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Class: NucleicAcidExtraction (NucleicAcidExtraction)

Metadata describing a nucleic acid extraction experiment

URI: microbial_experiment_schema:NucleicAcidExtraction

classDiagram class NucleicAcidExtraction click NucleicAcidExtraction href "../NucleicAcidExtraction" ExperimentWithInstrument <|-- NucleicAcidExtraction click ExperimentWithInstrument href "../ExperimentWithInstrument" NucleicAcidExtraction : core_data_path NucleicAcidExtraction --> "1" StringValue : core_data_path click StringValue href "../StringValue" NucleicAcidExtraction : data_acquisition_date NucleicAcidExtraction --> "1" DateValue : data_acquisition_date click DateValue href "../DateValue" NucleicAcidExtraction : elab_experiment NucleicAcidExtraction --> "1" ELabExperiment : elab_experiment click ELabExperiment href "../ELabExperiment" NucleicAcidExtraction : instrument_id NucleicAcidExtraction --> "1" ELabItemValue : instrument_id click ELabItemValue href "../ELabItemValue" NucleicAcidExtraction : kit_lot_number NucleicAcidExtraction --> "0..1" ELabItemValue : kit_lot_number click ELabItemValue href "../ELabItemValue" NucleicAcidExtraction : microbial_material_id NucleicAcidExtraction --> "0..1" MicrobialMaterialIDValue : microbial_material_id click MicrobialMaterialIDValue href "../MicrobialMaterialIDValue" NucleicAcidExtraction : nucleic_acid_type NucleicAcidExtraction --> "0..1" NucleicAcidTypeValue : nucleic_acid_type click NucleicAcidTypeValue href "../NucleicAcidTypeValue" NucleicAcidExtraction : operator_id NucleicAcidExtraction --> "1" OperatorIDValue : operator_id click OperatorIDValue href "../OperatorIDValue" NucleicAcidExtraction : project_id NucleicAcidExtraction --> "1" ELabItemValue : project_id click ELabItemValue href "../ELabItemValue" NucleicAcidExtraction : sample_purpose_codes NucleicAcidExtraction --> "0..1" SamplePurposeCodesValue : sample_purpose_codes click SamplePurposeCodesValue href "../SamplePurposeCodesValue" NucleicAcidExtraction : specific_data_path NucleicAcidExtraction --> "1" StringValue : specific_data_path click StringValue href "../StringValue" NucleicAcidExtraction : template_name NucleicAcidExtraction --> "1" NucleicAcidExtractionTemplateNameValue : template_name click NucleicAcidExtractionTemplateNameValue href "../NucleicAcidExtractionTemplateNameValue"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
kit_lot_number 0..1
ELabItemValue		 The lot number of any relevant kits (linked item from ELabFTW) direct
microbial_material_id 0..1
MicrobialMaterialIDValue		 Cell material(s) used in experiment as named in the eLabFTW database (linked ... direct
nucleic_acid_type 0..1
NucleicAcidTypeValue		 The type of nucleic acid used in an extraction experiment direct
sample_purpose_codes 0..1
SamplePurposeCodesValue		 The types of samples acquired in an experiment (from a controlled list) direct
instrument_id 1
ELabItemValue		 The instrument used to acquire the data in an experiment (linked item from EL... ExperimentWithInstrument
core_data_path 1
StringValue		 Portion of the data pathway that will not change as the template is used to g... ExperimentWithData
specific_data_path 1
StringValue		 Portion of the data pathway specific to data from a given experimental record... ExperimentWithData
data_acquisition_date 1
DateValue		 Date on which data were acquired according to eLabFTW record Experiment
elab_experiment 1
ELabExperiment		 A self-reference to this experiment record Experiment
operator_id 1
OperatorIDValue		 Instrument operator during an experiment (a linked item from ELabFTW) Experiment
project_id 1
ELabItemValue		 The project that an experiment supports (link to an ELabFTW item) Experiment
template_name 1
NucleicAcidExtractionTemplateNameValue		 The name of the template used to collect metadata for an experiment in ELabFT... Experiment

Identifier and Mapping Information

Annotations

property value
elabftw_template True

Schema Source

  • from schema: https://w3id.org/usnistgov/microbial-experiment-schema

Mappings

Mapping Type Mapped Value
self microbial_experiment_schema:NucleicAcidExtraction
native microbial_experiment_schema:NucleicAcidExtraction

LinkML Source

Direct

name: NucleicAcidExtraction
annotations:
  elabftw_template:
    tag: elabftw_template
    value: true
description: Metadata describing a nucleic acid extraction experiment
title: NucleicAcidExtraction
from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
is_a: ExperimentWithInstrument
slots:
- kit_lot_number
- microbial_material_id
- nucleic_acid_type
- sample_purpose_codes
slot_usage:
  template_name:
    name: template_name
    range: NucleicAcidExtractionTemplateNameValue

Induced

name: NucleicAcidExtraction
annotations:
  elabftw_template:
    tag: elabftw_template
    value: true
description: Metadata describing a nucleic acid extraction experiment
title: NucleicAcidExtraction
from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
is_a: ExperimentWithInstrument
slot_usage:
  template_name:
    name: template_name
    range: NucleicAcidExtractionTemplateNameValue
attributes:
  kit_lot_number:
    name: kit_lot_number
    description: The lot number of any relevant kits (linked item from ELabFTW)
    title: KitLotNumber
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: kit_lot_number
    owner: NucleicAcidExtraction
    domain_of:
    - NucleicAcidExtraction
    - GenericTemplateDeprecated
    - GenericTemplate
    range: ELabItemValue
    required: false
  microbial_material_id:
    name: microbial_material_id
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: LabCAS
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: Cell material(s) used in experiment as named in the eLabFTW database
      (linked items)
    title: MicrobialMaterialID
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: microbial_material_id
    owner: NucleicAcidExtraction
    domain_of:
    - CytoFLEXAcquisition
    - NucleicAcidExtraction
    - CellCultureInBroth
    - GenericTemplateDeprecated
    - FormaldehydeFixation
    - MicroscopyAcquisition
    - GenericTemplate
    - CoulterAcquisition
    - BactoBoxAcquisition
    - LogCOMETSamplePrep
    - CFU
    - InitiateGrowthOfBSpizizenii
    range: MicrobialMaterialIDValue
    required: false
  nucleic_acid_type:
    name: nucleic_acid_type
    description: The type of nucleic acid used in an extraction experiment
    title: NucleicAcidType
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: nucleic_acid_type
    owner: NucleicAcidExtraction
    domain_of:
    - NucleicAcidExtraction
    - GenericTemplateDeprecated
    - GenericTemplate
    range: NucleicAcidTypeValue
    required: false
  sample_purpose_codes:
    name: sample_purpose_codes
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: Generic Microbial
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: The types of samples acquired in an experiment (from a controlled
      list)
    title: SamplePurposeCodes
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    ifabsent: Positive control
    alias: sample_purpose_codes
    owner: NucleicAcidExtraction
    domain_of:
    - CytoFLEXAcquisition
    - NucleicAcidExtraction
    - CellCultureInBroth
    - GenericTemplateDeprecated
    - FormaldehydeFixation
    - MicroscopyAcquisition
    - GenericTemplate
    - CoulterAcquisition
    - BactoBoxAcquisition
    - LogCOMETSamplePrep
    - CFU
    - InitiateGrowthOfBSpizizenii
    range: SamplePurposeCodesValue
    required: false
  instrument_id:
    name: instrument_id
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: LabCAS
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: The instrument used to acquire the data in an experiment (linked
      item from ELabFTW)
    title: InstrumentID
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: instrument_id
    owner: NucleicAcidExtraction
    domain_of:
    - ExperimentWithInstrument
    - ExperimentWithInstrumentNoData
    range: ELabItemValue
    required: true
  core_data_path:
    name: core_data_path
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: LabCAS
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
      read_only:
        tag: read_only
        value: true
    description: Portion of the data pathway that will not change as the template
      is used to generate experimental records (should be network-resolvable)
    title: CoreDataPath
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: core_data_path
    owner: NucleicAcidExtraction
    domain_of:
    - ExperimentWithData
    range: StringValue
    required: true
  specific_data_path:
    name: specific_data_path
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: LabCAS
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: Portion of the data pathway specific to data from a given experimental
      record  (should be a sub-path of the location specified by `CoreDataPath`)
    title: SpecificDataPath
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: specific_data_path
    owner: NucleicAcidExtraction
    domain_of:
    - ExperimentWithData
    range: StringValue
    required: true
  data_acquisition_date:
    name: data_acquisition_date
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: LabCAS
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: Date on which data were acquired according to eLabFTW record
    title: DataAcquisitionDate
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: data_acquisition_date
    owner: NucleicAcidExtraction
    domain_of:
    - Experiment
    range: DateValue
    required: true
  elab_experiment:
    name: elab_experiment
    annotations:
      elabftw_user_input:
        tag: elabftw_user_input
        value: false
    description: A self-reference to this experiment record
    title: ELabFTW Experiment
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: elab_experiment
    owner: NucleicAcidExtraction
    domain_of:
    - Experiment
    range: ELabExperiment
    required: true
    inlined: true
    inlined_as_list: true
  operator_id:
    name: operator_id
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: LabCAS
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: Instrument operator during an experiment (a linked item from ELabFTW)
    title: OperatorID
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: operator_id
    owner: NucleicAcidExtraction
    domain_of:
    - Experiment
    range: OperatorIDValue
    required: true
  project_id:
    name: project_id
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: LabCAS
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: The project that an experiment supports (link to an ELabFTW item)
    title: ProjectID
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: project_id
    owner: NucleicAcidExtraction
    domain_of:
    - Experiment
    range: ELabItemValue
    required: true
  template_name:
    name: template_name
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: LabCAS
      read_only:
        tag: read_only
        value: true
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: The name of the template used to collect metadata for an experiment
      in ELabFTW. This value controls what specific metadata fields are allowed.
    title: TemplateName
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: template_name
    owner: NucleicAcidExtraction
    domain_of:
    - Experiment
    range: NucleicAcidExtractionTemplateNameValue
    required: true