be described
  by a chemical formula.
title: chemical entity
comments:
- Does not encompass chemical grouping classes, such as "amino acid". Use the class
  ChemicalGrouping for this.
- In common chemical usage generic and specific chemical names (such as radical or
  hydroxide ion) or chemical formulae refer either to a chemical species or to a molecular
  entity[https://goldbook.iupac.org/terms/view/CT01038]
from_schema: https://w3id.org/chemrof
aliases:
- specific chemical entity
- chemical
- chemical species
mappings:
- CHEBI:24431
- CHEMINF:000000
- OntoRxn:ChemSpecies
exact_mappings:
- SIO:010004
- wdeschema:E239
is_a: PhysicochemicalEntity
abstract: true
mixins:
- OwlClass
slot_usage:
  inchi_chemical_sublayer:
    name: inchi_chemical_sublayer
    required: false
    recommended: true
attributes:
  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: ChemicalEntity
    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: ChemicalEntity
    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: ChemicalEntity
    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: ChemicalEntity
    domain_of:
    - ChemicalEntity
    range: ChemicalEncoding
  inchi_chemical_sublayer:
    name: inchi_chemical_sublayer
    annotations:
      inchi.index:
        tag: inchi.index
        value: 2
    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
    comments:
    - in the case of hydrates, the dot separates the formula of the compound from
      the water molecules. For example, CuSO₄·5H₂O represents copper(II) sulfate pentahydrate,
      indicating that there are five water molecules associated with each copper(II)
      sulfate unit in the crystal.
    - 'Salt Formulations: Dots can also be used to denote the proportions in which
      different components are combined to form a salt. For instance, "CaCl₂·2AgNO₃"
      would suggest a complex formed from one unit of calcium chloride and two units
      of silver nitrate, though this particular example is more illustrative than
      practical.'
    - 'Coordination Complexes: In coordination chemistry, dots can separate the metal
      complex from its counterions or ligands that are not directly bonded to the
      metal center. For example, "[Co(NH₃)₆]Cl₃" indicates a complex of cobalt with
      six ammonia ligands, and the three chloride ions are counterions. If written
      as "[Co(NH₃)₆]·3Cl", it would similarly denote the presence of three chloride
      ions associated with the complex, though this notation is less common'
    - 'Molecular Assemblies: For certain supramolecular structures or assemblies,
      dots might be used to indicate a non-covalent association of components. This
      usage is less common and more context-dependent'
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: inchi_sublayer_in_main_layer
    alias: inchi_chemical_sublayer
    owner: ChemicalEntity
    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
    alias: smiles_string
    owner: ChemicalEntity
    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: ChemicalEntity
    domain_of:
    - ChemicalEntity
    range: ChemicalEncoding
  has_major_microspecies_at_pH7_3:
    name: has_major_microspecies_at_pH7_3
    description: Links different variants of the same chemical in different protonation
      states, where the target of this link is the (predicited) to be most common
      protonation state for this chemical at a pH of 7.3. This link may point to it's
      source. 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: ChemicalEntity
    alias: has_major_microspecies_at_pH7_3
    owner: ChemicalEntity
    domain_of:
    - ChemicalEntity
    inverse: major_microspecies_at_pH7_3_of
    range: ChemicalEntity
    multivalued: true
  molecular_mass:
    name: molecular_mass
    description: The sum of the relative atomic masses of the constituent atoms of
      a molecule.
    title: molecular mass
    from_schema: https://w3id.org/chemrof
    exact_mappings:
    - NCIT:C28272
    - FIX:0000270
    - chebi.property:mass
    rank: 1000
    is_a: molecular_property
    alias: molecular_mass
    owner: ChemicalEntity
    domain_of:
    - ChemicalEntity
    range: float
    unit:
      ucum_code: u
  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: ChemicalEntity
    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: ChemicalEntity
    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: ChemicalEntity
    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: ChemicalEntity
    domain_of:
    - DomainEntity
    range: uriorcurie
unique_keys:
  smiles_string:
    unique_key_name: smiles_string
    unique_key_slots:
    - smiles_string