openminds.ephys

In-depth metadata for electrophysiology recordings.

class CellPatching(lookup_label=None, bath_temperature=None, custom_property_sets=None, description=None, devices=None, end_time=None, inputs=None, is_part_of=None, outputs=None, performed_by=None, preparation_design=None, protocols=None, start_time=None, study_targets=None, target_position=None, tissue_bath_solution=None, variation=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, CellPatching

<description not available>

Parameters:

• bath_temperature (QuantitativeValue, QuantitativeValueRange) – no description available

• custom_property_sets (CustomPropertySet) – no description available

• description (str) – Longer statement or account giving the characteristics of the cell patching.

• devices (ElectrodeArrayUsage, ElectrodeUsage, PipetteUsage, SlicingDeviceUsage) – Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.

• end_time (datetime, time) – no description available

• inputs (TissueSampleState, SubjectState) – Something or someone that is put into or participates in a process or machine.

• is_part_of (DatasetVersion) – Reference to the ensemble of multiple things or beings.

• lookup_label (str) – no description available

• outputs (TissueSampleState, SubjectState) – Something or someone that comes out of, is delivered or produced by a process or machine.

• performed_by (SoftwareAgent, Person) – no description available

• preparation_design (PreparationType) – no description available

• protocols (Protocol) – Plan that describes the process of a scientific or medical experiment, treatment, or procedure.

• start_time (datetime, time) – no description available

• study_targets (AuditoryStimulusType, BiologicalOrder, BiologicalSex, BreedingType, CellCultureType, CellType, Disease, DiseaseModel, ElectricalStimulusType, GeneticStrainType, GustatoryStimulusType, Handedness, MolecularEntity, OlfactoryStimulusType, OpticalStimulusType, Organ, OrganismSubstance, OrganismSystem, Species, SubcellularEntity, TactileStimulusType, TermSuggestion, TissueSampleType, UBERONParcellation, VisualStimulusType, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Structure or function that was targeted within a study.

• target_position (AnatomicalTargetPosition) – no description available

• tissue_bath_solution (ChemicalMixture) – no description available

• variation (PatchClampVariation) – no description available

class ElectrodePlacement(lookup_label=None, custom_property_sets=None, description=None, devices=None, end_time=None, inputs=None, is_part_of=None, outputs=None, performed_by=None, preparation_design=None, protocols=None, start_time=None, study_targets=None, target_position=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, ElectrodePlacement

<description not available>

Parameters:

• custom_property_sets (CustomPropertySet) – no description available

• description (str) – Longer statement or account giving the characteristics of the electrode placement.

• devices (ElectrodeArrayUsage, ElectrodeUsage, PipetteUsage, SlicingDeviceUsage) – Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.

• end_time (datetime, time) – no description available

• inputs (TissueSampleState, SubjectState) – Something or someone that is put into or participates in a process or machine.

• is_part_of (DatasetVersion) – Reference to the ensemble of multiple things or beings.

• lookup_label (str) – no description available

• outputs (TissueSampleState, SubjectState) – Something or someone that comes out of, is delivered or produced by a process or machine.

• performed_by (SoftwareAgent, Person) – no description available

• preparation_design (PreparationType) – no description available

• protocols (Protocol) – Plan that describes the process of a scientific or medical experiment, treatment, or procedure.

• start_time (datetime, time) – no description available

• study_targets (AuditoryStimulusType, BiologicalOrder, BiologicalSex, BreedingType, CellCultureType, CellType, Disease, DiseaseModel, ElectricalStimulusType, GeneticStrainType, GustatoryStimulusType, Handedness, MolecularEntity, OlfactoryStimulusType, OpticalStimulusType, Organ, OrganismSubstance, OrganismSystem, Species, SubcellularEntity, TactileStimulusType, TermSuggestion, TissueSampleType, UBERONParcellation, VisualStimulusType, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Structure or function that was targeted within a study.

• target_position (AnatomicalTargetPosition) – no description available

class RecordingActivity(lookup_label=None, custom_property_sets=None, description=None, devices=None, end_time=None, inputs=None, internal_identifier=None, is_part_of=None, outputs=None, performed_by=None, preparation_design=None, protocols=None, start_time=None, study_targets=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, RecordingActivity

<description not available>

Parameters:

• custom_property_sets (CustomPropertySet) – no description available

• description (str) – Longer statement or account giving the characteristics of the recording activity.

• devices (ElectrodeArrayUsage, ElectrodeUsage, PipetteUsage) – Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.

• end_time (datetime, time) – no description available

• inputs (SubjectGroupState, SubjectState, TissueSampleCollectionState, TissueSampleState) – Something or someone that is put into or participates in a process or machine.

• internal_identifier (str) – Term or code that identifies the recording activity within a particular product.

• is_part_of (DatasetVersion) – Reference to the ensemble of multiple things or beings.

• lookup_label (str) – no description available

• outputs (File, FileBundle) – Something or someone that comes out of, is delivered or produced by a process or machine.

• performed_by (SoftwareAgent, Person) – no description available

• preparation_design (PreparationType) – no description available

• protocols (Protocol) – Plan that describes the process of a scientific or medical experiment, treatment, or procedure.

• start_time (datetime, time) – no description available

• study_targets (AuditoryStimulusType, BiologicalOrder, BiologicalSex, BreedingType, CellCultureType, CellType, Disease, DiseaseModel, ElectricalStimulusType, GeneticStrainType, GustatoryStimulusType, Handedness, MolecularEntity, OlfactoryStimulusType, OpticalStimulusType, Organ, OrganismSubstance, OrganismSystem, Species, SubcellularEntity, TactileStimulusType, TermSuggestion, TissueSampleType, UBERONParcellation, VisualStimulusType, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – Structure or function that was targeted within a study.

class Pipette(name=None, lookup_label=None, description=None, device_type=None, digital_identifier=None, external_diameter=None, internal_diameter=None, internal_identifier=None, is_part_of=None, manufacturers=None, material=None, owners=None, serial_number=None, usage=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, Pipette

<description not available>

Parameters:

• description (str) – Longer statement or account giving the characteristics of the pipette.

• device_type (DeviceType) – no description available

• digital_identifier (DOI, RRID) – Digital handle to identify objects or legal persons.

• external_diameter (QuantitativeValue) – no description available

• internal_diameter (QuantitativeValue) – no description available

• internal_identifier (str) – Term or code that identifies the pipette within a particular product.

• lookup_label (str) – no description available

• manufacturers (Consortium, Organization, Person) – no description available

• material (ChemicalMixture, ChemicalSubstance, MolecularEntity) – no description available

• name (str) – Word or phrase that constitutes the distinctive designation of the pipette.

• owners (Consortium, Organization, Person) – no description available

• serial_number (str) – no description available

• is_part_of (Setup) – reverse of ‘has_parts’

• usage (PipetteUsage) – reverse of ‘device’

class PipetteUsage(lookup_label=None, anatomical_location=None, chloride_reversal_potentials=None, compensation_current=None, device=None, end_membrane_potential=None, generation_device=None, holding_potential=None, input_resistance=None, labeling_compound=None, liquid_junction_potential=None, metadata_locations=None, pipette_resistance=None, pipette_solution=None, placed_by=None, seal_resistance=None, series_resistance=None, spatial_location=None, start_membrane_potential=None, used_in=None, used_specimen=None, used_to_measure=None, used_to_record=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, PipetteUsage

<description not available>

Parameters:

• anatomical_location (CellType, Organ, OrganismSubstance, SubcellularEntity, UBERONParcellation, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – no description available

• chloride_reversal_potentials (Measurement) – no description available

• compensation_current (Measurement) – no description available

• device (Pipette) – Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.

• end_membrane_potential (Measurement) – no description available

• holding_potential (Measurement) – no description available

• input_resistance (Measurement) – no description available

• labeling_compound (ChemicalMixture, ChemicalSubstance, MolecularEntity) – no description available

• liquid_junction_potential (Measurement) – no description available

• lookup_label (str) – no description available

• metadata_locations (File, FileBundle) – no description available

• pipette_resistance (QuantitativeValue, QuantitativeValueRange) – no description available

• pipette_solution (ChemicalMixture) – no description available

• seal_resistance (Measurement) – no description available

• series_resistance (Measurement) – no description available

• spatial_location (CoordinatePoint) – no description available

• start_membrane_potential (Measurement) – no description available

• used_specimen (SubjectState, TissueSampleState) – no description available

• generation_device (EphysStimulus) – reverse of ‘generated_by’

• placed_by (ElectrodePlacement) – reverse of ‘devices’

• used_in (CellPatching, RecordingActivity) – reverse of ‘devices’

• used_to_measure (Measurement) – reverse of ‘measured_with’

• used_to_record (Recording) – reverse of ‘recorded_with’

class Electrode(name=None, lookup_label=None, conductor_material=None, description=None, device_type=None, digital_identifier=None, insulator_material=None, internal_identifier=None, intrinsic_resistance=None, is_part_of=None, manufacturers=None, owners=None, serial_number=None, usage=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, Electrode

Structured information on an electrode.

Parameters:

• conductor_material (ChemicalMixture, ChemicalSubstance, MolecularEntity) – no description available

• description (str) – Longer statement or account giving the characteristics of the electrode.

• device_type (DeviceType) – no description available

• digital_identifier (DOI, RRID) – Digital handle to identify objects or legal persons.

• insulator_material (ChemicalMixture, ChemicalSubstance, MolecularEntity) – no description available

• internal_identifier (str) – Term or code that identifies the electrode within a particular product.

• intrinsic_resistance (QuantitativeValue, QuantitativeValueRange) – no description available

• lookup_label (str) – no description available

• manufacturers (Consortium, Organization, Person) – no description available

• name (str) – Word or phrase that constitutes the distinctive designation of the electrode.

• owners (Consortium, Organization, Person) – no description available

• serial_number (str) – no description available

• is_part_of (Setup) – reverse of ‘has_parts’

• usage (ElectrodeUsage) – reverse of ‘device’

class ElectrodeUsage(lookup_label=None, anatomical_location=None, contact_resistance=None, device=None, generation_device=None, metadata_locations=None, placed_by=None, spatial_location=None, used_in=None, used_specimen=None, used_to_measure=None, used_to_record=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, ElectrodeUsage

<description not available>

Parameters:

• anatomical_location (CellType, Organ, OrganismSubstance, SubcellularEntity, UBERONParcellation, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – no description available

• contact_resistance (QuantitativeValue, QuantitativeValueRange) – no description available

• device (Electrode) – Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.

• lookup_label (str) – no description available

• metadata_locations (File, FileBundle) – no description available

• spatial_location (CoordinatePoint) – no description available

• used_specimen (SubjectState, TissueSampleState) – no description available

• generation_device (EphysStimulus) – reverse of ‘generated_by’

• placed_by (ElectrodePlacement) – reverse of ‘devices’

• used_in (CellPatching, RecordingActivity) – reverse of ‘devices’

• used_to_measure (Measurement) – reverse of ‘measured_with’

• used_to_record (Recording) – reverse of ‘recorded_with’

class ElectrodeArray(name=None, lookup_label=None, conductor_material=None, description=None, device_type=None, digital_identifier=None, electrode_identifiers=None, insulator_material=None, internal_identifier=None, intrinsic_resistance=None, is_part_of=None, manufacturers=None, number_of_electrodes=None, owners=None, serial_number=None, usage=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, ElectrodeArray

Structured information on an electrode array.

Parameters:

• conductor_material (ChemicalMixture, ChemicalSubstance, MolecularEntity) – no description available

• description (str) – Longer statement or account giving the characteristics of the electrode array.

• device_type (DeviceType) – no description available

• digital_identifier (DOI, RRID) – Digital handle to identify objects or legal persons.

• electrode_identifiers (str) – no description available

• insulator_material (ChemicalMixture, ChemicalSubstance, MolecularEntity) – no description available

• internal_identifier (str) – Term or code that identifies the electrode array within a particular product.

• intrinsic_resistance (QuantitativeValue, QuantitativeValueRange) – no description available

• lookup_label (str) – no description available

• manufacturers (Consortium, Organization, Person) – no description available

• name (str) – Word or phrase that constitutes the distinctive designation of the electrode array.

• number_of_electrodes (int) – no description available

• owners (Consortium, Organization, Person) – no description available

• serial_number (str) – no description available

• is_part_of (Setup) – reverse of ‘has_parts’

• usage (ElectrodeArrayUsage) – reverse of ‘device’

class ElectrodeArrayUsage(lookup_label=None, anatomical_locations_of_arrays=None, anatomical_locations_of_electrodes=None, contact_resistances=None, device=None, generation_device=None, metadata_locations=None, placed_by=None, spatial_locations_of_electrodes=None, used_electrodes=None, used_in=None, used_specimen=None, used_to_measure=None, used_to_record=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, ElectrodeArrayUsage

<description not available>

Parameters:

• anatomical_locations_of_arrays (CellType, Organ, OrganismSubstance, SubcellularEntity, UBERONParcellation, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – no description available

• anatomical_locations_of_electrodes (CellType, Organ, OrganismSubstance, SubcellularEntity, UBERONParcellation, CustomAnatomicalEntity, ParcellationEntity, ParcellationEntityVersion) – no description available

• contact_resistances (QuantitativeValue, QuantitativeValueRange) – no description available

• device (ElectrodeArray) – Piece of equipment or mechanism (hardware) designed to serve a special purpose or perform a special function.

• lookup_label (str) – no description available

• metadata_locations (File, FileBundle) – no description available

• spatial_locations_of_electrodes (CoordinatePoint) – no description available

• used_electrodes (str) – no description available

• used_specimen (SubjectState, TissueSampleState) – no description available

• generation_device (EphysStimulus) – reverse of ‘generated_by’

• placed_by (ElectrodePlacement) – reverse of ‘devices’

• used_in (CellPatching, RecordingActivity) – reverse of ‘devices’

• used_to_measure (Measurement) – reverse of ‘measured_with’

• used_to_record (Recording) – reverse of ‘recorded_with’

class Channel(internal_identifier=None, unit=None, id=None, data=None, space=None, release_status=None)

Bases: KGEmbedded, Channel

<description not available>

Parameters:

• internal_identifier (str) – Term or code that identifies the channel within a particular product.

• unit (UnitOfMeasurement) – Determinate quantity adopted as a standard of measurement.

class Recording(name=None, additional_remarks=None, channels=None, data_location=None, internal_identifier=None, next_recording=None, previous_recording=None, recorded_with=None, sampling_frequency=None, id=None, data=None, space=None, release_status=None)

Bases: KGObject, Recording

<description not available>

Parameters:

• additional_remarks (str) – Mention of what deserves additional attention or notice.

• channels (Channel) – no description available

• data_location (File, FileBundle) – no description available

• internal_identifier (str) – Term or code that identifies the recording within a particular product.

• name (str) – Word or phrase that constitutes the distinctive designation of the recording.

• previous_recording (Recording) – no description available

• recorded_with (ElectrodeArrayUsage, ElectrodeUsage, PipetteUsage, SlicingDeviceUsage) – no description available

• sampling_frequency (QuantitativeValue) – no description available

• next_recording (Recording) – reverse of ‘previous_recording’