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Class: NucleotideSequencing

A lab activity in which DNA or RNA that was extracted from a sample is sequenced.

URI: basalt_schema:NucleotideSequencing

 classDiagram
    class NucleotideSequencing
    click NucleotideSequencing href "../NucleotideSequencing/"
      DataGenerationActivity <|-- NucleotideSequencing
        click DataGenerationActivity href "../DataGenerationActivity/"

      NucleotideSequencing : acquisition_end_time

      NucleotideSequencing : acquisition_start_time

      NucleotideSequencing : analyte_id





        NucleotideSequencing --> "0..1" ProcessedSample : analyte_id
        click ProcessedSample href "../ProcessedSample/"



      NucleotideSequencing : description

      NucleotideSequencing : external_identifiers

      NucleotideSequencing : id

      NucleotideSequencing : instrument_operator_id





        NucleotideSequencing --> "0..1" PersonValue : instrument_operator_id
        click PersonValue href "../PersonValue/"



      NucleotideSequencing : instrument_used





        NucleotideSequencing --> "0..1" Instrument : instrument_used
        click Instrument href "../Instrument/"



      NucleotideSequencing : name

      NucleotideSequencing : nucleotide_sequencing_category





        NucleotideSequencing --> "0..1" NucleotideSequencingEnum : nucleotide_sequencing_category
        click NucleotideSequencingEnum href "../NucleotideSequencingEnum/"



      NucleotideSequencing : protocol_url

      NucleotideSequencing : protocol_version

      NucleotideSequencing : sequence_order

Inheritance

Slots

Name Cardinality and Range Description Inheritance
nucleotide_sequencing_category 0..1
NucleotideSequencingEnum		 The category of nucleotide sequencing performed (e direct
external_identifiers *
Uriorcurie		 List of external identifiers (e direct
sequence_order 0..1
Integer		 Integer ordering within a temporal series for the same analyte DataGenerationActivity
name 1
String		 Human-readable name for the entity or activity DataGenerationActivity
description 0..1
String		 Human-readable description for the entity or activity DataGenerationActivity
protocol_url 0..1
String		 URL pointing to the protocol used in the activity, if applicable DataGenerationActivity
protocol_version 0..1
String		 Version of the protocol used in the activity, if applicable DataGenerationActivity
id 1
Uuid		 DataGenerationActivity
analyte_id 0..1
ProcessedSample		 DataGenerationActivity
acquisition_start_time 1
Datetime		 DataGenerationActivity
acquisition_end_time 1
Datetime		 DataGenerationActivity
instrument_used 0..1
Instrument		 DataGenerationActivity
instrument_operator_id 0..1
PersonValue		 DataGenerationActivity

Usages

used by used in type used
NucleotideSequencingInstrumentData produced_by_sequencing_activity range NucleotideSequencing

Identifier and Mapping Information

Schema Source

Mappings

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

LinkML Source

Direct

name: NucleotideSequencing
description: A lab activity in which DNA or RNA that was extracted from a sample is
  sequenced.
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: DataGenerationActivity
slots:
- nucleotide_sequencing_category
- external_identifiers
slot_usage:
  external_identifiers:
    name: external_identifiers
    description: List of external identifiers (e.g., GOLD sequencing project, NCBI
      BioProject) associated with this sequencing activity.

Induced

name: NucleotideSequencing
description: A lab activity in which DNA or RNA that was extracted from a sample is
  sequenced.
from_schema: https://EMSL-Computing.github.io/BASALT-Schema
is_a: DataGenerationActivity
slot_usage:
  external_identifiers:
    name: external_identifiers
    description: List of external identifiers (e.g., GOLD sequencing project, NCBI
      BioProject) associated with this sequencing activity.
attributes:
  nucleotide_sequencing_category:
    name: nucleotide_sequencing_category
    description: The category of nucleotide sequencing performed (e.g., amplicon,
      shotgun).
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: nucleotide_sequencing_category
    owner: NucleotideSequencing
    domain_of:
    - NucleotideSequencing
    range: NucleotideSequencingEnum
  external_identifiers:
    name: external_identifiers
    description: List of external identifiers (e.g., GOLD sequencing project, NCBI
      BioProject) associated with this sequencing activity.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: external_identifiers
    owner: NucleotideSequencing
    domain_of:
    - NucleotideSequencing
    - AerosolArmSample
    - AerosolSample
    - CommerciallyPurchasedSample
    - CultureEnvironmentalSample
    - EngineeredStrainSample
    - FieldDeployedTerraformSample
    - MixedCultureSample
    - MonetSoilSample
    - OtherUndescribedSample
    - PlantSample
    - PureCultureSample
    - SedimentSample
    - SoilSample
    - SynthesizedMaterialSample
    - TerraformSample
    - WaterSample
    - Study
    range: uriorcurie
    multivalued: true
  sequence_order:
    name: sequence_order
    description: "Integer ordering within a temporal series for the same analyte.\n\
      Lower = earlier in series. Use when acquisition_time alone is insufficient.\n\
      \nDDL: ALTER TABLE \"DataGenerationActivity\"\n       ADD COLUMN sequence_order\
      \ INTEGER;"
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: sequence_order
    owner: NucleotideSequencing
    domain_of:
    - DataGenerationActivity
    range: integer
    required: false
  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: NucleotideSequencing
    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: NucleotideSequencing
    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
  protocol_url:
    name: protocol_url
    description: URL pointing to the protocol used in the activity, if applicable.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: protocol_url
    owner: NucleotideSequencing
    domain_of:
    - DataGenerationActivity
    - SampleProcessing
    range: string
  protocol_version:
    name: protocol_version
    description: Version of the protocol used in the activity, if applicable.
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: protocol_version
    owner: NucleotideSequencing
    domain_of:
    - DataGenerationActivity
    - SampleProcessing
    range: string
  id:
    name: id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    identifier: true
    alias: id
    owner: NucleotideSequencing
    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
  analyte_id:
    name: analyte_id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: analyte_id
    owner: NucleotideSequencing
    domain_of:
    - DataGenerationActivity
    range: ProcessedSample
  acquisition_start_time:
    name: acquisition_start_time
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: acquisition_start_time
    owner: NucleotideSequencing
    domain_of:
    - DataGenerationActivity
    range: datetime
    required: true
  acquisition_end_time:
    name: acquisition_end_time
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: acquisition_end_time
    owner: NucleotideSequencing
    domain_of:
    - DataGenerationActivity
    range: datetime
    required: true
  instrument_used:
    name: instrument_used
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: instrument_used
    owner: NucleotideSequencing
    domain_of:
    - DataGenerationActivity
    range: Instrument
  instrument_operator_id:
    name: instrument_operator_id
    from_schema: https://EMSL-Computing.github.io/BASALT-Schema
    rank: 1000
    alias: instrument_operator_id
    owner: NucleotideSequencing
    domain_of:
    - DataGenerationActivity
    range: PersonValue