Class: imprecise chemical mixture (ImpreciseChemicalMixture)
A macroscopic polyatomic entity that consists of multiple chemical entities where the stoichiometry is not specified and the spatial arrangement of the ingredients is not defined. Examples include coal, tea tree oil, toothpaste, organometallic compounds, heterogeneous metals
URI: chemrof:ImpreciseChemicalMixture
classDiagram
class ImpreciseChemicalMixture
click ImpreciseChemicalMixture href "../ImpreciseChemicalMixture"
ChemicalMixture <|-- ImpreciseChemicalMixture
click ChemicalMixture href "../ChemicalMixture"
ImpreciseChemicalMixture : empirical_formula
ImpreciseChemicalMixture : has_chemical_role
ImpreciseChemicalMixture --> "0..1" ChemicalRole : has_chemical_role
click ChemicalRole href "../ChemicalRole"
ImpreciseChemicalMixture : has_minchi_representation
ImpreciseChemicalMixture : has_mixfile_location
ImpreciseChemicalMixture : has_physiologically_stable_form
ImpreciseChemicalMixture --> "*" MoleculeByChargeState : has_physiologically_stable_form
click MoleculeByChargeState href "../MoleculeByChargeState"
ImpreciseChemicalMixture : has_proportional_parts
ImpreciseChemicalMixture --> "*" ProportionalPart : has_proportional_parts
click ProportionalPart href "../ProportionalPart"
ImpreciseChemicalMixture : id
ImpreciseChemicalMixture : inchi_atom_connections_sublayer
ImpreciseChemicalMixture : inchi_chemical_sublayer
ImpreciseChemicalMixture : inchi_string
ImpreciseChemicalMixture : is_radical
ImpreciseChemicalMixture : IUPAC_name
ImpreciseChemicalMixture : name
ImpreciseChemicalMixture : owl_subclass_of
ImpreciseChemicalMixture --> "0..1" OwlClass : owl_subclass_of
click OwlClass href "../OwlClass"
ImpreciseChemicalMixture : smiles_string
ImpreciseChemicalMixture : type
Inheritance
- DomainEntity
- PhysicochemicalEntity
- ChemicalEntity [ OwlClass]
- PolyatomicEntity
- ChemicalMixture
- ImpreciseChemicalMixture
- ChemicalMixture
- PolyatomicEntity
- ChemicalEntity [ OwlClass]
- PhysicochemicalEntity
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
has_proportional_parts | * ProportionalPart |
Relationship between a complex mixture and its parts | direct |
has_mixfile_location | 0..1 FileLocation |
Location of a MixFile representing a chemical mixture | direct |
has_minchi_representation | 0..1 ChemicalEncoding |
Proposed new Mixtures InChI | direct |
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 | * 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 | * 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 String |
DomainEntity | |
name | 0..1 String |
name of chemical entity | DomainEntity |
type | 0..1 Uriorcurie |
DomainEntity |
Usages
used by | used in | type | used |
---|---|---|---|
ImpreciseChemicalMixture | has_proportional_parts | domain | ImpreciseChemicalMixture |
Aliases
- portion of matter
Examples
Value |
---|
toothpaste (sodium fluoride 0.243 w/v%[active] + H2O[inactive] + ... ) |
Comments
- although the stoichiometry is not known rough percentage parts can be provided
See Also
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/chemrof
Mappings
Mapping Type | Mapped Value |
---|---|
self | chemrof:ImpreciseChemicalMixture |
native | chemrof:ImpreciseChemicalMixture |
LinkML Source
Direct
name: ImpreciseChemicalMixture
description: A macroscopic polyatomic entity that consists of multiple chemical entities
where the stoichiometry is not specified and the spatial arrangement of the ingredients
is not defined. Examples include coal, tea tree oil, toothpaste, organometallic
compounds, heterogeneous metals
title: imprecise chemical mixture
comments:
- although the stoichiometry is not known rough percentage parts can be provided
examples:
- value: toothpaste (sodium fluoride 0.243 w/v%[active] + H2O[inactive] + ... )
from_schema: https://w3id.org/chemrof
see_also:
- https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0357-4
aliases:
- portion of matter
is_a: ChemicalMixture
slots:
- has_proportional_parts
- has_mixfile_location
- has_minchi_representation
Induced
name: ImpreciseChemicalMixture
description: A macroscopic polyatomic entity that consists of multiple chemical entities
where the stoichiometry is not specified and the spatial arrangement of the ingredients
is not defined. Examples include coal, tea tree oil, toothpaste, organometallic
compounds, heterogeneous metals
title: imprecise chemical mixture
comments:
- although the stoichiometry is not known rough percentage parts can be provided
examples:
- value: toothpaste (sodium fluoride 0.243 w/v%[active] + H2O[inactive] + ... )
from_schema: https://w3id.org/chemrof
see_also:
- https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0357-4
aliases:
- portion of matter
is_a: ChemicalMixture
attributes:
has_proportional_parts:
name: has_proportional_parts
description: Relationship between a complex mixture and its parts
title: has proportional parts
from_schema: https://w3id.org/chemrof
aliases:
- has ingredients
rank: 1000
domain: ImpreciseChemicalMixture
alias: has_proportional_parts
owner: ImpreciseChemicalMixture
domain_of:
- ImpreciseChemicalMixture
range: ProportionalPart
multivalued: true
has_mixfile_location:
name: has_mixfile_location
description: Location of a MixFile representing a chemical mixture
title: has mixfile location
from_schema: https://w3id.org/chemrof
see_also:
- https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0357-4
- https://github.com/cdd/mixtures
rank: 1000
is_a: information_property
alias: has_mixfile_location
owner: ImpreciseChemicalMixture
domain_of:
- ImpreciseChemicalMixture
range: FileLocation
has_minchi_representation:
name: has_minchi_representation
description: Proposed new Mixtures InChI
title: has minchi representation
from_schema: https://w3id.org/chemrof
see_also:
- https://cheminf20.org/2018/08/27/mixtures-cheminformatics/
aliases:
- MInChi
rank: 1000
is_a: chemical_representation
domain: ChemicalEntity
alias: has_minchi_representation
owner: ImpreciseChemicalMixture
domain_of:
- ImpreciseChemicalMixture
range: ChemicalEncoding
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: ImpreciseChemicalMixture
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: ImpreciseChemicalMixture
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: ImpreciseChemicalMixture
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: ImpreciseChemicalMixture
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: ImpreciseChemicalMixture
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: ImpreciseChemicalMixture
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: ImpreciseChemicalMixture
domain_of:
- ChemicalEntity
range: ChemicalEncoding
multivalued: true
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: ImpreciseChemicalMixture
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
alias: has_physiologically_stable_form
owner: ImpreciseChemicalMixture
domain_of:
- ChemicalEntity
range: MoleculeByChargeState
multivalued: true
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: ImpreciseChemicalMixture
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: ImpreciseChemicalMixture
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: ImpreciseChemicalMixture
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: ImpreciseChemicalMixture
domain_of:
- DomainEntity
range: uriorcurie