Class: ChemicalSubstanceMixin

A LinkML mixin used to pass down properties common to all material entities that are described in a chemical context via being composed of chemical entities (e.g. atom, molecule, ion, ion pair, radical, complex, conformer etc., ) of the same type or of different types.

NOTE: this is an abstract class and should not be instantiated directly

URI: coremeta4cat:class/ChemicalSubstanceMixin

 classDiagram
    class ChemicalSubstanceMixin
    click ChemicalSubstanceMixin href "../../classes/ChemicalSubstanceMixin/"
      MaterialisticMixin <|-- ChemicalSubstanceMixin
        click MaterialisticMixin href "../../classes/MaterialisticMixin/"


      ChemicalSubstanceMixin <|-- SubstanceSample
        click SubstanceSample href "../../classes/SubstanceSample/"
      ChemicalSubstanceMixin <|-- PolymerMixin
        click PolymerMixin href "../../classes/PolymerMixin/"
      ChemicalSubstanceMixin <|-- StartingMaterial
        click StartingMaterial href "../../classes/StartingMaterial/"
      ChemicalSubstanceMixin <|-- DissolvingSubstance
        click DissolvingSubstance href "../../classes/DissolvingSubstance/"
      ChemicalSubstanceMixin <|-- Reagent
        click Reagent href "../../classes/Reagent/"
      ChemicalSubstanceMixin <|-- ChemicalProduct
        click ChemicalProduct href "../../classes/ChemicalProduct/"
      ChemicalSubstanceMixin <|-- Catalyst
        click Catalyst href "../../classes/Catalyst/"


      ChemicalSubstanceMixin : alternative_label

      ChemicalSubstanceMixin : composed_of





        ChemicalSubstanceMixin --> "* _recommended_" ChemicalEntity : composed_of
        click ChemicalEntity href "../../classes/ChemicalEntity/"



      ChemicalSubstanceMixin : has_amount





        ChemicalSubstanceMixin --> "* _recommended_" AmountOfSubstance : has_amount
        click AmountOfSubstance href "../../classes/AmountOfSubstance/"



      ChemicalSubstanceMixin : has_concentration





        ChemicalSubstanceMixin --> "* _recommended_" Concentration : has_concentration
        click Concentration href "../../classes/Concentration/"



      ChemicalSubstanceMixin : has_density





        ChemicalSubstanceMixin --> "* _recommended_" Density : has_density
        click Density href "../../classes/Density/"



      ChemicalSubstanceMixin : has_mass





        ChemicalSubstanceMixin --> "* _recommended_" Mass : has_mass
        click Mass href "../../classes/Mass/"



      ChemicalSubstanceMixin : has_ph_value





        ChemicalSubstanceMixin --> "* _recommended_" PHValue : has_ph_value
        click PHValue href "../../classes/PHValue/"



      ChemicalSubstanceMixin : has_physical_state





        ChemicalSubstanceMixin --> "0..1" PhysicalStateEnum : has_physical_state
        click PhysicalStateEnum href "../../enums/PhysicalStateEnum/"



      ChemicalSubstanceMixin : has_pressure





        ChemicalSubstanceMixin --> "* _recommended_" Pressure : has_pressure
        click Pressure href "../../classes/Pressure/"



      ChemicalSubstanceMixin : has_temperature





        ChemicalSubstanceMixin --> "* _recommended_" Temperature : has_temperature
        click Temperature href "../../classes/Temperature/"



      ChemicalSubstanceMixin : has_volume





        ChemicalSubstanceMixin --> "* _recommended_" Volume : has_volume
        click Volume href "../../classes/Volume/"

Inheritance

MaterialisticMixin
- ChemicalSubstanceMixin
  - PolymerMixin

Slots

Name	Cardinality and Range	Description	Inheritance
has_concentration	* recommended Concentration	The slot to provide the Concentration of a ChemicalSubstance.	direct
has_ph_value	* recommended PHValue	The slot to provide the PHValue of a ChemicalSubstance.	direct
composed_of	* recommended ChemicalEntity	The slot to provide the chemical entities of which a ChemicalSubstance is composed of.	direct
has_amount	* recommended AmountOfSubstance	The slot to provide the AmountConcentration of a ChemicalSubstance.	direct
alternative_label	0..1 String	The slot to specify an alternative label, name or title for a MaterialEntity.	MaterialisticMixin
has_physical_state	0..1 PhysicalStateEnum	The slot to specify the physical state of a MaterialEntity.	MaterialisticMixin
has_temperature	* recommended Temperature	The slot to provide the Temperature of a MaterialEntity or an Activity, whereas the temperature of the Activity is ontologically rooted in the temperature of the material entities that participate in the Activity.	MaterialisticMixin
has_mass	* recommended Mass	The slot to provide the Mass of a MaterialEntity.	MaterialisticMixin
has_volume	* recommended Volume	The slot to provide the Volume of a MaterialEntity.	MaterialisticMixin
has_density	* recommended Density	The slot to provide the Density of a MaterialEntity.	MaterialisticMixin
has_pressure	* recommended Pressure	The slot to provide data about the pressure of a MaterialEntity or an Activity, whereas the Pressure of an Activity is ontologically a quality borne by the material entities participating in the Activity.	MaterialisticMixin

Mixin Usage

mixed into	description
SubstanceSample	A MaterialSample derived from a chemical substance that is of interest in an analytical procedure.
StartingMaterial	A ChemicalSubstance with that has a starting material role in a synthesis.
DissolvingSubstance	A liquid ChemicalSubstance that dissolves or that is capable of dissolving a ChemicalSubstance.
Reagent	A ChemicalSubstance that is consumed or transformed in a ChemicalReaction.
ChemicalProduct	A chemical substance that is produced by a ChemicalReaction.
Catalyst	A ChemicalSubstance or MaterialEntity that initiates or accelerates a ChemicalReaction without itself being affected.

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/nfdi4cat/coremeta4cat

Mappings

Mapping Type	Mapped Value
self	coremeta4cat:ChemicalSubstanceMixin
native	coremeta4cat:ChemicalSubstanceMixin

LinkML Source

Direct

name: ChemicalSubstanceMixin
description: A LinkML mixin used to pass down properties common to all material entities
  that are described in a chemical context via being composed of chemical entities
  (e.g. atom, molecule, ion, ion pair, radical, complex, conformer etc., ) of the
  same type or of different types.
from_schema: https://w3id.org/nfdi4cat/coremeta4cat
is_a: MaterialisticMixin
abstract: true
mixin: true
slots:
- has_concentration
- has_ph_value
- composed_of
- has_amount

Induced

name: ChemicalSubstanceMixin
description: A LinkML mixin used to pass down properties common to all material entities
  that are described in a chemical context via being composed of chemical entities
  (e.g. atom, molecule, ion, ion pair, radical, complex, conformer etc., ) of the
  same type or of different types.
from_schema: https://w3id.org/nfdi4cat/coremeta4cat
is_a: MaterialisticMixin
abstract: true
mixin: true
attributes:
  has_concentration:
    name: has_concentration
    description: The slot to provide the Concentration of a ChemicalSubstance.
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008
    alias: has_concentration
    owner: ChemicalSubstanceMixin
    domain_of:
    - ChemicalSubstanceMixin
    range: Concentration
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_ph_value:
    name: has_ph_value
    description: The slot to provide the PHValue of a ChemicalSubstance.
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008
    alias: has_ph_value
    owner: ChemicalSubstanceMixin
    domain_of:
    - ChemicalSubstanceMixin
    range: PHValue
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  composed_of:
    name: composed_of
    description: The slot to provide the chemical entities of which a ChemicalSubstance
      is composed of.
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    close_mappings:
    - AFX:0000940
    rank: 1000
    is_a: has_part
    slot_uri: BFO:0000051
    alias: composed_of
    owner: ChemicalSubstanceMixin
    domain_of:
    - ChemicalSubstanceMixin
    range: ChemicalEntity
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_amount:
    name: has_amount
    description: The slot to provide the AmountConcentration of a ChemicalSubstance.
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008
    alias: has_amount
    owner: ChemicalSubstanceMixin
    domain_of:
    - ChemicalSubstanceMixin
    range: AmountOfSubstance
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  alternative_label:
    name: alternative_label
    description: The slot to specify an alternative label, name or title for a MaterialEntity.
    todos:
    - Should probably rather declared on Entity or in some common metadata mixin instead.
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    slot_uri: skos:altLabel
    alias: alternative_label
    owner: ChemicalSubstanceMixin
    domain_of:
    - MaterialisticMixin
    range: string
  has_physical_state:
    name: has_physical_state
    description: The slot to specify the physical state of a MaterialEntity.
    todos:
    - Find out how to make this a subproperty of has_qualitative_attribute, as it
      currently throws the error 'physical_state enumerations cannot be inlined' due
      to the fact that we are using an enum here.
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    slot_uri: SIO:000008
    alias: has_physical_state
    owner: ChemicalSubstanceMixin
    domain_of:
    - MaterialisticMixin
    range: PhysicalStateEnum
    multivalued: false
    inlined: false
  has_temperature:
    name: has_temperature
    description: The slot to provide the Temperature of a MaterialEntity or an Activity,
      whereas the temperature of the Activity is ontologically rooted in the temperature
      of the material entities that participate in the Activity.
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008
    alias: has_temperature
    owner: ChemicalSubstanceMixin
    domain_of:
    - MaterialisticMixin
    - ChemicalReaction
    range: Temperature
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_mass:
    name: has_mass
    description: The slot to provide the Mass of a MaterialEntity.
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008
    alias: has_mass
    owner: ChemicalSubstanceMixin
    domain_of:
    - MaterialisticMixin
    range: Mass
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_volume:
    name: has_volume
    description: The slot to provide the Volume of a MaterialEntity.
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008
    alias: has_volume
    owner: ChemicalSubstanceMixin
    domain_of:
    - MaterialisticMixin
    range: Volume
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_density:
    name: has_density
    description: The slot to provide the Density of a MaterialEntity.
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008
    alias: has_density
    owner: ChemicalSubstanceMixin
    domain_of:
    - MaterialisticMixin
    range: Density
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_pressure:
    name: has_pressure
    description: The slot to provide data about the pressure of a MaterialEntity or
      an Activity, whereas the Pressure of an Activity is ontologically a quality
      borne by the material entities participating in the Activity.
    from_schema: https://w3id.org/nfdi4cat/coremeta4cat
    rank: 1000
    is_a: has_quantitative_attribute
    slot_uri: SIO:000008
    alias: has_pressure
    owner: ChemicalSubstanceMixin
    domain_of:
    - MaterialisticMixin
    - ChemicalReaction
    range: Pressure
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true