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Class: GenericTemplate_Deprecated (GenericTemplateDeprecated) (DEPRECATED) (Abstract)

A retired version of a generic experiment template used to create other templates

  • NOTE: this is an abstract class and should not be instantiated directly

  • NOTE this element has been deprecated with the following note:

    • (2024 June) this is no longer used, use GenericTemplate instead
    • Element has been replaced by GenericTemplate

URI: microbial_experiment_schema:GenericTemplateDeprecated

classDiagram class GenericTemplateDeprecated click GenericTemplateDeprecated href "../GenericTemplateDeprecated" ExperimentWithInstrument <|-- GenericTemplateDeprecated click ExperimentWithInstrument href "../ExperimentWithInstrument" GenericTemplateDeprecated : acquisition_time GenericTemplateDeprecated --> "0..1" DurationValue : acquisition_time click DurationValue href "../DurationValue" GenericTemplateDeprecated : acquisition_volume GenericTemplateDeprecated --> "0..1" VolumeValue : acquisition_volume click VolumeValue href "../VolumeValue" GenericTemplateDeprecated : bead_lot_number_concentration_qc GenericTemplateDeprecated --> "0..1" StringValue : bead_lot_number_concentration_qc click StringValue href "../StringValue" GenericTemplateDeprecated : bead_lot_number_size_qc GenericTemplateDeprecated --> "0..1" StringValue : bead_lot_number_size_qc click StringValue href "../StringValue" GenericTemplateDeprecated : cell_volume GenericTemplateDeprecated --> "0..1" VolumeValue : cell_volume click VolumeValue href "../VolumeValue" GenericTemplateDeprecated : cfu_method GenericTemplateDeprecated --> "0..1" CFUMethodValue : cfu_method click CFUMethodValue href "../CFUMethodValue" GenericTemplateDeprecated : core_data_path GenericTemplateDeprecated --> "1" StringValue : core_data_path click StringValue href "../StringValue" GenericTemplateDeprecated : coulter_aperture_size GenericTemplateDeprecated --> "0..1" LengthValue : coulter_aperture_size click LengthValue href "../LengthValue" GenericTemplateDeprecated : data_acquisition_date GenericTemplateDeprecated --> "1" DateValue : data_acquisition_date click DateValue href "../DateValue" GenericTemplateDeprecated : diluent_name GenericTemplateDeprecated --> "0..1" ELabItemValue : diluent_name click ELabItemValue href "../ELabItemValue" GenericTemplateDeprecated : diluent_volume GenericTemplateDeprecated --> "0..1" VolumeValue : diluent_volume click VolumeValue href "../VolumeValue" GenericTemplateDeprecated : elab_experiment GenericTemplateDeprecated --> "1" ELabExperiment : elab_experiment click ELabExperiment href "../ELabExperiment" GenericTemplateDeprecated : error_flag GenericTemplateDeprecated --> "0..1" BooleanValue : error_flag click BooleanValue href "../BooleanValue" GenericTemplateDeprecated : fc_acquisition_count_target GenericTemplateDeprecated --> "0..1" CountValue : fc_acquisition_count_target click CountValue href "../CountValue" GenericTemplateDeprecated : fc_acquisition_threshold_channel GenericTemplateDeprecated --> "0..1" StringValue : fc_acquisition_threshold_channel click StringValue href "../StringValue" GenericTemplateDeprecated : fc_acquisition_threshold_value GenericTemplateDeprecated --> "0..1" NumberValue : fc_acquisition_threshold_value click NumberValue href "../NumberValue" GenericTemplateDeprecated : fc_flow_rate_setting GenericTemplateDeprecated --> "0..1" FlowRateValue : fc_flow_rate_setting click FlowRateValue href "../FlowRateValue" GenericTemplateDeprecated : fc_fluorescent_channels GenericTemplateDeprecated --> "0..1" StringValue : fc_fluorescent_channels click StringValue href "../StringValue" GenericTemplateDeprecated : fc_injection_mode GenericTemplateDeprecated --> "0..1" FCInjectionModeValue : fc_injection_mode click FCInjectionModeValue href "../FCInjectionModeValue" GenericTemplateDeprecated : fixation_method GenericTemplateDeprecated --> "0..1" FixationMethodValue : fixation_method click FixationMethodValue href "../FixationMethodValue" GenericTemplateDeprecated : fluorescent_probe GenericTemplateDeprecated --> "0..1" FluorescentProbeValue : fluorescent_probe click FluorescentProbeValue href "../FluorescentProbeValue" GenericTemplateDeprecated : growth_duration GenericTemplateDeprecated --> "0..1" DurationValue : growth_duration click DurationValue href "../DurationValue" GenericTemplateDeprecated : growth_media_name GenericTemplateDeprecated --> "0..1" ELabItemValue : growth_media_name click ELabItemValue href "../ELabItemValue" GenericTemplateDeprecated : incubation_agitation GenericTemplateDeprecated --> "0..1" AgitationValue : incubation_agitation click AgitationValue href "../AgitationValue" GenericTemplateDeprecated : incubation_atmosphere GenericTemplateDeprecated --> "0..1" IncubationAtmosphereValue : incubation_atmosphere click IncubationAtmosphereValue href "../IncubationAtmosphereValue" GenericTemplateDeprecated : incubation_duration GenericTemplateDeprecated --> "0..1" DurationValue : incubation_duration click DurationValue href "../DurationValue" GenericTemplateDeprecated : incubation_temperature GenericTemplateDeprecated --> "0..1" TemperatureValue : incubation_temperature click TemperatureValue href "../TemperatureValue" GenericTemplateDeprecated : instrument_id GenericTemplateDeprecated --> "1" ELabItemValue : instrument_id click ELabItemValue href "../ELabItemValue" GenericTemplateDeprecated : kit_lot_number GenericTemplateDeprecated --> "0..1" ELabItemValue : kit_lot_number click ELabItemValue href "../ELabItemValue" GenericTemplateDeprecated : labcas_data_acquisition_date GenericTemplateDeprecated --> "0..1" DateValue : labcas_data_acquisition_date click DateValue href "../DateValue" GenericTemplateDeprecated : labcas_instrument GenericTemplateDeprecated --> "0..1" LabCASInstrumentValue : labcas_instrument click LabCASInstrumentValue href "../LabCASInstrumentValue" GenericTemplateDeprecated : labcas_microbial_material_id GenericTemplateDeprecated --> "0..1" LabCASMicrobialMaterialIDValue : labcas_microbial_material_id click LabCASMicrobialMaterialIDValue href "../LabCASMicrobialMaterialIDValue" GenericTemplateDeprecated : labcas_operator GenericTemplateDeprecated --> "0..1" LabCASOperatorValue : labcas_operator click LabCASOperatorValue href "../LabCASOperatorValue" GenericTemplateDeprecated : labcas_project GenericTemplateDeprecated --> "0..1" LabCASProjectValue : labcas_project click LabCASProjectValue href "../LabCASProjectValue" GenericTemplateDeprecated : library_prep GenericTemplateDeprecated --> "0..1" StringValue : library_prep click StringValue href "../StringValue" GenericTemplateDeprecated : microbial_material_id GenericTemplateDeprecated --> "0..1" MicrobialMaterialIDValue : microbial_material_id click MicrobialMaterialIDValue href "../MicrobialMaterialIDValue" GenericTemplateDeprecated : nucleic_acid_type GenericTemplateDeprecated --> "0..1" NucleicAcidTypeValue : nucleic_acid_type click NucleicAcidTypeValue href "../NucleicAcidTypeValue" GenericTemplateDeprecated : objective GenericTemplateDeprecated --> "0..1" ObjectivesValue : objective click ObjectivesValue href "../ObjectivesValue" GenericTemplateDeprecated : operator_id GenericTemplateDeprecated --> "1" OperatorIDValue : operator_id click OperatorIDValue href "../OperatorIDValue" GenericTemplateDeprecated : project_id GenericTemplateDeprecated --> "1" ELabItemValue : project_id click ELabItemValue href "../ELabItemValue" GenericTemplateDeprecated : qc_reagent_lot_number GenericTemplateDeprecated --> "0..1" StringValue : qc_reagent_lot_number click StringValue href "../StringValue" GenericTemplateDeprecated : sample_purpose_codes GenericTemplateDeprecated --> "0..1" SamplePurposeCodesValue : sample_purpose_codes click SamplePurposeCodesValue href "../SamplePurposeCodesValue" GenericTemplateDeprecated : specific_data_path GenericTemplateDeprecated --> "1" StringValue : specific_data_path click StringValue href "../StringValue" GenericTemplateDeprecated : template_name GenericTemplateDeprecated --> "1" StringValue : template_name click StringValue href "../StringValue" GenericTemplateDeprecated : transmission_mode GenericTemplateDeprecated --> "0..1" TransmissionModeValue : transmission_mode click TransmissionModeValue href "../TransmissionModeValue"

Inheritance

Slots

Name Cardinality and Range Description Inheritance
acquisition_time 0..1
DurationValue		 Data acquisition time as set by instrument direct
acquisition_volume 0..1
VolumeValue		 Data acquisition volume as set by instrument direct
bead_lot_number_concentration_qc 0..1
StringValue		 Lot number of beads used for quality control of concentration measurements direct
bead_lot_number_size_qc 0..1
StringValue		 Lot number of beads used for quality control of size measurements direct
cell_volume 0..1
VolumeValue		 Volume of cell stock added to acquisition vessel direct
cfu_method 0..1
CFUMethodValue		 Describes deposition format of cells on agar plate direct
coulter_aperture_size 0..1
LengthValue		 Aperture installed on Coulter counter during measurement direct
diluent_name 0..1
ELabItemValue		 Which diluent was used to suspend cells for acquisition (linked item) direct
diluent_volume 0..1
VolumeValue		 Volume of diluent added to acquisition vessel direct
error_flag 0..1
BooleanValue		 Indicates if a known error appears in the dataset direct
fc_acquisition_count_target 0..1
CountValue		 Set number of events to acquire in a particular gate on flow cytometer direct
fc_acquisition_threshold_channel 0..1
StringValue		 Which channel as named by the manufacturer was used to threshold the data acq... direct
fc_acquisition_threshold_value 0..1
NumberValue		 Threshold value in arbitrary units that defines the lower limit of data acqui... direct
fc_flow_rate_setting 0..1
FlowRateValue		 Set flow rate of data acquisition on flow cytometer direct
fc_fluorescent_channels 0..1
StringValue		 List of fluorescent channels acquired during a flow cytometry experiment as n... direct
fc_injection_mode 0..1
FCInjectionModeValue		 Sample acquisition format in flow cytometer direct
fixation_method 0..1
FixationMethodValue		 Specific treatment applied to cells to prevent future changes direct
fluorescent_probe 0..1
FluorescentProbeValue		 Fluorescent probe(s) used in the experiment, as linked item(s) from ELabFTW direct
growth_duration 0..1
DurationValue		 Time that cells were incubated to encourage growth direct
growth_media_name 0..1
ELabItemValue		 Name of media used to culture cells (linked item from ELabFTW) direct
incubation_agitation 0..1
AgitationValue		 Speed of agitation that cells were incubated during an experiment direct
incubation_atmosphere 0..1
IncubationAtmosphereValue		 Atmosphere that cells were incubated in to encourage growth direct
incubation_duration 0..1
DurationValue		 Length of time that cells were incubated during an experiment direct
incubation_temperature 0..1
TemperatureValue		 Temperature at which cells were incubated during an experiment or culture direct
kit_lot_number 0..1
ELabItemValue		 The lot number of any relevant kits (linked item from ELabFTW) direct
labcas_data_acquisition_date 0..1
DateValue		 Date on which data were acquired according to eLabFTW record direct
labcas_instrument 0..1
LabCASInstrumentValue		 Date on which data were acquired according to eLabFTW record direct
labcas_microbial_material_id 0..1
LabCASMicrobialMaterialIDValue		 Cell material(s) used in experiment as named in the eLabFTW database (linked ... direct
labcas_operator 0..1
LabCASOperatorValue		 Instrument operator during an experiment (a linked item from ELabFTW) direct
labcas_project 0..1
LabCASProjectValue		 The project that an experiment supports (link to an ELabFTW item) direct
library_prep 0..1
StringValue		 The name of a specific kit used for sequencing preparation steps 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
objective 0..1
ObjectivesValue		 The microscope objectives used in a microscopy acquisition experiment direct
qc_reagent_lot_number 0..1
StringValue		 The lot number for a QC reagent (link to an ELabFTW item) direct
sample_purpose_codes 0..1
SamplePurposeCodesValue		 The types of samples acquired in an experiment (from a controlled list) direct
transmission_mode 0..1
TransmissionModeValue		 The type (modality) of a microscopy acquisition experiment 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
StringValue		 The name of the template used to collect metadata for an experiment in ELabFT... Experiment

Identifier and Mapping Information

Schema Source

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

Mappings

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

LinkML Source

Direct

name: GenericTemplateDeprecated
description: A retired version of a generic experiment template used to create other
  templates
title: GenericTemplate_Deprecated
deprecated: (2024 June) this is no longer used, use GenericTemplate instead
from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
deprecated_element_has_exact_replacement: GenericTemplate
is_a: ExperimentWithInstrument
abstract: true
slots:
- acquisition_time
- acquisition_volume
- bead_lot_number_concentration_qc
- bead_lot_number_size_qc
- cell_volume
- cfu_method
- coulter_aperture_size
- diluent_name
- diluent_volume
- error_flag
- fc_acquisition_count_target
- fc_acquisition_threshold_channel
- fc_acquisition_threshold_value
- fc_flow_rate_setting
- fc_fluorescent_channels
- fc_injection_mode
- fixation_method
- fluorescent_probe
- growth_duration
- growth_media_name
- incubation_agitation
- incubation_atmosphere
- incubation_duration
- incubation_temperature
- kit_lot_number
- labcas_data_acquisition_date
- labcas_instrument
- labcas_microbial_material_id
- labcas_operator
- labcas_project
- library_prep
- microbial_material_id
- nucleic_acid_type
- objective
- qc_reagent_lot_number
- sample_purpose_codes
- transmission_mode

Induced

name: GenericTemplateDeprecated
description: A retired version of a generic experiment template used to create other
  templates
title: GenericTemplate_Deprecated
deprecated: (2024 June) this is no longer used, use GenericTemplate instead
from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
deprecated_element_has_exact_replacement: GenericTemplate
is_a: ExperimentWithInstrument
abstract: true
attributes:
  acquisition_time:
    name: acquisition_time
    description: Data acquisition time as set by instrument
    title: AcquisitionTime
    deprecated: (2024 June) unnecessary and unused
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: acquisition_time
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: DurationValue
    required: false
  acquisition_volume:
    name: acquisition_volume
    description: Data acquisition volume as set by instrument
    title: AcquisitionVolume
    deprecated: (2024 June) unnecessary and unused
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: acquisition_volume
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: VolumeValue
    required: false
  bead_lot_number_concentration_qc:
    name: bead_lot_number_concentration_qc
    description: Lot number of beads used for quality control of concentration measurements
    title: BeadLotNumber_ConcentrationQC
    deprecated: (2024 June) unnecessary and unused
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: bead_lot_number_concentration_qc
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: StringValue
    required: false
  bead_lot_number_size_qc:
    name: bead_lot_number_size_qc
    description: Lot number of beads used for quality control of size measurements
    title: BeadLotNumber_SizeQC
    deprecated: (2024 June) unnecessary and unused
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: bead_lot_number_size_qc
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: StringValue
    required: false
  cell_volume:
    name: cell_volume
    description: Volume of cell stock added to acquisition vessel
    title: CellVolume
    deprecated: (2024 June) unnecessary and unused
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: cell_volume
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: VolumeValue
    required: false
  cfu_method:
    name: cfu_method
    description: Describes deposition format of cells on agar plate
    title: CFUMethod
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: cfu_method
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    - GenericTemplate
    - CFU
    range: CFUMethodValue
    required: false
  coulter_aperture_size:
    name: coulter_aperture_size
    description: Aperture installed on Coulter counter during measurement
    title: CoulterApertureSize
    deprecated: (2024 June) unnecessary and unused
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: coulter_aperture_size
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: LengthValue
    required: false
  diluent_name:
    name: diluent_name
    description: Which diluent was used to suspend cells for acquisition (linked item)
    title: DiluentName
    deprecated: (2024 June) unnecessary and unused
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: diluent_name
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: ELabItemValue
    required: false
  diluent_volume:
    name: diluent_volume
    description: Volume of diluent added to acquisition vessel
    title: DiluentVolume
    deprecated: (2024 June) unnecessary and unused
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: diluent_volume
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: VolumeValue
    required: false
  error_flag:
    name: error_flag
    description: Indicates if a known error appears in the dataset
    title: ErrorFlag
    deprecated: (2024 June) unnecessary and unused
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: error_flag
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: BooleanValue
    required: false
  fc_acquisition_count_target:
    name: fc_acquisition_count_target
    description: Set number of events to acquire in a particular gate on flow cytometer
    title: FCAcquisitionCountTarget
    deprecated: (2024 June) unnecessary and unused
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: fc_acquisition_count_target
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: CountValue
    required: false
  fc_acquisition_threshold_channel:
    name: fc_acquisition_threshold_channel
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: Fluorescence FC
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: Which channel as named by the manufacturer was used to threshold
      the data acquisition
    title: FCAcquisitionThresholdChannel
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: fc_acquisition_threshold_channel
    owner: GenericTemplateDeprecated
    domain_of:
    - CytoFLEXAcquisition
    - GenericTemplateDeprecated
    - GenericTemplate
    range: StringValue
    required: false
  fc_acquisition_threshold_value:
    name: fc_acquisition_threshold_value
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: Fluorescence FC
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: Threshold value in arbitrary units that defines the lower limit of
      data acquisition in flow cytometry
    title: FCAcquisitionThresholdValue
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: fc_acquisition_threshold_value
    owner: GenericTemplateDeprecated
    domain_of:
    - CytoFLEXAcquisition
    - GenericTemplateDeprecated
    - GenericTemplate
    range: NumberValue
    required: false
  fc_flow_rate_setting:
    name: fc_flow_rate_setting
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: Fluorescence FC
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
      elabftw_default_unit:
        tag: elabftw_default_unit
        value: µL/min
    description: Set flow rate of data acquisition on flow cytometer
    title: FCFlowRateSetting
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: fc_flow_rate_setting
    owner: GenericTemplateDeprecated
    domain_of:
    - CytoFLEXAcquisition
    - CytoFLEXVolumeCalibration
    - GenericTemplateDeprecated
    - GenericTemplate
    range: FlowRateValue
    required: false
  fc_fluorescent_channels:
    name: fc_fluorescent_channels
    description: List of fluorescent channels acquired during a flow cytometry experiment
      as named by the manufacturer (separated by semicolons)
    title: FCFluorescentChannels
    deprecated: (2024 June) unnecessary and unused
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: fc_fluorescent_channels
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: StringValue
    required: false
  fc_injection_mode:
    name: fc_injection_mode
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: Fluorescence FC
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: Sample acquisition format in flow cytometer
    title: FCInjectionMode
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    ifabsent: Tube
    alias: fc_injection_mode
    owner: GenericTemplateDeprecated
    domain_of:
    - CytoFLEXAcquisition
    - CytoFLEXVolumeCalibration
    - GenericTemplateDeprecated
    - GenericTemplate
    range: FCInjectionModeValue
    required: false
  fixation_method:
    name: fixation_method
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: Generic Microbial
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: Specific treatment applied to cells to prevent future changes
    title: FixationMethod
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    ifabsent: None
    alias: fixation_method
    owner: GenericTemplateDeprecated
    domain_of:
    - CytoFLEXAcquisition
    - GenericTemplateDeprecated
    - FormaldehydeFixation
    - MicroscopyAcquisition
    - GenericTemplate
    - CoulterAcquisition
    - BactoBoxAcquisition
    - LogCOMETSamplePrep
    - CFU
    range: FixationMethodValue
    required: false
  fluorescent_probe:
    name: fluorescent_probe
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: Generic Microbial
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: Fluorescent probe(s) used in the experiment, as linked item(s) from
      ELabFTW
    title: FluorescentProbe
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: fluorescent_probe
    owner: GenericTemplateDeprecated
    domain_of:
    - CytoFLEXAcquisition
    - GenericTemplateDeprecated
    - MicroscopyAcquisition
    - GenericTemplate
    range: FluorescentProbeValue
    required: false
  growth_duration:
    name: growth_duration
    description: Time that cells were incubated to encourage growth
    title: GrowthDuration
    deprecated: (2024 June) unnecessary and unused
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: growth_duration
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: DurationValue
    required: false
  growth_media_name:
    name: growth_media_name
    description: Name of media used to culture cells (linked item from ELabFTW)
    title: GrowthMediaName
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: growth_media_name
    owner: GenericTemplateDeprecated
    domain_of:
    - CellCultureInBroth
    - GenericTemplateDeprecated
    - GenericTemplate
    - CFU
    - InitiateGrowthOfBSpizizenii
    range: ELabItemValue
    required: false
  incubation_agitation:
    name: incubation_agitation
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: Generic Microbial
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
      elabftw_default_unit:
        tag: elabftw_default_unit
        value: rpm
    description: Speed of agitation that cells were incubated during an experiment
    title: IncubationAgitation
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: incubation_agitation
    owner: GenericTemplateDeprecated
    domain_of:
    - CytoFLEXAcquisition
    - CellCultureInBroth
    - GenericTemplateDeprecated
    - FormaldehydeFixation
    - MicroscopyAcquisition
    - GenericTemplate
    - InitiateGrowthOfBSpizizenii
    range: AgitationValue
    required: false
  incubation_atmosphere:
    name: incubation_atmosphere
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: Generic Microbial
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
    description: Atmosphere that cells were incubated in to encourage growth
    title: IncubationAtmosphere
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: incubation_atmosphere
    owner: GenericTemplateDeprecated
    domain_of:
    - CytoFLEXAcquisition
    - CellCultureInBroth
    - GenericTemplateDeprecated
    - FormaldehydeFixation
    - MicroscopyAcquisition
    - GenericTemplate
    - CFU
    - InitiateGrowthOfBSpizizenii
    range: IncubationAtmosphereValue
    required: false
  incubation_duration:
    name: incubation_duration
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: Generic Microbial
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
      elabftw_default_unit:
        tag: elabftw_default_unit
        value: hr
    description: Length of time that cells were incubated during an experiment
    title: IncubationDuration
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: incubation_duration
    owner: GenericTemplateDeprecated
    domain_of:
    - CytoFLEXAcquisition
    - CellCultureInBroth
    - GenericTemplateDeprecated
    - FormaldehydeFixation
    - MicroscopyAcquisition
    - GenericTemplate
    - CFU
    - InitiateGrowthOfBSpizizenii
    range: DurationValue
    required: false
  incubation_temperature:
    name: incubation_temperature
    annotations:
      elabftw_group:
        tag: elabftw_group
        value: Generic Microbial
      elabftw_user_input:
        tag: elabftw_user_input
        value: true
      elabftw_default_unit:
        tag: elabftw_default_unit
        value: oC
    description: Temperature at which cells were incubated during an experiment or
      culture
    title: IncubationTemperature
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: incubation_temperature
    owner: GenericTemplateDeprecated
    domain_of:
    - CytoFLEXAcquisition
    - CellCultureInBroth
    - GenericTemplateDeprecated
    - FormaldehydeFixation
    - MicroscopyAcquisition
    - GenericTemplate
    - CFU
    - InitiateGrowthOfBSpizizenii
    range: TemperatureValue
    required: false
  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: GenericTemplateDeprecated
    domain_of:
    - NucleicAcidExtraction
    - GenericTemplateDeprecated
    - GenericTemplate
    range: ELabItemValue
    required: false
  labcas_data_acquisition_date:
    name: labcas_data_acquisition_date
    description: Date on which data were acquired according to eLabFTW record
    title: LabCAS-DataAcquisitionDate
    deprecated: (2024 June) this is too specific, use data_acquisition_date instead
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    deprecated_element_has_exact_replacement: data_acquisition_date
    rank: 1000
    alias: labcas_data_acquisition_date
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: DateValue
    required: false
  labcas_instrument:
    name: labcas_instrument
    description: Date on which data were acquired according to eLabFTW record
    title: LabCAS-Instrument
    deprecated: (2024 June) this is too specific, use instrument_id instead
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    deprecated_element_has_exact_replacement: instrument_id
    rank: 1000
    alias: labcas_instrument
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: LabCASInstrumentValue
    required: false
  labcas_microbial_material_id:
    name: labcas_microbial_material_id
    description: Cell material(s) used in experiment as named in the eLabFTW database
      (linked items)
    title: LabCAS-MicrobialMaterialID
    deprecated: (2024 June) this is too specific, use microbial_material_id instead
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    deprecated_element_has_exact_replacement: microbial_material_id
    rank: 1000
    alias: labcas_microbial_material_id
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: LabCASMicrobialMaterialIDValue
    required: false
  labcas_operator:
    name: labcas_operator
    description: Instrument operator during an experiment (a linked item from ELabFTW)
    title: LabCAS-Operator
    deprecated: (2024 June) this is too specific, use operator_id instead
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    deprecated_element_has_exact_replacement: operator_id
    rank: 1000
    alias: labcas_operator
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: LabCASOperatorValue
    required: false
  labcas_project:
    name: labcas_project
    description: The project that an experiment supports (link to an ELabFTW item)
    title: LabCAS-Project
    deprecated: (2024 June) this is too specific, use project_id instead
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    deprecated_element_has_exact_replacement: project_id
    rank: 1000
    alias: labcas_project
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: LabCASProjectValue
    required: false
  library_prep:
    name: library_prep
    description: The name of a specific kit used for sequencing preparation steps
    title: LibraryPrep
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: library_prep
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    - GenericTemplate
    range: StringValue
    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: GenericTemplateDeprecated
    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: GenericTemplateDeprecated
    domain_of:
    - NucleicAcidExtraction
    - GenericTemplateDeprecated
    - GenericTemplate
    range: NucleicAcidTypeValue
    required: false
  objective:
    name: objective
    description: The microscope objectives used in a microscopy acquisition experiment
    title: Objective
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: objective
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    - MicroscopyAcquisition
    - GenericTemplate
    range: ObjectivesValue
    required: false
  qc_reagent_lot_number:
    name: qc_reagent_lot_number
    description: The lot number for a QC reagent (link to an ELabFTW item)
    title: QCReagentLotNumber
    deprecated: (2024 June) this metadata term was determined to be unneeded, do not
      use
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    rank: 1000
    alias: qc_reagent_lot_number
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: StringValue
    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: GenericTemplateDeprecated
    domain_of:
    - CytoFLEXAcquisition
    - NucleicAcidExtraction
    - CellCultureInBroth
    - GenericTemplateDeprecated
    - FormaldehydeFixation
    - MicroscopyAcquisition
    - GenericTemplate
    - CoulterAcquisition
    - BactoBoxAcquisition
    - LogCOMETSamplePrep
    - CFU
    - InitiateGrowthOfBSpizizenii
    range: SamplePurposeCodesValue
    required: false
  transmission_mode:
    name: transmission_mode
    description: The type (modality) of a microscopy acquisition experiment
    title: TransmissionMode
    deprecated: (2024 June) this is too specific, use modalities instead
    from_schema: https://w3id.org/usnistgov/microbial-experiment-schema
    deprecated_element_has_exact_replacement: modalities
    rank: 1000
    alias: transmission_mode
    owner: GenericTemplateDeprecated
    domain_of:
    - GenericTemplateDeprecated
    range: TransmissionModeValue
    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: GenericTemplateDeprecated
    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: GenericTemplateDeprecated
    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: GenericTemplateDeprecated
    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: GenericTemplateDeprecated
    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: GenericTemplateDeprecated
    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: GenericTemplateDeprecated
    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: GenericTemplateDeprecated
    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: GenericTemplateDeprecated
    domain_of:
    - Experiment
    range: StringValue
    required: true