Class: MixingProcess

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

__

classDiagram class MixingProcess click MixingProcess href "../MixingProcess" PlannedProcess <|-- MixingProcess click PlannedProcess href "../PlannedProcess" MixingProcess : alternative_identifiers MixingProcess : description MixingProcess : designated_class MixingProcess : duration MixingProcess --> "0..1" QuantityValue : duration click QuantityValue href "../QuantityValue" MixingProcess : end_date MixingProcess : has_failure_categorization MixingProcess --> "0..*" FailureCategorization : has_failure_categorization click FailureCategorization href "../FailureCategorization" MixingProcess : has_input MixingProcess --> "0..*" NamedThing : has_input click NamedThing href "../NamedThing" MixingProcess : has_output MixingProcess --> "0..*" ProcessedSample : has_output click ProcessedSample href "../ProcessedSample" MixingProcess : id MixingProcess : instrument_name 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

Inheritance

NamedThing
- PlannedProcess
  - MixingProcess

Slots

Name	Cardinality and Range	Description	Inheritance
duration	0..1 QuantityValue	The elapsed time of an activity	direct
designated_class	0..1 Uriorcurie		PlannedProcess
end_date	0..1 String	The date on which any process or activity was ended	PlannedProcess
has_input	0..* NamedThing	An input to a process	PlannedProcess
has_output	0..* 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
instrument_name	0..1 String	The name of the instrument that was used for processing the sample	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	0..* FailureCategorization		PlannedProcess
id	1..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	0..* Uriorcurie	A list of alternative identifiers for the entity	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

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

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: PlannedProcess
slots:
- duration
slot_usage:
  has_input:
    name: has_input
    domain_of:
    - BiosampleProcessing
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    any_of:
    - range: Biosample
    - range: ProcessedSample
  has_output:
    name: has_output
    description: The mixed sample.
    domain_of:
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    range: ProcessedSample

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: PlannedProcess
slot_usage:
  has_input:
    name: has_input
    domain_of:
    - BiosampleProcessing
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    any_of:
    - range: Biosample
    - range: ProcessedSample
  has_output:
    name: has_output
    description: The mixed sample.
    domain_of:
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    range: ProcessedSample
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
    domain: PlannedProcess
    alias: duration
    owner: MixingProcess
    domain_of:
    - MixingProcess
    range: QuantityValue
  designated_class:
    name: designated_class
    comments:
    - required on all instances in a polymorphic Database slot like planned_process_set
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    designates_type: true
    alias: designated_class
    owner: MixingProcess
    domain_of:
    - PlannedProcess
    range: uriorcurie
  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
  has_input:
    name: has_input
    description: An input to a process.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: NamedThing
    multivalued: true
    alias: has_input
    owner: MixingProcess
    domain_of:
    - BiosampleProcessing
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    range: NamedThing
    any_of:
    - range: Biosample
    - range: ProcessedSample
  has_output:
    name: has_output
    description: The mixed sample.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: NamedThing
    multivalued: true
    alias: has_output
    owner: MixingProcess
    domain_of:
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    range: ProcessedSample
  processing_institution:
    name: processing_institution
    description: The organization that processed the sample.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: PlannedProcess
    alias: processing_institution
    owner: MixingProcess
    domain_of:
    - OmicsProcessing
    - PlannedProcess
    range: processing_institution_enum
  protocol_link:
    name: protocol_link
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: PlannedProcess
    alias: protocol_link
    owner: MixingProcess
    domain_of:
    - PlannedProcess
    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
  instrument_name:
    name: instrument_name
    description: The name of the instrument that was used for processing the sample.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: PlannedProcess
    alias: instrument_name
    owner: MixingProcess
    domain_of:
    - OmicsProcessing
    - 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
    - WorkflowExecutionActivity
    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
    - WorkflowExecutionActivity
    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: MixingProcess
    domain_of:
    - PlannedProcess
    - WorkflowExecutionActivity
    range: FailureCategorization
  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: MixingProcess
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - Activity
    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: MixingProcess
    domain_of:
    - Protocol
    - NamedThing
    - PersonValue
    - Activity
    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:
    - Study
    - NamedThing
    - ImageValue
    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: MixingProcess
    domain_of:
    - Biosample
    - Study
    - NamedThing
    - MetaboliteQuantification
    range: uriorcurie
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$