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Class: SubSamplingProcess

Separating a sample aliquot from the starting material for downstream activity.

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URI: nmdc:SubSamplingProcess

classDiagram class SubSamplingProcess click SubSamplingProcess href "../SubSamplingProcess" PlannedProcess <|-- SubSamplingProcess click PlannedProcess href "../PlannedProcess" SubSamplingProcess : alternative_identifiers SubSamplingProcess : contained_in SubSamplingProcess --> "0..1" ContainerCategoryEnum : contained_in click ContainerCategoryEnum href "../ContainerCategoryEnum" SubSamplingProcess : container_size SubSamplingProcess --> "0..1" QuantityValue : container_size click QuantityValue href "../QuantityValue" SubSamplingProcess : description SubSamplingProcess : designated_class SubSamplingProcess : end_date SubSamplingProcess : has_failure_categorization SubSamplingProcess --> "0..*" FailureCategorization : has_failure_categorization click FailureCategorization href "../FailureCategorization" SubSamplingProcess : has_input SubSamplingProcess --> "0..*" NamedThing : has_input click NamedThing href "../NamedThing" SubSamplingProcess : has_output SubSamplingProcess --> "0..*" ProcessedSample : has_output click ProcessedSample href "../ProcessedSample" SubSamplingProcess : id SubSamplingProcess : instrument_name SubSamplingProcess : mass SubSamplingProcess --> "0..1" QuantityValue : mass click QuantityValue href "../QuantityValue" SubSamplingProcess : name SubSamplingProcess : processing_institution SubSamplingProcess --> "0..1" ProcessingInstitutionEnum : processing_institution click ProcessingInstitutionEnum href "../ProcessingInstitutionEnum" SubSamplingProcess : protocol_link SubSamplingProcess --> "0..1" Protocol : protocol_link click Protocol href "../Protocol" SubSamplingProcess : qc_comment SubSamplingProcess : qc_status SubSamplingProcess --> "0..1" StatusEnum : qc_status click StatusEnum href "../StatusEnum" SubSamplingProcess : start_date SubSamplingProcess : temperature SubSamplingProcess --> "0..1" QuantityValue : temperature click QuantityValue href "../QuantityValue" SubSamplingProcess : volume SubSamplingProcess --> "0..1" QuantityValue : volume click QuantityValue href "../QuantityValue"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
container_size 0..1
QuantityValue		 The volume of the container an analyte is stored in or an activity takes plac... direct
contained_in 0..1
ContainerCategoryEnum		 A type of container direct
temperature 0..1
QuantityValue		 The value of a temperature measurement or temperature used in a process direct
volume 0..1
QuantityValue		 The output volume of the SubSampling Process direct
mass 0..1
QuantityValue		 The output mass of the SubSampling Process 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 subsample 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

TODOs

  • add intermediate class between PlannedProcess and this (MaterialProcessing potentially)
  • Montana to visit slot descriptions
  • add 'has_output' usage for processed sample - James

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value
self nmdc:SubSamplingProcess
native nmdc:SubSamplingProcess
related OBI:0000744

LinkML Source

Direct

name: SubSamplingProcess
description: 'Separating a sample aliquot from the starting material for downstream
  activity.

  '
todos:
- add intermediate class between PlannedProcess and this (MaterialProcessing potentially)
- Montana to visit slot descriptions
- add 'has_output' usage for processed sample - James
notes:
- A subsample may be (a) a portion of the sample obtained by selection or division;
  (b) an individual unit of the lot taken as part of the sample; (c) the final unit
  of multistage sampling. The term 'subsample' is used either in the sense of a 'sample
  of a sample' or as a synonym for 'unit'. In practice, the meaning is usually apparent
  from the context or is defined.
from_schema: https://w3id.org/nmdc/nmdc
related_mappings:
- OBI:0000744
contributors:
- ORCID:0009-0001-1555-1601
- ORCID:0000-0002-8683-0050
- ORCID:0000-0001-9076-6066
- ORCID:0009-0008-4013-7737
is_a: PlannedProcess
slots:
- container_size
- contained_in
- temperature
- volume
- mass
slot_usage:
  volume:
    name: volume
    description: The output volume of the SubSampling Process.
    domain_of:
    - Extraction
    - Solution
    - SubSamplingProcess
    - FiltrationProcess
  mass:
    name: mass
    description: The output mass of the SubSampling Process.
    domain_of:
    - SubSamplingProcess
  has_input:
    name: has_input
    domain_of:
    - BiosampleProcessing
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    any_of:
    - range: Biosample
    - range: ProcessedSample
  has_output:
    name: has_output
    description: The subsample.
    domain_of:
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    range: ProcessedSample

Induced

name: SubSamplingProcess
description: 'Separating a sample aliquot from the starting material for downstream
  activity.

  '
todos:
- add intermediate class between PlannedProcess and this (MaterialProcessing potentially)
- Montana to visit slot descriptions
- add 'has_output' usage for processed sample - James
notes:
- A subsample may be (a) a portion of the sample obtained by selection or division;
  (b) an individual unit of the lot taken as part of the sample; (c) the final unit
  of multistage sampling. The term 'subsample' is used either in the sense of a 'sample
  of a sample' or as a synonym for 'unit'. In practice, the meaning is usually apparent
  from the context or is defined.
from_schema: https://w3id.org/nmdc/nmdc
related_mappings:
- OBI:0000744
contributors:
- ORCID:0009-0001-1555-1601
- ORCID:0000-0002-8683-0050
- ORCID:0000-0001-9076-6066
- ORCID:0009-0008-4013-7737
is_a: PlannedProcess
slot_usage:
  volume:
    name: volume
    description: The output volume of the SubSampling Process.
    domain_of:
    - Extraction
    - Solution
    - SubSamplingProcess
    - FiltrationProcess
  mass:
    name: mass
    description: The output mass of the SubSampling Process.
    domain_of:
    - SubSamplingProcess
  has_input:
    name: has_input
    domain_of:
    - BiosampleProcessing
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    any_of:
    - range: Biosample
    - range: ProcessedSample
  has_output:
    name: has_output
    description: The subsample.
    domain_of:
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    range: ProcessedSample
attributes:
  container_size:
    name: container_size
    description: The volume of the container an analyte is stored in or an activity
      takes place in
    from_schema: https://w3id.org/nmdc/nmdc
    contributors:
    - ORCID:0009-0001-1555-1601
    - ORCID:0000-0002-8683-0050
    rank: 1000
    alias: container_size
    owner: SubSamplingProcess
    domain_of:
    - SubSamplingProcess
    - FiltrationProcess
    range: QuantityValue
  contained_in:
    name: contained_in
    description: A type of container. i.e. test tube, falcon tube, etc.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: contained_in
    owner: SubSamplingProcess
    domain_of:
    - SubSamplingProcess
    range: ContainerCategoryEnum
  temperature:
    name: temperature
    description: The value of a temperature measurement or temperature used in a process.
    notes:
    - Not to be confused with the MIXS:0000113
    from_schema: https://w3id.org/nmdc/nmdc
    contributors:
    - ORCID:0009-0001-1555-1601
    - ORCID:0000-0002-8683-0050
    rank: 1000
    alias: temperature
    owner: SubSamplingProcess
    domain_of:
    - SubSamplingProcess
    - ChromatographicSeparationProcess
    range: QuantityValue
  volume:
    name: volume
    description: The output volume of the SubSampling Process.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: PlannedProcess
    alias: volume
    owner: SubSamplingProcess
    domain_of:
    - Extraction
    - Solution
    - SubSamplingProcess
    - FiltrationProcess
    range: QuantityValue
  mass:
    name: mass
    description: The output mass of the SubSampling Process.
    title: mass
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: mass
    owner: SubSamplingProcess
    domain_of:
    - SubSamplingProcess
    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: SubSamplingProcess
    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: SubSamplingProcess
    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: SubSamplingProcess
    domain_of:
    - BiosampleProcessing
    - OmicsProcessing
    - PlannedProcess
    - WorkflowExecutionActivity
    range: NamedThing
    any_of:
    - range: Biosample
    - range: ProcessedSample
  has_output:
    name: has_output
    description: The subsample.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    domain: NamedThing
    multivalued: true
    alias: has_output
    owner: SubSamplingProcess
    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: SubSamplingProcess
    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: SubSamplingProcess
    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: SubSamplingProcess
    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: SubSamplingProcess
    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: SubSamplingProcess
    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: SubSamplingProcess
    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: SubSamplingProcess
    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: SubSamplingProcess
    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: SubSamplingProcess
    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: SubSamplingProcess
    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: SubSamplingProcess
    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_\-\/\.,]*$