Skip to content

Class: Extraction

A material separation in which a desired component of an input material is separated from the remainder.

URI: nmdc:Extraction

classDiagram class Extraction click Extraction href "../Extraction" MaterialProcessing <|-- Extraction click MaterialProcessing href "../MaterialProcessing" Extraction : alternative_identifiers Extraction : description Extraction : end_date Extraction : extraction_targets Extraction --> "*" ExtractionTargetEnum : extraction_targets click ExtractionTargetEnum href "../ExtractionTargetEnum" Extraction : has_failure_categorization Extraction --> "*" FailureCategorization : has_failure_categorization click FailureCategorization href "../FailureCategorization" Extraction : has_input Extraction --> "1..*" NamedThing : has_input click NamedThing href "../NamedThing" Extraction : has_output Extraction --> "1..*" ProcessedSample : has_output click ProcessedSample href "../ProcessedSample" Extraction : id Extraction : input_mass Extraction --> "0..1" QuantityValue : input_mass click QuantityValue href "../QuantityValue" Extraction : instrument_used Extraction --> "*" Instrument : instrument_used click Instrument href "../Instrument" Extraction : name Extraction : processing_institution Extraction --> "0..1" ProcessingInstitutionEnum : processing_institution click ProcessingInstitutionEnum href "../ProcessingInstitutionEnum" Extraction : protocol_link Extraction --> "0..1" Protocol : protocol_link click Protocol href "../Protocol" Extraction : qc_comment Extraction : qc_status Extraction --> "0..1" StatusEnum : qc_status click StatusEnum href "../StatusEnum" Extraction : start_date Extraction : substances_used Extraction --> "*" PortionOfSubstance : substances_used click PortionOfSubstance href "../PortionOfSubstance" Extraction : type Extraction : volume Extraction --> "0..1" QuantityValue : volume click QuantityValue href "../QuantityValue"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
substances_used *
PortionOfSubstance		 The substances that are combined to enable a ChemicalConversionProcess direct
extraction_targets *
ExtractionTargetEnum		 Provides the target biomolecule that has been separated from a sample during ... direct
input_mass 0..1
QuantityValue		 Total mass of sample used in activity direct
volume 0..1
QuantityValue		 The volume of the solvent/solute being used, not the input direct
instrument_used *
Instrument		 What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing
has_input 1..*
NamedThing or 
Biosample or 
ProcessedSample		 An input to a process PlannedProcess
has_output 1..*
ProcessedSample		 An output from a process PlannedProcess
processing_institution 0..1
ProcessingInstitutionEnum		 The organization that processed the sample PlannedProcess
protocol_link 0..1
Protocol		 PlannedProcess
start_date 0..1
String		 The date on which any process or activity was started PlannedProcess
end_date 0..1
String		 The date on which any process or activity was ended PlannedProcess
qc_status 0..1
StatusEnum		 Stores information about the result of a process (ie the process of sequencin... PlannedProcess
qc_comment 0..1
String		 Slot to store additional comments about laboratory or workflow output PlannedProcess
has_failure_categorization *
FailureCategorization		 PlannedProcess
id 1
Uriorcurie		 A unique identifier for a thing NamedThing
name 0..1
String		 A human readable label for an entity NamedThing
description 0..1
String		 a human-readable description of a thing NamedThing
alternative_identifiers *
Uriorcurie		 A list of alternative identifiers for the entity NamedThing
type 1
Uriorcurie		 the class_uri of the class that has been instantiated NamedThing

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self nmdc:Extraction
native nmdc:Extraction
exact OBI:0302884

LinkML Source

Direct

name: Extraction
description: A material separation in which a desired component of an input material
  is separated from the remainder.
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- OBI:0302884
is_a: MaterialProcessing
slots:
- substances_used
- extraction_targets
- input_mass
- volume
slot_usage:
  has_input:
    name: has_input
    domain_of:
    - PlannedProcess
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
    any_of:
    - range: Biosample
    - range: ProcessedSample
  has_output:
    name: has_output
    domain_of:
    - PlannedProcess
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
  id:
    name: id
    domain_of:
    - NamedThing
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$'
      interpolated: true
  volume:
    name: volume
    description: The volume of the solvent/solute being used, not the input.
    domain_of:
    - Extraction
    - SubSamplingProcess
    - FiltrationProcess
    - MobilePhaseSegment
    - PortionOfSubstance
class_uri: nmdc:Extraction

Induced

name: Extraction
description: A material separation in which a desired component of an input material
  is separated from the remainder.
from_schema: https://w3id.org/nmdc/nmdc
exact_mappings:
- OBI:0302884
is_a: MaterialProcessing
slot_usage:
  has_input:
    name: has_input
    domain_of:
    - PlannedProcess
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
    any_of:
    - range: Biosample
    - range: ProcessedSample
  has_output:
    name: has_output
    domain_of:
    - PlannedProcess
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
  id:
    name: id
    domain_of:
    - NamedThing
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$'
      interpolated: true
  volume:
    name: volume
    description: The volume of the solvent/solute being used, not the input.
    domain_of:
    - Extraction
    - SubSamplingProcess
    - FiltrationProcess
    - MobilePhaseSegment
    - PortionOfSubstance
attributes:
  substances_used:
    name: substances_used
    description: The substances that are combined to enable a ChemicalConversionProcess.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    multivalued: true
    alias: substances_used
    owner: Extraction
    domain_of:
    - Extraction
    - StorageProcess
    - DissolvingProcess
    - ChemicalConversionProcess
    - MobilePhaseSegment
    range: PortionOfSubstance
    inlined: true
    inlined_as_list: true
  extraction_targets:
    name: extraction_targets
    description: Provides the target biomolecule that has been separated from a sample
      during an extraction process.
    notes:
    - todos, remove nucl_acid_ext from OmicsProcessing (DataGeneration)
    from_schema: https://w3id.org/nmdc/nmdc
    narrow_mappings:
    - NCIT:C177560
    - MIXS:0000037
    rank: 1000
    multivalued: true
    alias: extraction_targets
    owner: Extraction
    domain_of:
    - Extraction
    range: ExtractionTargetEnum
  input_mass:
    name: input_mass
    description: Total mass of sample used in activity.
    title: sample mass used
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - sample mass
    - sample weight
    exact_mappings:
    - MS:1000004
    narrow_mappings:
    - MIXS:0000111
    rank: 1000
    alias: input_mass
    owner: Extraction
    domain_of:
    - Extraction
    range: QuantityValue
  volume:
    name: volume
    description: The volume of the solvent/solute being used, not the input.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: volume
    owner: Extraction
    domain_of:
    - Extraction
    - SubSamplingProcess
    - FiltrationProcess
    - MobilePhaseSegment
    - PortionOfSubstance
    range: QuantityValue
  instrument_used:
    name: instrument_used
    description: What instrument was used during DataGeneration or MaterialProcessing.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    multivalued: true
    alias: instrument_used
    owner: Extraction
    domain_of:
    - MaterialProcessing
    - DataGeneration
    range: Instrument
  has_input:
    name: has_input
    description: An input to a process.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    multivalued: true
    alias: has_input
    owner: Extraction
    domain_of:
    - PlannedProcess
    range: NamedThing
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
    any_of:
    - range: Biosample
    - range: ProcessedSample
  has_output:
    name: has_output
    description: An output from a process.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    multivalued: true
    alias: has_output
    owner: Extraction
    domain_of:
    - PlannedProcess
    range: ProcessedSample
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
  processing_institution:
    name: processing_institution
    description: The organization that processed the sample.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: processing_institution
    owner: Extraction
    domain_of:
    - PlannedProcess
    range: ProcessingInstitutionEnum
  protocol_link:
    name: protocol_link
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: protocol_link
    owner: Extraction
    domain_of:
    - PlannedProcess
    - Study
    range: Protocol
  start_date:
    name: start_date
    description: The date on which any process or activity was started
    todos:
    - add date string validation pattern
    comments:
    - We are using string representations of dates until all components of our ecosystem
      can handle ISO 8610 dates
    - The date should be formatted as YYYY-MM-DD
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: start_date
    owner: Extraction
    domain_of:
    - PlannedProcess
    range: string
  end_date:
    name: end_date
    description: The date on which any process or activity was ended
    todos:
    - add date string validation pattern
    comments:
    - We are using string representations of dates until all components of our ecosystem
      can handle ISO 8610 dates
    - The date should be formatted as YYYY-MM-DD
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: end_date
    owner: Extraction
    domain_of:
    - PlannedProcess
    range: string
  qc_status:
    name: qc_status
    description: Stores information about the result of a process (ie the process
      of sequencing a library may have for qc_status of 'fail' if not enough data
      was generated)
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: qc_status
    owner: Extraction
    domain_of:
    - PlannedProcess
    range: StatusEnum
  qc_comment:
    name: qc_comment
    description: Slot to store additional comments about laboratory or workflow output.
      For workflow output it may describe the particular workflow stage that failed.
      (ie Failed at call-stage due to a malformed fastq file).
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: qc_comment
    owner: Extraction
    domain_of:
    - PlannedProcess
    range: string
  has_failure_categorization:
    name: has_failure_categorization
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    multivalued: true
    alias: has_failure_categorization
    owner: Extraction
    domain_of:
    - PlannedProcess
    range: FailureCategorization
    inlined: true
    inlined_as_list: true
  id:
    name: id
    description: A unique identifier for a thing. Must be either a CURIE shorthand
      for a URI or a complete URI
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    identifier: true
    alias: id
    owner: Extraction
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
    structured_pattern:
      syntax: '{id_nmdc_prefix}:extrp-{id_shoulder}-{id_blade}$'
      interpolated: true
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: name
    owner: Extraction
    domain_of:
    - PersonValue
    - NamedThing
    - Protocol
    range: string
  description:
    name: description
    description: a human-readable description of a thing
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: Extraction
    domain_of:
    - ImageValue
    - NamedThing
    range: string
  alternative_identifiers:
    name: alternative_identifiers
    description: A list of alternative identifiers for the entity.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    multivalued: true
    alias: alternative_identifiers
    owner: Extraction
    domain_of:
    - MetaboliteIdentification
    - NamedThing
    range: uriorcurie
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
  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: Extraction
    domain_of:
    - FunctionalAnnotationAggMember
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - PeptideQuantification
    - ProteinQuantification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
class_uri: nmdc:Extraction