Class: molecule (Molecule)
A chemical entity that consists of two or more atoms where all atoms are connected via covalent bonds.
URI: chemrof:Molecule
classDiagram
class Molecule
click Molecule href "../Molecule"
FullyCovalentlyBonded <|-- Molecule
click FullyCovalentlyBonded href "../FullyCovalentlyBonded"
PolyatomicEntity <|-- Molecule
click PolyatomicEntity href "../PolyatomicEntity"
Molecule <|-- SmallMolecule
click SmallMolecule href "../SmallMolecule"
Molecule <|-- Macromolecule
click Macromolecule href "../Macromolecule"
Molecule <|-- NaturalProduct
click NaturalProduct href "../NaturalProduct"
Molecule <|-- MolecularSpecies
click MolecularSpecies href "../MolecularSpecies"
Molecule <|-- NonSpeciesMolecule
click NonSpeciesMolecule href "../NonSpeciesMolecule"
Molecule <|-- MoleculeByChargeState
click MoleculeByChargeState href "../MoleculeByChargeState"
Molecule <|-- Ester
click Ester href "../Ester"
Molecule <|-- Stereoisomer
click Stereoisomer href "../Stereoisomer"
Molecule <|-- Allotrope
click Allotrope href "../Allotrope"
Molecule : empirical_formula
Molecule : has_atom_occurrences
Molecule --> "2..*" AtomOccurrence : has_atom_occurrences
click AtomOccurrence href "../AtomOccurrence"
Molecule : has_atoms
Molecule --> "*" Atom : has_atoms
click Atom href "../Atom"
Molecule : has_bonds
Molecule --> "*" AtomicBond : has_bonds
click AtomicBond href "../AtomicBond"
Molecule : has_chemical_role
Molecule --> "0..1" ChemicalRole : has_chemical_role
click ChemicalRole href "../ChemicalRole"
Molecule : has_physiologically_stable_form
Molecule --> "*" MoleculeByChargeState : has_physiologically_stable_form
click MoleculeByChargeState href "../MoleculeByChargeState"
Molecule : has_submolecules
Molecule --> "*" Molecule : has_submolecules
click Molecule href "../Molecule"
Molecule : id
Molecule : inchi_atom_connections_sublayer
Molecule : inchi_chemical_sublayer
Molecule : inchi_string
Molecule : is_organic
Molecule : is_radical
Molecule : IUPAC_name
Molecule : name
Molecule : owl_subclass_of
Molecule --> "0..1" OwlClass : owl_subclass_of
click OwlClass href "../OwlClass"
Molecule : smiles_string
Molecule : type
Inheritance
Slots
| Name | Cardinality and Range | Description | Inheritance |
|---|---|---|---|
| has_atom_occurrences | 2..* AtomOccurrence |
An individuated atom in the context of a chemical structure | direct |
| has_bonds | * AtomicBond |
The set of all bonds connecting atoms in a molecule | direct |
| has_submolecules | * Molecule |
Relation between a molecule and the molecules it is made from | direct |
| has_atoms | * Atom |
Relation between a molecule and the atoms it contains | direct |
| is_organic | 0..1 Boolean |
An organic molecule is a molecule composed of organic atoms (at least carbon,... | 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
Aliases
- molecular entity
- monomolecular entity
Examples
| Value |
|---|
| dioxygen |
| cysteine |
| phosphene |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/chemrof
Mappings
| Mapping Type | Mapped Value |
|---|---|
| self | chemrof:Molecule |
| native | chemrof:Molecule |
| exact | SIO:011125, biotop:MonoMolecularEntity, gc:Molecule |
| undefined | COB:0000013 |
LinkML Source
Direct
name: Molecule
description: A chemical entity that consists of two or more atoms where all atoms
are connected via covalent bonds.
title: molecule
examples:
- value: dioxygen
- value: cysteine
- value: phosphene
from_schema: https://w3id.org/chemrof
aliases:
- molecular entity
- monomolecular entity
mappings:
- COB:0000013
exact_mappings:
- SIO:011125
- biotop:MonoMolecularEntity
- gc:Molecule
is_a: PolyatomicEntity
mixins:
- FullyCovalentlyBonded
slots:
- has_atom_occurrences
- has_bonds
- has_submolecules
- has_atoms
- is_organic
slot_usage:
has_atom_occurrences:
name: has_atom_occurrences
domain_of:
- Molecule
minimum_cardinality: 2
has_bonds:
name: has_bonds
description: The set of all bonds connecting atoms in a molecule
aliases:
- adjacency matrix
domain_of:
- Molecule
has_part:
name: has_part
minimum_value: 1
Induced
name: Molecule
description: A chemical entity that consists of two or more atoms where all atoms
are connected via covalent bonds.
title: molecule
examples:
- value: dioxygen
- value: cysteine
- value: phosphene
from_schema: https://w3id.org/chemrof
aliases:
- molecular entity
- monomolecular entity
mappings:
- COB:0000013
exact_mappings:
- SIO:011125
- biotop:MonoMolecularEntity
- gc:Molecule
is_a: PolyatomicEntity
mixins:
- FullyCovalentlyBonded
slot_usage:
has_atom_occurrences:
name: has_atom_occurrences
domain_of:
- Molecule
minimum_cardinality: 2
has_bonds:
name: has_bonds
description: The set of all bonds connecting atoms in a molecule
aliases:
- adjacency matrix
domain_of:
- Molecule
has_part:
name: has_part
minimum_value: 1
attributes:
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: Molecule
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: Molecule
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: Molecule
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: Molecule
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: Molecule
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: Molecule
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: Molecule
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: Molecule
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: Molecule
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: Molecule
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: Molecule
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: Molecule
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: Molecule
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: Molecule
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: Molecule
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: Molecule
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: Molecule
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: Molecule
domain_of:
- DomainEntity
range: uriorcurie