Class: MassSpectrometryConfiguration
A set of parameters that define and control the actions of a mass spectrometry process.
URI: nmdc:MassSpectrometryConfiguration
classDiagram
class MassSpectrometryConfiguration
click MassSpectrometryConfiguration href "../MassSpectrometryConfiguration"
Configuration <|-- MassSpectrometryConfiguration
click Configuration href "../Configuration"
MassSpectrometryConfiguration : alternative_identifiers
MassSpectrometryConfiguration : description
MassSpectrometryConfiguration : id
MassSpectrometryConfiguration : ionization_source
MassSpectrometryConfiguration --> "0..1" IonizationSourceEnum : ionization_source
click IonizationSourceEnum href "../IonizationSourceEnum"
MassSpectrometryConfiguration : mass_analyzers
MassSpectrometryConfiguration --> "*" MassAnalyzerEnum : mass_analyzers
click MassAnalyzerEnum href "../MassAnalyzerEnum"
MassSpectrometryConfiguration : mass_spectrometry_acquisition_strategy
MassSpectrometryConfiguration --> "0..1" MassSpectrometryAcquisitionStrategyEnum : mass_spectrometry_acquisition_strategy
click MassSpectrometryAcquisitionStrategyEnum href "../MassSpectrometryAcquisitionStrategyEnum"
MassSpectrometryConfiguration : mass_spectrum_collection_modes
MassSpectrometryConfiguration --> "*" MassSpectrumCollectionModeEnum : mass_spectrum_collection_modes
click MassSpectrumCollectionModeEnum href "../MassSpectrumCollectionModeEnum"
MassSpectrometryConfiguration : name
MassSpectrometryConfiguration : polarity_mode
MassSpectrometryConfiguration --> "0..1" PolarityModeEnum : polarity_mode
click PolarityModeEnum href "../PolarityModeEnum"
MassSpectrometryConfiguration : resolution_categories
MassSpectrometryConfiguration --> "*" ResolutionCategoryEnum : resolution_categories
click ResolutionCategoryEnum href "../ResolutionCategoryEnum"
MassSpectrometryConfiguration : type
Inheritance
- NamedThing
- InformationObject
- Configuration
- MassSpectrometryConfiguration
- Configuration
- InformationObject
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
mass_spectrometry_acquisition_strategy | 0..1 MassSpectrometryAcquisitionStrategyEnum |
Mode of running a mass spectrometer method by which m/z ranges are selected a... | direct |
resolution_categories | * ResolutionCategoryEnum |
The relative resolution at which spectra were collected | direct |
mass_analyzers | * MassAnalyzerEnum |
The kind of mass analyzer(s) used during the spectra collection | direct |
ionization_source | 0..1 IonizationSourceEnum |
The ionization source used to introduce processed samples into a mass spectro... | direct |
mass_spectrum_collection_modes | * MassSpectrumCollectionModeEnum |
Indicates whether mass spectra were collected in full profile, reduced profil... | direct |
polarity_mode | 0..1 PolarityModeEnum |
the polarity of which ions are generated and detected | direct |
id | 1 Uriorcurie |
A unique identifier for a thing | NamedThing |
name | 1 String |
A human readable label for an entity | NamedThing |
description | 1 String |
a human-readable description of a thing | NamedThing |
alternative_identifiers | * Uriorcurie |
A list of alternative identifiers for the entity | NamedThing |
type | 1 Uriorcurie |
the class_uri of the class that has been instantiated | NamedThing |
Usages
used by | used in | type | used |
---|---|---|---|
MassSpectrometry | has_mass_spectrometry_configuration | range | MassSpectrometryConfiguration |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/nmdc/nmdc
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc:MassSpectrometryConfiguration |
native | nmdc:MassSpectrometryConfiguration |
LinkML Source
Direct
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
domain_of:
- PersonValue
- NamedThing
- Protocol
required: true
description:
name: description
domain_of:
- ImageValue
- NamedThing
required: true
id:
name: id
domain_of:
- NamedThing
structured_pattern:
syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'
interpolated: true
class_uri: nmdc:MassSpectrometryConfiguration
Induced
name: MassSpectrometryConfiguration
description: A set of parameters that define and control the actions of a mass spectrometry
process.
notes:
- This class is intended to represent a mass spectrometry method file that controls
a mass spectrometry process.
from_schema: https://w3id.org/nmdc/nmdc
is_a: Configuration
slot_usage:
name:
name: name
domain_of:
- PersonValue
- NamedThing
- Protocol
required: true
description:
name: description
domain_of:
- ImageValue
- NamedThing
required: true
id:
name: id
domain_of:
- NamedThing
structured_pattern:
syntax: '{id_nmdc_prefix}:mscon-{id_shoulder}-{id_blade}$'
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
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