Class: natural product (NaturalProduct)

name: NaturalProduct
title: natural product
from_schema: https://w3id.org/chemrof
exact_mappings:
- wdeschema:E240
is_a: Molecule
attributes:
  derived_from_organisms:
    name: derived_from_organisms
    from_schema: https://w3id.org/chemrof
    rank: 1000
    domain_of:
    - NaturalProduct
    range: uriorcurie
    multivalued: true

name: NaturalProduct
title: natural product
from_schema: https://w3id.org/chemrof
exact_mappings:
- wdeschema:E240
is_a: Molecule
attributes:
  derived_from_organisms:
    name: derived_from_organisms
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: derived_from_organisms
    owner: NaturalProduct
    domain_of:
    - NaturalProduct
    range: uriorcurie
    multivalued: true
  has_atom_occurrences:
    name: has_atom_occurrences
    description: An individuated atom in the context of a chemical structure.
    title: has atom occurrences
    from_schema: https://w3id.org/chemrof
    rank: 1000
    alias: has_atom_occurrences
    owner: NaturalProduct
    domain_of:
    - Molecule
    range: AtomOccurrence
    multivalued: true
    inlined: true
    inlined_as_list: true
    minimum_cardinality: 2
  has_bonds:
    name: has_bonds
    description: The set of all bonds connecting atoms in a molecule
    title: has bonds
    from_schema: https://w3id.org/chemrof
    aliases:
    - adjacency matrix
    rank: 1000
    domain: Molecule
    alias: has_bonds
    owner: NaturalProduct
    domain_of:
    - Molecule
    range: AtomicBond
    multivalued: true
  has_submolecules:
    name: has_submolecules
    description: Relation between a molecule and the molecules it is made from.
    title: has submolecules
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: has_part
    domain: Molecule
    alias: has_submolecules
    owner: NaturalProduct
    domain_of:
    - Molecule
    range: Molecule
    multivalued: true
  has_atoms:
    name: has_atoms
    description: 'Relation between a molecule and the atoms it contains. Note that
      this is a shortcut relation: for granular representations go via atom occurrences'
    title: has atoms
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: has_part
    domain: Molecule
    alias: has_atoms
    owner: NaturalProduct
    domain_of:
    - Molecule
    range: Atom
    multivalued: true
  is_organic:
    name: is_organic
    description: An organic molecule is a molecule composed of organic atoms (at least
      carbon, hydrogen, and optionally oxygen, phosphorus, nitrogen, sulfur) [SIO]
    title: is organic
    from_schema: https://w3id.org/chemrof
    close_mappings:
    - SIO:010072
    rank: 1000
    domain: ChemicalEntity
    alias: is_organic
    owner: NaturalProduct
    domain_of:
    - Molecule
    range: boolean
  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: NaturalProduct
    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: NaturalProduct
    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: NaturalProduct
    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: NaturalProduct
    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: NaturalProduct
    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: NaturalProduct
    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: NaturalProduct
    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: NaturalProduct
    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: NaturalProduct
    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: NaturalProduct
    domain_of:
    - ChemicalEntity
    range: float
    unit:
      ucum_code: u
  water_solubility:
    name: water_solubility
    description: The maximum amount of a substance that can dissolve in water at 25°C,
      expressed in grams per liter (g/L).
    title: water solubility
    comments:
    - Standard temperature is 25°C (298.15 K)
    - This property represents the maximum equilibrium solubility in pure water
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: molecular_property
    alias: water_solubility
    owner: NaturalProduct
    domain_of:
    - ChemicalEntity
    range: float
    unit:
      ucum_code: g/L
  pka_ionization_constant:
    name: pka_ionization_constant
    description: The negative logarithm of the acid dissociation constant (Ka) for
      ionizable groups in a molecule. Multiple pKa values may exist for molecules
      with multiple ionizable groups.
    title: pKa ionization constant
    comments:
    - Lower pKa values indicate stronger acids
    - For molecules with multiple ionizable groups, this field can contain multiple
      values
    - 'Standard conditions: aqueous solution at 25°C'
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: molecular_property
    alias: pka_ionization_constant
    owner: NaturalProduct
    domain_of:
    - ChemicalEntity
    range: float
    multivalued: true
  pka_temperature:
    name: pka_temperature
    description: Temperature in Celsius at which pKa was measured. Default is 25°C
      if not specified.
    title: pKa temperature
    comments:
    - Standard temperature is 25°C (298.15 K)
    - pKa values can shift significantly with temperature following the van't Hoff
      equation
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: molecular_property
    alias: pka_temperature
    owner: NaturalProduct
    domain_of:
    - ChemicalEntity
    range: float
    unit:
      ucum_code: Cel
  pka_ionic_strength:
    name: pka_ionic_strength
    description: Ionic strength of solution in mol/L at which pKa was measured. Default
      is 0.0 M if not specified.
    title: pKa ionic strength
    comments:
    - Standard ionic strength is 0.0 M (zero ionic strength corresponding to distilled
      water)
    - Salt concentration affects pKa through electrostatic shielding of charges
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: molecular_property
    alias: pka_ionic_strength
    owner: NaturalProduct
    domain_of:
    - ChemicalEntity
    range: float
    unit:
      ucum_code: mol/L
  pka_solvent:
    name: pka_solvent
    description: Solvent system for pKa measurement. Default is water (H₂O) if not
      specified.
    title: pKa solvent
    comments:
    - Standard solvent is water (H₂O)
    - pKa values in non-aqueous solvents can be dramatically different due to polarity
      effects
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: molecular_property
    alias: pka_solvent
    owner: NaturalProduct
    domain_of:
    - ChemicalEntity
    range: string
  pka_pressure:
    name: pka_pressure
    description: Pressure in atmospheres at which pKa was measured. Default is 1 atm
      if not specified.
    title: pKa pressure
    comments:
    - Standard pressure is 1 atm
    - Generally minor effect under standard laboratory conditions
    from_schema: https://w3id.org/chemrof
    rank: 1000
    is_a: molecular_property
    alias: pka_pressure
    owner: NaturalProduct
    domain_of:
    - ChemicalEntity
    range: float
    unit:
      ucum_code: atm
  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: NaturalProduct
    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: NaturalProduct
    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: NaturalProduct
    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: NaturalProduct
    domain_of:
    - DomainEntity
    range: uriorcurie