Class: Portion of a Substance (PortionOfSubstance)

A portion of any matter of defined composition that has discrete existence, whose origin may be biological, mineral or chemical.

URI: nmdc:PortionOfSubstance

classDiagram class PortionOfSubstance click PortionOfSubstance href "../PortionOfSubstance" PortionOfSubstance : final_concentration PortionOfSubstance --> "0..1" QuantityValue : final_concentration click QuantityValue href "../QuantityValue" PortionOfSubstance : known_as PortionOfSubstance --> "0..1" ChemicalEntity : known_as click ChemicalEntity href "../ChemicalEntity" PortionOfSubstance : mass PortionOfSubstance --> "0..1" QuantityValue : mass click QuantityValue href "../QuantityValue" PortionOfSubstance : sample_state_information PortionOfSubstance --> "0..1" SampleStateEnum : sample_state_information click SampleStateEnum href "../SampleStateEnum" PortionOfSubstance : source_concentration PortionOfSubstance --> "0..1" QuantityValue : source_concentration click QuantityValue href "../QuantityValue" PortionOfSubstance : substance_role PortionOfSubstance --> "0..1" SubstanceRoleEnum : substance_role click SubstanceRoleEnum href "../SubstanceRoleEnum" PortionOfSubstance : type PortionOfSubstance : volume PortionOfSubstance --> "0..1" QuantityValue : volume click QuantityValue href "../QuantityValue"

Slots

Name	Cardinality and Range	Description	Inheritance
final_concentration	0..1 QuantityValue	When solutions A (containing substance X) and B are combined together, this s...	direct
known_as	0..1 ChemicalEntity		direct
mass	0..1 QuantityValue	A physical quality that inheres in a bearer by virtue of the proportion of th...	direct
sample_state_information	0..1 SampleStateEnum	The chemical phase of a pure sample, or the state of a mixed sample	direct
source_concentration	0..1 QuantityValue	When solutions A (containing substance X) and B are combined together, this s...	direct
substance_role	0..1 SubstanceRoleEnum	The role of a substance in a process	direct
type	1 Uriorcurie	the class_uri of the class that has been instantiated	direct
volume	0..1 QuantityValue	The volume of a substance	direct

Usages

used by	used in	type	used
Extraction	substances_used	range	PortionOfSubstance
StorageProcess	substances_used	range	PortionOfSubstance
DissolvingProcess	substances_used	range	PortionOfSubstance
ChemicalConversionProcess	substances_used	range	PortionOfSubstance
MobilePhaseSegment	substances_used	range	PortionOfSubstance

Identifier and Mapping Information

Schema Source

from schema: https://w3id.org/nmdc/nmdc

Mappings

Mapping Type	Mapped Value
self	nmdc:PortionOfSubstance
native	nmdc:PortionOfSubstance
undefined	schema:Substance

LinkML Source

Direct

name: PortionOfSubstance
description: A portion of any matter of defined composition that has discrete existence,
  whose origin may be biological, mineral or chemical.
title: Portion of a Substance
from_schema: https://w3id.org/nmdc/nmdc
mappings:
- schema:Substance
slots:
- final_concentration
- known_as
- mass
- sample_state_information
- source_concentration
- substance_role
- type
- volume
class_uri: nmdc:PortionOfSubstance

Induced

name: PortionOfSubstance
description: A portion of any matter of defined composition that has discrete existence,
  whose origin may be biological, mineral or chemical.
title: Portion of a Substance
from_schema: https://w3id.org/nmdc/nmdc
mappings:
- schema:Substance
attributes:
  final_concentration:
    name: final_concentration
    description: When solutions A (containing substance X) and B are combined together,
      this slot captures the concentration of X in the combination
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    is_a: concentration
    alias: final_concentration
    owner: PortionOfSubstance
    domain_of:
    - PortionOfSubstance
    range: QuantityValue
  known_as:
    name: known_as
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: known_as
    owner: PortionOfSubstance
    domain_of:
    - PortionOfSubstance
    range: ChemicalEntity
  mass:
    name: mass
    description: A physical quality that inheres in a bearer by virtue of the proportion
      of the bearer's amount of matter.
    title: mass
    from_schema: https://w3id.org/nmdc/nmdc
    exact_mappings:
    - PATO:0000125
    rank: 1000
    alias: mass
    owner: PortionOfSubstance
    domain_of:
    - SubSamplingProcess
    - PortionOfSubstance
    range: QuantityValue
  sample_state_information:
    name: sample_state_information
    description: The chemical phase of a pure sample, or the state of a mixed sample
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: sample_state_information
    owner: PortionOfSubstance
    domain_of:
    - PortionOfSubstance
    range: SampleStateEnum
  source_concentration:
    name: source_concentration
    description: When solutions A (containing substance X) and B are combined together,
      this slot captures the concentration of X in solution A
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    is_a: concentration
    alias: source_concentration
    owner: PortionOfSubstance
    domain_of:
    - PortionOfSubstance
    range: QuantityValue
  substance_role:
    name: substance_role
    description: The role of a substance in a process
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: substance_role
    owner: PortionOfSubstance
    domain_of:
    - PortionOfSubstance
    range: SubstanceRoleEnum
  type:
    name: type
    description: the class_uri of the class that has been instantiated
    notes:
    - replaces legacy nmdc:type slot
    - makes it easier to read example data files
    - required for polymorphic MongoDB collections
    examples:
    - value: nmdc:Biosample
    - value: nmdc:Study
    from_schema: https://w3id.org/nmdc/nmdc
    see_also:
    - https://github.com/microbiomedata/nmdc-schema/issues/1048
    - https://github.com/microbiomedata/nmdc-schema/issues/1233
    - https://github.com/microbiomedata/nmdc-schema/issues/248
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: type
    owner: PortionOfSubstance
    domain_of:
    - FunctionalAnnotationAggMember
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - PeptideQuantification
    - ProteinQuantification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
  volume:
    name: volume
    description: The volume of a substance.
    from_schema: https://w3id.org/nmdc/nmdc
    contributors:
    - ORCID:0009-0001-1555-1601
    - ORCID:0000-0002-8683-0050
    rank: 1000
    alias: volume
    owner: PortionOfSubstance
    domain_of:
    - Extraction
    - SubSamplingProcess
    - FiltrationProcess
    - MobilePhaseSegment
    - PortionOfSubstance
    range: QuantityValue
class_uri: nmdc:PortionOfSubstance