Class: MassSpectrometryConfiguration

name: MassSpectrometryConfiguration
description: A set of parameters that define and control the actions of a mass spectrometry
  process.
notes:
- This class is intended to represent a mass spectrometry method file that controls
  a mass spectrometry process.
from_schema: https://w3id.org/nmdc/nmdc
is_a: Configuration
slots:
- mass_spectrometry_acquisition_strategy
- resolution_categories
- mass_analyzers
- ionization_source
- mass_spectrum_collection_modes
- polarity_mode
slot_usage:
  name:
    name: name
    required: true
  description:
    name: description
    required: true
  id:
    name: id
    structured_pattern:
      syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'
      interpolated: true
class_uri: nmdc:MassSpectrometryConfiguration

name: MassSpectrometryConfiguration
description: A set of parameters that define and control the actions of a mass spectrometry
  process.
notes:
- This class is intended to represent a mass spectrometry method file that controls
  a mass spectrometry process.
from_schema: https://w3id.org/nmdc/nmdc
is_a: Configuration
slot_usage:
  name:
    name: name
    required: true
  description:
    name: description
    required: true
  id:
    name: id
    structured_pattern:
      syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'
      interpolated: true
attributes:
  mass_spectrometry_acquisition_strategy:
    name: mass_spectrometry_acquisition_strategy
    description: Mode of running a mass spectrometer method by which m/z ranges are
      selected and ions possibly fragment.
    from_schema: https://w3id.org/nmdc/nmdc
    exact_mappings:
    - MS:1003213
    rank: 1000
    alias: mass_spectrometry_acquisition_strategy
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: MassSpectrometryAcquisitionStrategyEnum
  resolution_categories:
    name: resolution_categories
    description: The relative resolution at which spectra were collected.
    examples:
    - value: '[''high'', ''low'']'
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: resolution_categories
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: ResolutionCategoryEnum
    multivalued: true
  mass_analyzers:
    name: mass_analyzers
    description: The kind of mass analyzer(s) used during the spectra collection.
    from_schema: https://w3id.org/nmdc/nmdc
    exact_mappings:
    - MS:1000443
    rank: 1000
    alias: mass_analyzers
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: MassAnalyzerEnum
    multivalued: true
  ionization_source:
    name: ionization_source
    description: The ionization source used to introduce processed samples into a
      mass spectrometer
    from_schema: https://w3id.org/nmdc/nmdc
    exact_mappings:
    - MS:1000008
    rank: 1000
    alias: ionization_source
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: IonizationSourceEnum
  mass_spectrum_collection_modes:
    name: mass_spectrum_collection_modes
    description: Indicates whether mass spectra were collected in full profile, reduced
      profile, or centroid mode during acquisition.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: mass_spectrum_collection_modes
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: MassSpectrumCollectionModeEnum
    multivalued: true
  polarity_mode:
    name: polarity_mode
    description: the polarity of which ions are generated and detected
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: polarity_mode
    owner: MassSpectrometryConfiguration
    domain_of:
    - MassSpectrometryConfiguration
    range: PolarityModeEnum
  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: MassSpectrometryConfiguration
    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}:mscon-{id_shoulder}-{id_blade}$'
      interpolated: true
  name:
    name: name
    description: A human readable label for an entity
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: name
    owner: MassSpectrometryConfiguration
    domain_of:
    - PersonValue
    - NamedThing
    - Protocol
    range: string
    required: true
  description:
    name: description
    description: a human-readable description of a thing
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: MassSpectrometryConfiguration
    domain_of:
    - ImageValue
    - NamedThing
    range: string
    required: true
  alternative_identifiers:
    name: alternative_identifiers
    description: A list of alternative identifiers for the entity.
    from_schema: https://w3id.org/nmdc/nmdc
    rank: 1000
    alias: alternative_identifiers
    owner: MassSpectrometryConfiguration
    domain_of:
    - MetaboliteIdentification
    - NamedThing
    range: uriorcurie
    multivalued: true
    pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
  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: MassSpectrometryConfiguration
    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:MassSpectrometryConfiguration