Class: SubSamplingProcess

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

  '
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.
- TODO - Montana to visit slot descriptions
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: MaterialProcessing
slots:
- container_size
- contained_in
- temperature
- volume
- mass
- sampled_portion
slot_usage:
  id:
    name: id
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$'
      interpolated: true
  volume:
    name: volume
    description: The output volume of the SubSampling Process.
  mass:
    name: mass
    description: The output mass of the SubSampling Process.
  has_input:
    name: has_input
    range: Sample
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
  has_output:
    name: has_output
    description: The subsample.
    range: ProcessedSample
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
class_uri: nmdc:SubSamplingProcess

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

  '
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.
- TODO - Montana to visit slot descriptions
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: MaterialProcessing
slot_usage:
  id:
    name: id
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:subspr-{id_shoulder}-{id_blade}$'
      interpolated: true
  volume:
    name: volume
    description: The output volume of the SubSampling Process.
  mass:
    name: mass
    description: The output mass of the SubSampling Process.
  has_input:
    name: has_input
    range: Sample
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
  has_output:
    name: has_output
    description: The subsample.
    range: ProcessedSample
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
attributes:
  container_size:
    name: container_size
    annotations:
      units_alignment_excuse:
        tag: units_alignment_excuse
        value: pending_analysis
    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.
    examples:
    - value: test tube
    - value: falcon tube
    - value: whirlpak
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: contained_in
    owner: SubSamplingProcess
    domain_of:
    - SubSamplingProcess
    - StorageProcess
    range: ContainerCategoryEnum
  temperature:
    name: temperature
    annotations:
      storage_units:
        tag: storage_units
        value: Cel
    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:
    - ChromatographyConfiguration
    - Extraction
    - SubSamplingProcess
    - StorageProcess
    - ChromatographicSeparationProcess
    - DissolvingProcess
    - ChemicalConversionProcess
    range: QuantityValue
  volume:
    name: volume
    annotations:
      storage_units:
        tag: storage_units
        value: mL|uL
    description: The output volume of the SubSampling Process.
    from_schema: https://w3id.org/nmdc/nmdc
    contributors:
    - ORCID:0009-0001-1555-1601
    - ORCID:0000-0002-8683-0050
    rank: 1000
    alias: volume
    owner: SubSamplingProcess
    domain_of:
    - Extraction
    - SubSamplingProcess
    - FiltrationProcess
    - MobilePhaseSegment
    - PortionOfSubstance
    range: QuantityValue
  mass:
    name: mass
    annotations:
      storage_units:
        tag: storage_units
        value: g
    description: The output mass of the SubSampling Process.
    title: mass
    from_schema: https://w3id.org/nmdc/nmdc
    exact_mappings:
    - PATO:0000125
    rank: 1000
    alias: mass
    owner: SubSamplingProcess
    domain_of:
    - SubSamplingProcess
    - PortionOfSubstance
    range: QuantityValue
  sampled_portion:
    name: sampled_portion
    description: The portion of the sample that is taken for downstream activity.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: sampled_portion
    owner: SubSamplingProcess
    domain_of:
    - SubSamplingProcess
    - ProcessedSample
    range: SamplePortionEnum
    multivalued: true
  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: SubSamplingProcess
    domain_of:
    - MaterialProcessing
    - DataGeneration
    range: Instrument
    multivalued: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:inst-{id_shoulder}-{id_blade}$'
      interpolated: true
  has_input:
    name: has_input
    description: An input to a process.
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - input
    rank: 1000
    alias: has_input
    owner: SubSamplingProcess
    domain_of:
    - PlannedProcess
    range: Sample
    multivalued: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}$'
      interpolated: true
  has_output:
    name: has_output
    description: The subsample.
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - output
    rank: 1000
    alias: has_output
    owner: SubSamplingProcess
    domain_of:
    - PlannedProcess
    range: ProcessedSample
    multivalued: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(procsm)-{id_shoulder}-{id_blade}$'
      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: SubSamplingProcess
    domain_of:
    - PlannedProcess
    range: ProcessingInstitutionEnum
  protocol_link:
    name: protocol_link
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: protocol_link
    owner: SubSamplingProcess
    domain_of:
    - Configuration
    - 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: SubSamplingProcess
    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: SubSamplingProcess
    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: SubSamplingProcess
    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: SubSamplingProcess
    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: SubSamplingProcess
    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
    structured_aliases:
      workflow_execution_id:
        literal_form: workflow_execution_id
        predicate: NARROW_SYNONYM
        contexts:
        - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
      data_object_id:
        literal_form: data_object_id
        predicate: NARROW_SYNONYM
        contexts:
        - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    rank: 1000
    identifier: true
    alias: id
    owner: SubSamplingProcess
    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}:subspr-{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: SubSamplingProcess
    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: SubSamplingProcess
    domain_of:
    - ImageValue
    - NamedThing
    - Protocol
    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: SubSamplingProcess
    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:
    - 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
    structured_aliases:
      workflow_execution_class:
        literal_form: workflow_execution_class
        predicate: NARROW_SYNONYM
        contexts:
        - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    alias: type
    owner: SubSamplingProcess
    domain_of:
    - EukEval
    - FunctionalAnnotationAggMember
    - PeptideQuantification
    - ProteinQuantification
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - OntologyRelation
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    range: uriorcurie
    required: true
class_uri: nmdc:SubSamplingProcess