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Class: MixingProcess

The combining of components, particles or layers into a more homogeneous state.

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URI: nmdc:MixingProcess

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

Inheritance

Slots

Name Cardinality and Range Description Inheritance
duration 0..1
QuantityValue		 The elapsed time of an activity direct
instrument_used *
Instrument		 What instrument was used during DataGeneration or MaterialProcessing MaterialProcessing
has_input *
NamedThing or 
Biosample or 
ProcessedSample		 An input to a process PlannedProcess
has_output *
ProcessedSample		 The mixed sample 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

Comments

  • The mixing may be achieved manually or mechanically by shifting the material with stirrers or pumps or by revolving or shaking the container.
  • The process must not permit segregation of particles of different size or properties.
  • Homogeneity may be considered to have been achieved in a practical sense when the sampling error of the processed portion is negligible compared to the total error of the measurement system.

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self nmdc:MixingProcess
native nmdc:MixingProcess

LinkML Source

Direct

name: MixingProcess
description: 'The combining of components, particles or layers into a more homogeneous
  state.

  '
comments:
- The mixing may be achieved manually or mechanically by shifting the material with
  stirrers or pumps or by revolving or shaking the container.
- The process must not permit segregation of particles of different size or properties.
- Homogeneity may be considered to have been achieved in a practical sense when the
  sampling error of the processed portion is negligible compared to the total error
  of the measurement system.
from_schema: https://w3id.org/nmdc/nmdc
contributors:
- ORCID:0009-0001-1555-1601
- ORCID:0000-0002-8683-0050
is_a: MaterialProcessing
slots:
- duration
slot_usage:
  id:
    name: id
    domain_of:
    - NamedThing
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:mixpro-{id_shoulder}-{id_blade}$'
  has_input:
    name: has_input
    domain_of:
    - PlannedProcess
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
    any_of:
    - range: Biosample
    - range: ProcessedSample
  has_output:
    name: has_output
    description: The mixed sample.
    domain_of:
    - PlannedProcess
    range: ProcessedSample
    structured_pattern:
      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'
      interpolated: true
class_uri: nmdc:MixingProcess

Induced

name: MixingProcess
description: 'The combining of components, particles or layers into a more homogeneous
  state.

  '
comments:
- The mixing may be achieved manually or mechanically by shifting the material with
  stirrers or pumps or by revolving or shaking the container.
- The process must not permit segregation of particles of different size or properties.
- Homogeneity may be considered to have been achieved in a practical sense when the
  sampling error of the processed portion is negligible compared to the total error
  of the measurement system.
from_schema: https://w3id.org/nmdc/nmdc
contributors:
- ORCID:0009-0001-1555-1601
- ORCID:0000-0002-8683-0050
is_a: MaterialProcessing
slot_usage:
  id:
    name: id
    domain_of:
    - NamedThing
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:mixpro-{id_shoulder}-{id_blade}$'
  has_input:
    name: has_input
    domain_of:
    - PlannedProcess
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
    any_of:
    - range: Biosample
    - range: ProcessedSample
  has_output:
    name: has_output
    description: The mixed sample.
    domain_of:
    - PlannedProcess
    range: ProcessedSample
    structured_pattern:
      syntax: '{id_nmdc_prefix}:procsm-{id_shoulder}-{id_blade}$'
      interpolated: true
attributes:
  duration:
    name: duration
    description: The elapsed time of an activity.
    examples:
    - value: JsonObj(has_numeric_value=2, has_unit='hours')
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: duration
    owner: MixingProcess
    domain_of:
    - MixingProcess
    - DissolvingProcess
    - ChemicalConversionProcess
    - MobilePhaseSegment
    range: QuantityValue
  instrument_used:
    name: instrument_used
    description: What instrument was used during DataGeneration or MaterialProcessing.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: instrument_used
    owner: MixingProcess
    domain_of:
    - MaterialProcessing
    - DataGeneration
    range: Instrument
    multivalued: true
  has_input:
    name: has_input
    description: An input to a process.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: has_input
    owner: MixingProcess
    domain_of:
    - PlannedProcess
    range: NamedThing
    multivalued: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
    any_of:
    - range: Biosample
    - range: ProcessedSample
  has_output:
    name: has_output
    description: The mixed sample.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: has_output
    owner: MixingProcess
    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: MixingProcess
    domain_of:
    - PlannedProcess
    range: ProcessingInstitutionEnum
  protocol_link:
    name: protocol_link
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: protocol_link
    owner: MixingProcess
    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: MixingProcess
    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: MixingProcess
    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: MixingProcess
    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: MixingProcess
    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: MixingProcess
    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
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    identifier: true
    alias: id
    owner: MixingProcess
    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}:mixpro-{id_shoulder}-{id_blade}$'
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: name
    owner: MixingProcess
    domain_of:
    - PersonValue
    - NamedThing
    - Protocol
    range: string
  description:
    name: description
    description: a human-readable description of a thing
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: MixingProcess
    domain_of:
    - ImageValue
    - NamedThing
    range: string
  alternative_identifiers:
    name: alternative_identifiers
    description: A list of alternative identifiers for the entity.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: alternative_identifiers
    owner: MixingProcess
    domain_of:
    - MetaboliteIdentification
    - NamedThing
    range: uriorcurie
    multivalued: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
  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: MixingProcess
    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:MixingProcess