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Class: MaterialProcessing

A process that takes one or more samples as inputs and generates one or more samples as outputs.

Note

This is an abstract class and should not be instantiated directly.

URI: nmdc:MaterialProcessing

classDiagram class MaterialProcessing click MaterialProcessing href "../MaterialProcessing" PlannedProcess <|-- MaterialProcessing click PlannedProcess href "../PlannedProcess" MaterialProcessing <|-- Pooling click Pooling href "../Pooling" MaterialProcessing <|-- Extraction click Extraction href "../Extraction" MaterialProcessing <|-- LibraryPreparation click LibraryPreparation href "../LibraryPreparation" MaterialProcessing <|-- SubSamplingProcess click SubSamplingProcess href "../SubSamplingProcess" MaterialProcessing <|-- MixingProcess click MixingProcess href "../MixingProcess" MaterialProcessing <|-- FiltrationProcess click FiltrationProcess href "../FiltrationProcess" MaterialProcessing <|-- ChromatographicSeparationProcess click ChromatographicSeparationProcess href "../ChromatographicSeparationProcess" MaterialProcessing <|-- DissolvingProcess click DissolvingProcess href "../DissolvingProcess" MaterialProcessing <|-- ChemicalConversionProcess click ChemicalConversionProcess href "../ChemicalConversionProcess" MaterialProcessing : alternative_identifiers MaterialProcessing : description MaterialProcessing : end_date MaterialProcessing : has_failure_categorization MaterialProcessing --> "*" FailureCategorization : has_failure_categorization click FailureCategorization href "../FailureCategorization" MaterialProcessing : has_input MaterialProcessing --> "*" NamedThing : has_input click NamedThing href "../NamedThing" MaterialProcessing : has_output MaterialProcessing --> "*" ProcessedSample : has_output click ProcessedSample href "../ProcessedSample" MaterialProcessing : id MaterialProcessing : instrument_used MaterialProcessing --> "*" Instrument : instrument_used click Instrument href "../Instrument" MaterialProcessing : name MaterialProcessing : processing_institution MaterialProcessing --> "0..1" ProcessingInstitutionEnum : processing_institution click ProcessingInstitutionEnum href "../ProcessingInstitutionEnum" MaterialProcessing : protocol_link MaterialProcessing --> "0..1" Protocol : protocol_link click Protocol href "../Protocol" MaterialProcessing : qc_comment MaterialProcessing : qc_status MaterialProcessing --> "0..1" StatusEnum : qc_status click StatusEnum href "../StatusEnum" MaterialProcessing : start_date MaterialProcessing : type

Inheritance

Slots

Name Cardinality and Range Description Inheritance
instrument_used *
Instrument		 What instrument was used during DataGeneration or MaterialProcessing direct
has_input *
NamedThing or 
Biosample or 
ProcessedSample		 An input to a process PlannedProcess
has_output *
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

Usages

used by used in type used
Database material_processing_set range MaterialProcessing

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self nmdc:MaterialProcessing
native nmdc:MaterialProcessing
broad OBI:0000094

LinkML Source

Direct

name: MaterialProcessing
description: A process that takes one or more samples as inputs and generates one
  or more samples as outputs.
notes:
- This class is a replacement for BiosampleProcessing.
from_schema: https://w3id.org/nmdc/nmdc
broad_mappings:
- OBI:0000094
is_a: PlannedProcess
abstract: true
slots:
- instrument_used
slot_usage:
  has_input:
    name: has_input
    domain_of:
    - PlannedProcess
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
    any_of:
    - range: Biosample
    - range: ProcessedSample
  has_output:
    name: has_output
    domain_of:
    - PlannedProcess
    range: ProcessedSample
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
class_uri: nmdc:MaterialProcessing

Induced

name: MaterialProcessing
description: A process that takes one or more samples as inputs and generates one
  or more samples as outputs.
notes:
- This class is a replacement for BiosampleProcessing.
from_schema: https://w3id.org/nmdc/nmdc
broad_mappings:
- OBI:0000094
is_a: PlannedProcess
abstract: true
slot_usage:
  has_input:
    name: has_input
    domain_of:
    - PlannedProcess
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
    any_of:
    - range: Biosample
    - range: ProcessedSample
  has_output:
    name: has_output
    domain_of:
    - PlannedProcess
    range: ProcessedSample
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
attributes:
  instrument_used:
    name: instrument_used
    description: What instrument was used during DataGeneration or MaterialProcessing.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: instrument_used
    owner: MaterialProcessing
    domain_of:
    - MaterialProcessing
    - DataGeneration
    range: Instrument
    multivalued: true
  has_input:
    name: has_input
    description: An input to a process.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: has_input
    owner: MaterialProcessing
    domain_of:
    - PlannedProcess
    range: NamedThing
    multivalued: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
    any_of:
    - range: Biosample
    - range: ProcessedSample
  has_output:
    name: has_output
    description: An output from a process.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: has_output
    owner: MaterialProcessing
    domain_of:
    - PlannedProcess
    range: ProcessedSample
    multivalued: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'
      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: MaterialProcessing
    domain_of:
    - PlannedProcess
    range: ProcessingInstitutionEnum
  protocol_link:
    name: protocol_link
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: protocol_link
    owner: MaterialProcessing
    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: MaterialProcessing
    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: MaterialProcessing
    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: MaterialProcessing
    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: MaterialProcessing
    domain_of:
    - PlannedProcess
    range: string
  has_failure_categorization:
    name: has_failure_categorization
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: has_failure_categorization
    owner: MaterialProcessing
    domain_of:
    - PlannedProcess
    range: FailureCategorization
    multivalued: true
    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
    notes:
    - 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'
    - a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters
      will be accepted
    - typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked
      via per-class id slot usage assertions
    - minting authority shoulders should probably be enumerated and checked in the
      pattern
    examples:
    - value: nmdc:mgmag-00-x012.1_7_c1
      description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    identifier: true
    alias: id
    owner: MaterialProcessing
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: name
    owner: MaterialProcessing
    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: MaterialProcessing
    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
    alias: alternative_identifiers
    owner: MaterialProcessing
    domain_of:
    - MetaboliteIdentification
    - NamedThing
    range: uriorcurie
    multivalued: true
    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: MaterialProcessing
    domain_of:
    - EukEval
    - FunctionalAnnotationAggMember
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - PeptideQuantification
    - ProteinQuantification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
class_uri: nmdc:MaterialProcessing