Class: chemical entity (ChemicalEntity)
A discrete structure that is one or more atoms that can be described by a chemical formula.
- NOTE: this is an abstract class and should not be instantiated directly
classDiagram
class ChemicalEntity
OwlClass <|-- ChemicalEntity
PhysicochemicalEntity <|-- ChemicalEntity
ChemicalEntity <|-- PolyatomicEntity
ChemicalEntity <|-- Atom
ChemicalEntity : empirical_formula
ChemicalEntity : has_chemical_role
ChemicalEntity --> ChemicalRole : has_chemical_role
ChemicalEntity : has_physiologically_stable_form
ChemicalEntity --> MoleculeByChargeState : has_physiologically_stable_form
ChemicalEntity : id
ChemicalEntity : inchi_chemical_sublayer
ChemicalEntity : inchi_string
ChemicalEntity : is_radical
ChemicalEntity : IUPAC_name
ChemicalEntity : name
ChemicalEntity : owl_subclass_of
ChemicalEntity --> OwlClass : owl_subclass_of
ChemicalEntity : smiles_string
ChemicalEntity : type
Inheritance
- DomainEntity
- PhysicochemicalEntity
- ChemicalEntity [ OwlClass]
- PhysicochemicalEntity
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| IUPAC_name | 0..1 String |
direct | |
| is_radical | 0..1 Boolean |
direct | |
| has_chemical_role | 0..1 ChemicalRole |
direct | |
| inchi_string | 0..1 ChemicalEncoding |
direct | |
| inchi_chemical_sublayer | 0..1 recommended String |
The part of an InChI string that represents the chemical formula, occurring a... | direct |
| smiles_string | 0..* ChemicalEncoding |
A string encoding of a molecular graph, no chiral or isotopic information | direct |
| empirical_formula | 0..1 ChemicalEncoding |
A chemical formula where numbers denote relative proportion of atoms | direct |
| has_physiologically_stable_form | 0..* MoleculeByChargeState |
connects an acid to the form that is stable at physiological pH (7 | direct |
| 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 |
Usages
Aliases
- specific chemical entity
- chemical
- chemical species
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]
Identifier and Mapping Information
Valid ID Prefixes
Instances of this class should have identifiers with one of the following prefixes:
-
CHEBI
-
CHEMBL.COMPOUND
-
DRUGBANK
-
PUBCHEM.COMPOUND
-
MESH
-
HMDB
-
INCHI
-
INCHIKEY
-
UNII
-
KEGG
-
SEED
-
MetaNetX.chemical
Schema Source
- from schema: https://w3id.org/chemrof
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | chemrof:ChemicalEntity |
| native | chemrof:ChemicalEntity |
| exact | SIO:010004, wdeschema:E239 |
| undefined | CHEBI:24431, CHEMINF:000000, OntoRxn:ChemSpecies |
LinkML Source
Direct
name: ChemicalEntity
id_prefixes:
- CHEBI
- CHEMBL.COMPOUND
- DRUGBANK
- PUBCHEM.COMPOUND
- MESH
- HMDB
- INCHI
- INCHIKEY
- UNII
- KEGG
- SEED
- MetaNetX.chemical
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_physiologically_stable_form
slot_usage:
inchi_chemical_sublayer:
name: inchi_chemical_sublayer
domain_of:
- ChemicalEntity
- StandardInchiObject
- EntityWithAtomsEnumerated
required: false
recommended: true
unique_keys:
smiles:
unique_key_name: smiles
unique_key_slots:
- smiles_string
Induced
name: ChemicalEntity
id_prefixes:
- CHEBI
- CHEMBL.COMPOUND
- DRUGBANK
- PUBCHEM.COMPOUND
- MESH
- HMDB
- INCHI
- INCHIKEY
- UNII
- KEGG
- SEED
- MetaNetX.chemical
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
domain_of:
- ChemicalEntity
- StandardInchiObject
- EntityWithAtomsEnumerated
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
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: 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
multivalued: true
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_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: ChemicalEntity
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: 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:
unique_key_name: smiles
unique_key_slots:
- smiles_string