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Class: MassSpectrometry

A mass spectrometry (MS) assay for the analysis of samples using a mass spectrometer.

__

URI: https://w3id.org/NFDI4Chem/ms-dcat-ap/MassSpectrometry

 classDiagram
    class MassSpectrometry
    click MassSpectrometry href "../MassSpectrometry/"
      DataGeneratingActivity <|-- MassSpectrometry
        click DataGeneratingActivity href "../DataGeneratingActivity/"

      MassSpectrometry : acquisition_mode





        MassSpectrometry --> "1" AcquisitionMode : acquisition_mode
        click AcquisitionMode href "../AcquisitionMode/"



      MassSpectrometry : carried_out_by





        MassSpectrometry --> "1..* _recommended_" MassSpectrometer : carried_out_by
        click MassSpectrometer href "../MassSpectrometer/"



      MassSpectrometry : description

      MassSpectrometry : evaluated_activity





        MassSpectrometry --> "* _recommended_" EvaluatedActivity : evaluated_activity
        click EvaluatedActivity href "../EvaluatedActivity/"



      MassSpectrometry : evaluated_entity





        MassSpectrometry --> "1 _recommended_" MSSample : evaluated_entity
        click MSSample href "../MSSample/"



      MassSpectrometry : had_input_activity





        MassSpectrometry --> "* _recommended_" Activity : had_input_activity
        click Activity href "../Activity/"



      MassSpectrometry : had_input_entity





        MassSpectrometry --> "* _recommended_" Entity : had_input_entity
        click Entity href "../Entity/"



      MassSpectrometry : had_output_entity





        MassSpectrometry --> "* _recommended_" Entity : had_output_entity
        click Entity href "../Entity/"



      MassSpectrometry : has_part





        MassSpectrometry --> "*" Activity : has_part
        click Activity href "../Activity/"



      MassSpectrometry : has_qualitative_attribute





        MassSpectrometry --> "* _recommended_" QualitativeAttribute : has_qualitative_attribute
        click QualitativeAttribute href "../QualitativeAttribute/"



      MassSpectrometry : has_quantitative_attribute





        MassSpectrometry --> "* _recommended_" QuantitativeAttribute : has_quantitative_attribute
        click QuantitativeAttribute href "../QuantitativeAttribute/"



      MassSpectrometry : id

      MassSpectrometry : occurred_in





        MassSpectrometry --> "0..1" Surrounding : occurred_in
        click Surrounding href "../Surrounding/"



      MassSpectrometry : other_identifier





        MassSpectrometry --> "*" Identifier : other_identifier
        click Identifier href "../Identifier/"



      MassSpectrometry : part_of





        MassSpectrometry --> "*" Activity : part_of
        click Activity href "../Activity/"



      MassSpectrometry : rdf_type





        MassSpectrometry --> "0..1 _recommended_" DefinedTerm : rdf_type
        click DefinedTerm href "../DefinedTerm/"



      MassSpectrometry : realized_plan





        MassSpectrometry --> "0..1" Plan : realized_plan
        click Plan href "../Plan/"



      MassSpectrometry : scan_polarity





        MassSpectrometry --> "1" ScanPolarity : scan_polarity
        click ScanPolarity href "../ScanPolarity/"



      MassSpectrometry : scan_window_lower_limit





        MassSpectrometry --> "1" ScanWindowLowerLimit : scan_window_lower_limit
        click ScanWindowLowerLimit href "../ScanWindowLowerLimit/"



      MassSpectrometry : scan_window_upper_limit





        MassSpectrometry --> "1" ScanWindowUpperLimit : scan_window_upper_limit
        click ScanWindowUpperLimit href "../ScanWindowUpperLimit/"



      MassSpectrometry : title

      MassSpectrometry : type





        MassSpectrometry --> "0..1" DefinedTerm : type
        click DefinedTerm href "../DefinedTerm/"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
acquisition_mode 1
AcquisitionMode		 The acquisition mode used during the mass spectrometry measurement. direct
scan_polarity 1
ScanPolarity		 The scan polarity used during the mass spectrometry measurement. direct
scan_window_lower_limit 1
ScanWindowLowerLimit		 The lower limit of the scan window used during the measurement, typically expressed in m/z. direct
scan_window_upper_limit 1
ScanWindowUpperLimit		 The upper limit of the scan window used during the measurement, typically expressed in m/z. direct
evaluated_entity 1 recommended
MSSample		 The slot to specify the Entity about which the DataGeneratingActivity produced information. DataGeneratingActivity
evaluated_activity * recommended
EvaluatedActivity		 The slot to specify the Activity about which the DataGeneratingActivity produced information. DataGeneratingActivity
realized_plan 0..1
Plan		 The slot to specify the Plan (i.e. directive information or procedure) that was realized by an Activity. DataGeneratingActivity
occurred_in 0..1
Surrounding		 The slot to specify the Surrounding in which an Activity took place. DataGeneratingActivity
id 1
Uriorcurie		 A slot to provide an URI for an entity within this schema. Activity
title *
String		 The slot to provide a title for the Activity. Activity
description *
String		 The slot to provide a description for the Activity. Activity
other_identifier *
Identifier		 The slot to provide a secondary identifier of the Activity. Activity
has_part *
Activity		 The slot to provide an Activity that is part of the Activity. Activity
had_input_entity * recommended
Entity		 The slot to specify the Entity that was used as an input of an Activity that is to be changed, consumed or transformed. Activity
had_output_entity * recommended
Entity		 The slot to specify the Entity that was generated as an output of an Activity. Activity
had_input_activity * recommended
Activity		 The slot to provide a previous Activity that informed the Activity by being causally via a shared participant. Activity
carried_out_by 1..* recommended
MassSpectrometer		 The slot to specify the AgenticEntity that played a certain part in carrying out the Activity, either via having a specific role, function or disposition that was realized in the Activity. Activity
has_qualitative_attribute * recommended
QualitativeAttribute		 The slot to relate a qualitative attribute to an EvaluatedEntity, EvaluatedActivity or AgenticEntity Activity
has_quantitative_attribute * recommended
QuantitativeAttribute		 The slot to relate a quantitative attribute to an EvaluatedEntity, EvaluatedActivity or AgenticEntity Activity
part_of *
Activity		 The slot to provide an Activity of which the Activity is a part. Activity
type 0..1
DefinedTerm		 This slot is described in more detail within the class in which it is used. ClassifierMixin
rdf_type 0..1 recommended
DefinedTerm		 The slot to specify the ontology class that is instantiated by an entity. ClassifierMixin

Usages

used by used in type used
MSSampleMeasurementDataset was_generated_by range MassSpectrometry

Identifier and Mapping Information

Schema Source

  • from schema: https://w3id.org/NFDI4Chem/ms-dcat-ap

Mappings

Mapping Type Mapped Value
self https://w3id.org/NFDI4Chem/ms-dcat-ap/MassSpectrometry
native https://w3id.org/NFDI4Chem/ms-dcat-ap/MassSpectrometry

LinkML Source

Direct

name: MassSpectrometry
description: 'A mass spectrometry (MS) assay for the analysis of samples using a mass
  spectrometer.

  '
from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
is_a: DataGeneratingActivity
slot_usage:
  carried_out_by:
    name: carried_out_by
    range: MassSpectrometer
    required: true
  evaluated_entity:
    name: evaluated_entity
    range: MSSample
    required: true
    multivalued: false
    inlined: false
    inlined_as_list: false
attributes:
  acquisition_mode:
    name: acquisition_mode
    description: The acquisition mode used during the mass spectrometry measurement.
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    is_a: has_qualitative_attribute
    domain_of:
    - MassSpectrometry
    range: AcquisitionMode
    required: true
  scan_polarity:
    name: scan_polarity
    description: The scan polarity used during the mass spectrometry measurement.
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    is_a: has_qualitative_attribute
    domain_of:
    - MassSpectrometry
    range: ScanPolarity
    required: true
  scan_window_lower_limit:
    name: scan_window_lower_limit
    description: The lower limit of the scan window used during the measurement, typically
      expressed in m/z.
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    is_a: has_quantitative_attribute
    domain_of:
    - MassSpectrometry
    range: ScanWindowLowerLimit
    required: true
  scan_window_upper_limit:
    name: scan_window_upper_limit
    description: The upper limit of the scan window used during the measurement, typically
      expressed in m/z.
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    is_a: has_quantitative_attribute
    domain_of:
    - MassSpectrometry
    range: ScanWindowUpperLimit
    required: true

Induced

name: MassSpectrometry
description: 'A mass spectrometry (MS) assay for the analysis of samples using a mass
  spectrometer.

  '
from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
is_a: DataGeneratingActivity
slot_usage:
  carried_out_by:
    name: carried_out_by
    range: MassSpectrometer
    required: true
  evaluated_entity:
    name: evaluated_entity
    range: MSSample
    required: true
    multivalued: false
    inlined: false
    inlined_as_list: false
attributes:
  acquisition_mode:
    name: acquisition_mode
    description: The acquisition mode used during the mass spectrometry measurement.
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    is_a: has_qualitative_attribute
    alias: acquisition_mode
    owner: MassSpectrometry
    domain_of:
    - MassSpectrometry
    range: AcquisitionMode
    required: true
  scan_polarity:
    name: scan_polarity
    description: The scan polarity used during the mass spectrometry measurement.
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    is_a: has_qualitative_attribute
    alias: scan_polarity
    owner: MassSpectrometry
    domain_of:
    - MassSpectrometry
    range: ScanPolarity
    required: true
  scan_window_lower_limit:
    name: scan_window_lower_limit
    description: The lower limit of the scan window used during the measurement, typically
      expressed in m/z.
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    is_a: has_quantitative_attribute
    alias: scan_window_lower_limit
    owner: MassSpectrometry
    domain_of:
    - MassSpectrometry
    range: ScanWindowLowerLimit
    required: true
  scan_window_upper_limit:
    name: scan_window_upper_limit
    description: The upper limit of the scan window used during the measurement, typically
      expressed in m/z.
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    is_a: has_quantitative_attribute
    alias: scan_window_upper_limit
    owner: MassSpectrometry
    domain_of:
    - MassSpectrometry
    range: ScanWindowUpperLimit
    required: true
  evaluated_entity:
    name: evaluated_entity
    description: The slot to specify the Entity about which the DataGeneratingActivity
      produced information.
    in_subset:
    - domain_agnostic_core
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    is_a: had_input_entity
    slot_uri: prov:used
    alias: evaluated_entity
    owner: MassSpectrometry
    domain_of:
    - DataGeneratingActivity
    range: MSSample
    required: true
    recommended: true
    multivalued: false
    inlined: false
    inlined_as_list: false
  evaluated_activity:
    name: evaluated_activity
    description: The slot to specify the Activity about which the DataGeneratingActivity
      produced information.
    in_subset:
    - domain_agnostic_core
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    is_a: had_input_activity
    slot_uri: prov:wasInformedBy
    alias: evaluated_activity
    owner: MassSpectrometry
    domain_of:
    - DataGeneratingActivity
    range: EvaluatedActivity
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  realized_plan:
    name: realized_plan
    description: The slot to specify the Plan (i.e. directive information or procedure)
      that was realized by an Activity.
    in_subset:
    - domain_agnostic_core
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    slot_uri: prov:used
    alias: realized_plan
    owner: MassSpectrometry
    domain_of:
    - DataGeneratingActivity
    range: Plan
  occurred_in:
    name: occurred_in
    description: The slot to specify the Surrounding in which an Activity took place.
    in_subset:
    - domain_agnostic_core
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    slot_uri: prov:atLocation
    alias: occurred_in
    owner: MassSpectrometry
    domain_of:
    - DataGeneratingActivity
    range: Surrounding
  id:
    name: id
    description: A slot to provide an URI for an entity within this schema.
    in_subset:
    - domain_agnostic_core
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    identifier: true
    alias: id
    owner: MassSpectrometry
    domain_of:
    - Activity
    - AgenticEntity
    - Dataset
    - DefinedTerm
    - Document
    - Entity
    - LegalResource
    - LicenseDocument
    - Resource
    range: uriorcurie
    required: true
  title:
    name: title
    description: The slot to provide a title for the Activity.
    notes:
    - not in DCAT-AP
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    slot_uri: dcterms:title
    alias: title
    owner: MassSpectrometry
    domain_of:
    - Activity
    - AgenticEntity
    - Any
    - Attribution
    - Catalogue
    - CatalogueRecord
    - ChecksumAlgorithm
    - Concept
    - ConceptScheme
    - DataService
    - Dataset
    - DatasetSeries
    - DefinedTerm
    - Distribution
    - Document
    - Entity
    - Frequency
    - Geometry
    - Identifier
    - LegalResource
    - LicenseDocument
    - LinguisticSystem
    - MediaType
    - MediaTypeOrExtent
    - PeriodOfTime
    - Plan
    - Policy
    - ProvenanceStatement
    - QualitativeAttribute
    - QuantitativeAttribute
    - Resource
    - RightsStatement
    - Role
    - Standard
    - SupportiveEntity
    - Surrounding
    - TimeInstant
    range: string
    multivalued: true
    inlined_as_list: true
  description:
    name: description
    description: The slot to provide a description for the Activity.
    notes:
    - not in DCAT-AP
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    slot_uri: dcterms:description
    alias: description
    owner: MassSpectrometry
    domain_of:
    - Activity
    - AgenticEntity
    - Any
    - Attribution
    - Catalogue
    - CatalogueRecord
    - ChecksumAlgorithm
    - Concept
    - ConceptScheme
    - DataService
    - Dataset
    - DatasetSeries
    - Distribution
    - Document
    - Entity
    - Frequency
    - Geometry
    - Identifier
    - LegalResource
    - LicenseDocument
    - LinguisticSystem
    - MediaType
    - MediaTypeOrExtent
    - PeriodOfTime
    - Plan
    - Policy
    - ProvenanceStatement
    - QualitativeAttribute
    - QuantitativeAttribute
    - Resource
    - RightsStatement
    - Role
    - Standard
    - SupportiveEntity
    - Surrounding
    - TimeInstant
    range: string
    multivalued: true
    inlined_as_list: true
  other_identifier:
    name: other_identifier
    description: The slot to provide a secondary identifier of the Activity.
    notes:
    - not in DCAT-AP
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    slot_uri: adms:identifier
    alias: other_identifier
    owner: MassSpectrometry
    domain_of:
    - Activity
    - AgenticEntity
    - Dataset
    - Entity
    range: Identifier
    multivalued: true
    inlined_as_list: true
  has_part:
    name: has_part
    description: The slot to provide an Activity that is part of the Activity.
    notes:
    - not in DCAT-AP
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    slot_uri: dcterms:hasPart
    alias: has_part
    owner: MassSpectrometry
    domain_of:
    - Activity
    - AgenticEntity
    - Catalogue
    - Entity
    range: Activity
    multivalued: true
    inlined_as_list: true
  had_input_entity:
    name: had_input_entity
    description: The slot to specify the Entity that was used as an input of an Activity
      that is to be changed, consumed or transformed.
    notes:
    - not in DCAT-AP
    in_subset:
    - domain_agnostic_core
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    slot_uri: prov:used
    alias: had_input_entity
    owner: MassSpectrometry
    domain_of:
    - Activity
    range: Entity
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  had_output_entity:
    name: had_output_entity
    description: The slot to specify the Entity that was generated as an output of
      an Activity.
    notes:
    - not in DCAT-AP
    in_subset:
    - domain_agnostic_core
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    slot_uri: prov:generated
    alias: had_output_entity
    owner: MassSpectrometry
    domain_of:
    - Activity
    range: Entity
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  had_input_activity:
    name: had_input_activity
    description: The slot to provide a previous Activity that informed the Activity
      by being causally via a shared participant.
    notes:
    - not in DCAT-AP
    in_subset:
    - domain_agnostic_core
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    slot_uri: prov:wasInformedBy
    alias: had_input_activity
    owner: MassSpectrometry
    domain_of:
    - Activity
    range: Activity
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  carried_out_by:
    name: carried_out_by
    description: The slot to specify the AgenticEntity that played a certain part
      in carrying out the Activity, either via having a specific role, function or
      disposition that was realized in the Activity.
    notes:
    - not in DCAT-AP
    in_subset:
    - domain_agnostic_core
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    slot_uri: prov:wasAssociatedWith
    alias: carried_out_by
    owner: MassSpectrometry
    domain_of:
    - Activity
    range: MassSpectrometer
    required: true
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_qualitative_attribute:
    name: has_qualitative_attribute
    description: The slot to relate a qualitative attribute to an EvaluatedEntity,
      EvaluatedActivity or AgenticEntity
    notes:
    - not in DCAT-AP
    in_subset:
    - domain_agnostic_core
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    slot_uri: dcterms:relation
    alias: has_qualitative_attribute
    owner: MassSpectrometry
    domain_of:
    - Activity
    - AgenticEntity
    - Entity
    range: QualitativeAttribute
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  has_quantitative_attribute:
    name: has_quantitative_attribute
    description: The slot to relate a quantitative attribute to an EvaluatedEntity,
      EvaluatedActivity or AgenticEntity
    notes:
    - not in DCAT-AP
    in_subset:
    - domain_agnostic_core
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    slot_uri: dcterms:relation
    alias: has_quantitative_attribute
    owner: MassSpectrometry
    domain_of:
    - Activity
    - AgenticEntity
    - Entity
    range: QuantitativeAttribute
    recommended: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  part_of:
    name: part_of
    description: The slot to provide an Activity of which the Activity is a part.
    notes:
    - not in DCAT-AP
    in_subset:
    - domain_agnostic_core
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    slot_uri: dcterms:isPartOf
    alias: part_of
    owner: MassSpectrometry
    domain_of:
    - Activity
    - AgenticEntity
    - Entity
    inverse: has_part
    range: Activity
    multivalued: true
    inlined_as_list: true
  type:
    name: type
    description: This slot is described in more detail within the class in which it
      is used.
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    slot_uri: dcterms:type
    alias: type
    owner: MassSpectrometry
    domain_of:
    - Agent
    - ClassifierMixin
    - Dataset
    - LicenseDocument
    range: DefinedTerm
    inlined: true
  rdf_type:
    name: rdf_type
    description: The slot to specify the ontology class that is instantiated by an
      entity.
    in_subset:
    - domain_agnostic_core
    from_schema: https://w3id.org/NFDI4Chem/ms-dcat-ap
    rank: 1000
    slot_uri: rdf:type
    alias: rdf_type
    owner: MassSpectrometry
    domain_of:
    - ClassifierMixin
    range: DefinedTerm
    recommended: true
    inlined: true