Class: DensityGradientFractionationProcess

name: DensityGradientFractionationProcess
description: A material processing that separates a sample, typically extracted nucleic
  acids, into fractions by buoyant density, usually by isopycnic centrifugation. The
  output fractions can record their gradient position, buoyant density and relative
  nucleic acid amount.
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- Isopycnic Centrifugation
- Density Gradient Centrifugation
is_a: MaterialProcessing
slots:
- internal_standard_method
slot_usage:
  id:
    name: id
    examples:
    - value: nmdc:fracp-99-labeled
      description: a DensityGradientFractionationProcess from the schema's example
        data; production has none
    structured_pattern:
      syntax: '{id_nmdc_prefix}:fracp-{id_shoulder}-{id_blade}'
      interpolated: true
  has_input:
    name: has_input
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|osm|procsm)-{id_shoulder}-{id_blade}'
      interpolated: true
  has_output:
    name: has_output
    required: true
class_uri: nmdc:DensityGradientFractionationProcess

name: DensityGradientFractionationProcess
description: A material processing that separates a sample, typically extracted nucleic
  acids, into fractions by buoyant density, usually by isopycnic centrifugation. The
  output fractions can record their gradient position, buoyant density and relative
  nucleic acid amount.
from_schema: https://w3id.org/nmdc/nmdc
aliases:
- Isopycnic Centrifugation
- Density Gradient Centrifugation
is_a: MaterialProcessing
slot_usage:
  id:
    name: id
    examples:
    - value: nmdc:fracp-99-labeled
      description: a DensityGradientFractionationProcess from the schema's example
        data; production has none
    structured_pattern:
      syntax: '{id_nmdc_prefix}:fracp-{id_shoulder}-{id_blade}'
      interpolated: true
  has_input:
    name: has_input
    required: true
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|osm|procsm)-{id_shoulder}-{id_blade}'
      interpolated: true
  has_output:
    name: has_output
    required: true
attributes:
  internal_standard_method:
    name: internal_standard_method
    description: Method used for internal standard for SIP fractionation, if an internal
      standard was used (i.e., spiking in a heavy-labelled DNA sequence).
    title: internal standard method
    from_schema: https://w3id.org/nmdc/nmdc
    exact_mappings:
    - MIXS:0001351
    rank: 1000
    owner: DensityGradientFractionationProcess
    domain_of:
    - DensityGradientFractionationProcess
    range: Protocol
  instrument_used:
    name: instrument_used
    description: What instrument was used during DataGeneration or MaterialProcessing.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    owner: DensityGradientFractionationProcess
    domain_of:
    - DataGeneration
    - MaterialProcessing
    range: Instrument
    multivalued: true
    pattern: ^(?:(nmdc):inst-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,}))$
    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
    owner: DensityGradientFractionationProcess
    domain_of:
    - PlannedProcess
    range: Sample
    required: true
    multivalued: true
    pattern: ^(?:(nmdc):(bsm|osm|procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,}))$
    structured_pattern:
      syntax: '{id_nmdc_prefix}:(bsm|osm|procsm)-{id_shoulder}-{id_blade}'
      interpolated: true
  has_output:
    name: has_output
    description: An output from a process.
    from_schema: https://w3id.org/nmdc/nmdc
    aliases:
    - output
    rank: 1000
    owner: DensityGradientFractionationProcess
    domain_of:
    - PlannedProcess
    range: ProcessedSample
    required: true
    multivalued: true
    pattern: ^(?:(nmdc):(procsm)-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,}))$
    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
    owner: DensityGradientFractionationProcess
    domain_of:
    - PlannedProcess
    range: ProcessingInstitutionEnum
  protocol_link:
    name: protocol_link
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    owner: DensityGradientFractionationProcess
    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
    owner: DensityGradientFractionationProcess
    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
    owner: DensityGradientFractionationProcess
    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
    owner: DensityGradientFractionationProcess
    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
    owner: DensityGradientFractionationProcess
    domain_of:
    - PlannedProcess
    range: string
  has_failure_categorization:
    name: has_failure_categorization
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    owner: DensityGradientFractionationProcess
    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
    title: ID
    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
    - This slot has no examples on purpose. linkml 1.12 copies a slot's examples into
      every class that uses it, and no single id matches every class id pattern (https://github.com/microbiomedata/nmdc-schema/issues/3540).
      Id examples belong in each class's slot_usage.
    examples:
    - value: nmdc:fracp-99-labeled
      description: a DensityGradientFractionationProcess from the schema's example
        data; production has none
    from_schema: https://w3id.org/nmdc/nmdc
    structured_aliases:
    - literal_form: workflow_execution_id
      predicate: NARROW_SYNONYM
      notes:
      - JGI Analysis Tracker (JAT) macro nmdc_metadata.yaml, in an access-restricted
        Bitbucket repository (https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml);
        source is the public NMDC page describing how JAT is used.
      source: https://github.com/microbiomedata/nmdc_automation/blob/main/data_management/README.md
    - literal_form: data_object_id
      predicate: NARROW_SYNONYM
      notes:
      - JGI Analysis Tracker (JAT) macro nmdc_metadata.yaml, in an access-restricted
        Bitbucket repository (https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml);
        source is the public NMDC page describing how JAT is used.
      source: https://github.com/microbiomedata/nmdc_automation/blob/main/data_management/README.md
    rank: 1000
    identifier: true
    owner: DensityGradientFractionationProcess
    domain_of:
    - NamedThing
    range: uriorcurie
    required: true
    pattern: ^(?:(nmdc):fracp-([0-9][a-z]{0,6}[0-9])-([A-Za-z0-9]{1,}))$
    structured_pattern:
      syntax: '{id_nmdc_prefix}:fracp-{id_shoulder}-{id_blade}'
      interpolated: true
  name:
    name: name
    description: A human readable label for an entity
    title: Name
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    owner: DensityGradientFractionationProcess
    domain_of:
    - Agent
    - NamedThing
    - Protocol
    range: string
  description:
    name: description
    description: a human-readable description of a thing
    title: Description
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: dcterms:description
    owner: DensityGradientFractionationProcess
    domain_of:
    - ImageValue
    - NamedThing
    - Protocol
    range: string
  alternative_identifiers:
    name: alternative_identifiers
    description: A list of alternative identifiers for the entity.
    title: Alternative Identifiers
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    owner: DensityGradientFractionationProcess
    domain_of:
    - NamedThing
    - MetaboliteIdentification
    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
    title: Type
    notes:
    - makes it easier to read example data files
    - required for polymorphic MongoDB collections
    comments:
    - 'Deprecating this slot was proposed and rejected: without it, a document read
      back from a polymorphic MongoDB collection cannot be resolved to the class it
      instantiates. It is required on every class for that reason, rather than as
      a convention inherited from LinkML.'
    examples:
    - value: nmdc:Biosample
    - value: nmdc:Study
    from_schema: https://w3id.org/nmdc/nmdc
    structured_aliases:
    - literal_form: workflow_execution_class
      predicate: NARROW_SYNONYM
      notes:
      - JGI Analysis Tracker (JAT) macro nmdc_metadata.yaml, in an access-restricted
        Bitbucket repository (https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml);
        source is the public NMDC page describing how JAT is used.
      source: https://github.com/microbiomedata/nmdc_automation/blob/main/data_management/README.md
    rank: 1000
    slot_uri: rdf:type
    designates_type: true
    owner: DensityGradientFractionationProcess
    domain_of:
    - Agent
    - EukEval
    - FunctionalAnnotationAggMember
    - IsotopologAddition
    - IsotopologComposition
    - PeptideQuantification
    - ProteinQuantification
    - GenomeFeature
    - FunctionalAnnotation
    - AttributeValue
    - NamedThing
    - OntologyRelation
    - FailureCategorization
    - Protocol
    - CreditAssociation
    - Doi
    - ProvenanceMetadata
    - MobilePhaseSegment
    - PortionOfSubstance
    - MagBin
    - MetaboliteIdentification
    range: uriorcurie
    required: true
class_uri: nmdc:DensityGradientFractionationProcess