Class: MassSpectrometryInstrumentData

Raw data files output from a mass spectrometry instrument.

URI: basalt_schema:MassSpectrometryInstrumentData

 classDiagram
    class MassSpectrometryInstrumentData
    click MassSpectrometryInstrumentData href "../MassSpectrometryInstrumentData/"
      InstrumentData <|-- MassSpectrometryInstrumentData
        click InstrumentData href "../InstrumentData/"

      MassSpectrometryInstrumentData : alternative_identifiers

      MassSpectrometryInstrumentData : collection_mode





        MassSpectrometryInstrumentData --> "0..1" MassSpectrumCollectionModeEnum : collection_mode
        click MassSpectrumCollectionModeEnum href "../MassSpectrumCollectionModeEnum/"



      MassSpectrometryInstrumentData : compression_type

      MassSpectrometryInstrumentData : core_section





        MassSpectrometryInstrumentData --> "0..1" CoreSectionEnum : core_section
        click CoreSectionEnum href "../CoreSectionEnum/"



      MassSpectrometryInstrumentData : description

      MassSpectrometryInstrumentData : file_curie

      MassSpectrometryInstrumentData : file_type





        MassSpectrometryInstrumentData --> "0..1" FileTypeEnum : file_type
        click FileTypeEnum href "../FileTypeEnum/"



      MassSpectrometryInstrumentData : filesize

      MassSpectrometryInstrumentData : id

      MassSpectrometryInstrumentData : md5checksum

      MassSpectrometryInstrumentData : ms_raw_file_type





        MassSpectrometryInstrumentData --> "0..1" MassSpecRawFileTypeEnum : ms_raw_file_type
        click MassSpecRawFileTypeEnum href "../MassSpecRawFileTypeEnum/"



      MassSpectrometryInstrumentData : name

      MassSpectrometryInstrumentData : produced_by_ms_run





        MassSpectrometryInstrumentData --> "0..1" MassSpectrometryDataGenerationActivity : produced_by_ms_run
        click MassSpectrometryDataGenerationActivity href "../MassSpectrometryDataGenerationActivity/"



      MassSpectrometryInstrumentData : project

      MassSpectrometryInstrumentData : s3_base_url

      MassSpectrometryInstrumentData : s3_bucket

      MassSpectrometryInstrumentData : s3_key

      MassSpectrometryInstrumentData : sample_name

      MassSpectrometryInstrumentData : sampling_set

      MassSpectrometryInstrumentData : software_version

Inheritance

DataProduct
- InstrumentData
  - MassSpectrometryInstrumentData

Slots

Name	Cardinality and Range	Description	Inheritance
produced_by_ms_run	0..1 MassSpectrometryDataGenerationActivity	a reference to the data generation activity that produced instrument data	direct
ms_raw_file_type	0..1 MassSpecRawFileTypeEnum	the filetype of the mass spectrometry instrument data	direct
collection_mode	0..1 MassSpectrumCollectionModeEnum	The collection mode for the mass spectrometry data (e	direct
file_curie	0..1 String	an identifier for a file that resolves to the file's accessible location	InstrumentData
alternative_identifiers	0..1 String		InstrumentData
compression_type	0..1 String		InstrumentData
file_type	0..1 FileTypeEnum		InstrumentData
software_version	0..1 String		InstrumentData
name	1 String	Human-readable name for the entity or activity	DataProduct
description	1 String	Human-readable description for the entity or activity	DataProduct
project	0..1 Integer	Identifier for the user project associated with the entity or activity	DataProduct
sampling_set	0..1 Integer	Sampling set number for grouping related samples collected together	DataProduct
core_section	0..1 CoreSectionEnum	The section of the core	DataProduct
sample_name	0..1 String	The name or label that is present on the shipped sample	DataProduct
s3_base_url	0..1 String		DataProduct
s3_bucket	0..1 String		DataProduct
s3_key	1 String	MinIO/S3 object key; required for all data products	DataProduct
filesize	0..1 Integer	Size of the file in bytes	DataProduct
md5checksum	0..1 String		DataProduct
id	1 Uuid		DataProduct

Usages

used by	used in	type	used
MassSpectrometryDataProcessingActivity	uses_raw_ms_data	range	MassSpectrometryInstrumentData
MassSpectrometryStandardRun	calibration_data	range	MassSpectrometryInstrumentData

Identifier and Mapping Information

Schema Source

from schema: https://EMSL-Computing.github.io/BASALT-Schema

Mappings

Mapping Type	Mapped Value
self	basalt_schema:MassSpectrometryInstrumentData
native	basalt_schema:MassSpectrometryInstrumentData

LinkML Source

Direct

name: MassSpectrometryInstrumentData
description: Raw data files output from a mass spectrometry instrument.
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: InstrumentData
slots:
- produced_by_ms_run
- ms_raw_file_type
- collection_mode

Induced

name: MassSpectrometryInstrumentData
description: Raw data files output from a mass spectrometry instrument.
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: InstrumentData
attributes:
  produced_by_ms_run:
    name: produced_by_ms_run
    description: a reference to the data generation activity that produced instrument
      data
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: produced_by_ms_run
    owner: MassSpectrometryInstrumentData
    domain_of:
    - MassSpectrometryInstrumentData
    range: MassSpectrometryDataGenerationActivity
  ms_raw_file_type:
    name: ms_raw_file_type
    description: the filetype of the mass spectrometry instrument data
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: ms_raw_file_type
    owner: MassSpectrometryInstrumentData
    domain_of:
    - MassSpectrometryInstrumentData
    range: MassSpecRawFileTypeEnum
  collection_mode:
    name: collection_mode
    description: The collection mode for the mass spectrometry data (e.g., profile,
      centroid)
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: collection_mode
    owner: MassSpectrometryInstrumentData
    domain_of:
    - MassSpectrometryInstrumentData
    range: MassSpectrumCollectionModeEnum
  file_curie:
    name: file_curie
    description: an identifier for a file that resolves to the file's accessible location
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: file_curie
    owner: MassSpectrometryInstrumentData
    domain_of:
    - InstrumentData
    range: string
  alternative_identifiers:
    name: alternative_identifiers
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: alternative_identifiers
    owner: MassSpectrometryInstrumentData
    domain_of:
    - InstrumentData
    - OntologyClass
    range: string
  compression_type:
    name: compression_type
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: compression_type
    owner: MassSpectrometryInstrumentData
    domain_of:
    - InstrumentData
    range: string
  file_type:
    name: file_type
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: file_type
    owner: MassSpectrometryInstrumentData
    domain_of:
    - InstrumentData
    range: FileTypeEnum
  software_version:
    name: software_version
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: software_version
    owner: MassSpectrometryInstrumentData
    domain_of:
    - InstrumentData
    - DataProcessingActivity
    range: string
  name:
    name: name
    description: Human-readable name for the entity or activity.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: name
    owner: MassSpectrometryInstrumentData
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - Instrument
    - OntologyClass
    - ContainerAxis
    - Configuration
    - MobilePhaseSegment
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - Study
    - SoftwareControlledTermValue
    range: string
    required: true
  description:
    name: description
    description: Human-readable description for the entity or activity
    title: description
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: description
    owner: MassSpectrometryInstrumentData
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - OntologyClass
    - ContainerType
    - LabDevice
    - Configuration
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - Site
    - Sample
    - SamplingActivity
    - SoilSamplingActivity
    - Study
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - QuantityValue
    range: string
    required: true
  project:
    name: project
    description: 'Identifier for the user project associated with the entity or activity. '
    title: Project
    todos:
    - should this be an ID? CURIE can use the one NMDC has https://bioregistry.io/reference/emsl.project:60141
      where emsl.project is the CURIE prefix
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    aliases:
    - study
    - study_id
    - project_id
    - proposal
    - proposal_id
    rank: 1000
    alias: project
    owner: MassSpectrometryInstrumentData
    domain_of:
    - DataProduct
    - AerosolArmSample
    - AerosolSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    - SamplingActivity
    range: integer
  sampling_set:
    name: sampling_set
    description: 'Sampling set number for grouping related samples collected together.

      This is a user-defined sequential integer that can be used to link samples collected

      in the same sampling event or campaign.'
    title: sampling set
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: sampling_set
    owner: MassSpectrometryInstrumentData
    domain_of:
    - DataProduct
    - MonetSoilSample
    range: integer
  core_section:
    name: core_section
    description: The section of the core.
    title: core section
    examples:
    - value: TOP
    - value: MID
    - value: BTM
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: core_section
    owner: MassSpectrometryInstrumentData
    domain_of:
    - DataProduct
    - CoreSection
    range: CoreSectionEnum
  sample_name:
    name: sample_name
    description: 'The name or label that is present on the shipped sample. This should

      be a human readable name.'
    title: sample name
    notes:
    - This is typically an alias for the inherited 'name' slot on Sample classes.
      Defined separately for compatibility with source data files using 'sample_name'
      column headers.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    aliases:
    - samp_name
    rank: 1000
    alias: sample_name
    owner: MassSpectrometryInstrumentData
    domain_of:
    - DataProduct
    - AerosolArmSample
    - AerosolSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    range: string
  s3_base_url:
    name: s3_base_url
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: s3_base_url
    owner: MassSpectrometryInstrumentData
    domain_of:
    - DataProduct
    range: string
  s3_bucket:
    name: s3_bucket
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: s3_bucket
    owner: MassSpectrometryInstrumentData
    domain_of:
    - DataProduct
    range: string
  s3_key:
    name: s3_key
    description: MinIO/S3 object key; required for all data products
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: s3_key
    owner: MassSpectrometryInstrumentData
    domain_of:
    - DataProduct
    range: string
    required: true
  filesize:
    name: filesize
    description: Size of the file in bytes
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: filesize
    owner: MassSpectrometryInstrumentData
    domain_of:
    - DataProduct
    range: integer
  md5checksum:
    name: md5checksum
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: md5checksum
    owner: MassSpectrometryInstrumentData
    domain_of:
    - DataProduct
    range: string
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: MassSpectrometryInstrumentData
    domain_of:
    - Activity
    - Entity
    - DataProduct
    - DataGenerationActivity
    - DataProcessingActivity
    - AlternativeIdentifier
    - FunctionalAnnotationIdentifier
    - Instrument
    - OntologyClass
    - ContainerType
    - Custodian
    - InstrumentAlternativeIdentifier
    - LabDevice
    - SampleProcessing
    - ProcessingSampleLink
    - Configuration
    - MobilePhaseSegment
    - MassSpectrometryStandardRun
    - PurchasedMaterial
    - LabProcessingActivity
    - organism
    - MAOMProduct
    - WEOMProduct
    - Site
    - Sample
    - AerosolArmSample
    - AerosolSample
    - AMP2UserSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - EngineeredStrainSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    - ProcessedSample
    - CoreSection
    - SamplingActivity
    - AerosolArmSamplingActivity
    - AerosolSamplingActivity
    - CommerciallyPurchasedSamplingActivity
    - CultureEnvironmentalSamplingActivity
    - EngineeredStrainSamplingActivity
    - FieldDeployedTerraformSamplingActivity
    - MixedCultureSamplingActivity
    - MonetSoilSamplingActivity
    - OtherUndescribedSamplingActivity
    - PlantSamplingActivity
    - PureCultureSamplingActivity
    - SedimentSamplingActivity
    - SoilSamplingActivity
    - SynthesizedMaterialSamplingActivity
    - TerraformSamplingActivity
    - WaterSamplingActivity
    - Study
    - ProjectParticipant
    - TimestampValue
    - TextValue
    - SoftwareControlledTermValue
    - ControlledTermValue
    - PersonValue
    - QuantityValue
    - ConditioningValue
    - zipDownload
    range: uuid
    required: true