nwb-linkml/nwb_linkml/schema/core.nwb.file.include.yaml

name: core.nwb.file.include
id: core.nwb.file.include
imports:
- core.nwb.base
- hdmf-common.table
- core.nwb.device
- core.nwb.ecephys
- core.nwb.icephys
- core.nwb.ogen
- core.nwb.ophys
- core.nwb.epoch
- core.nwb.misc
- nwb.language
- core.nwb.file.include
- core.nwb.file
default_prefix: core.nwb.file.include/
classes:
  NWBFile__file_create_date:
    name: NWBFile__file_create_date
    description: 'A record of the date the file was created and of subsequent modifications.
      The date is stored in UTC with local timezone offset as ISO 8601 extended formatted
      strings: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in "Z" with
      no timezone offset. Date accuracy is up to milliseconds. The file can be created
      after the experiment was run, so this may differ from the experiment start time.
      Each modification to the nwb file adds a new entry to the array.'
    attributes:
      file_create_date:
        name: file_create_date
        description: 'A record of the date the file was created and of subsequent
          modifications. The date is stored in UTC with local timezone offset as ISO
          8601 extended formatted strings: 2018-09-28T14:43:54.123+02:00. Dates stored
          in UTC end in "Z" with no timezone offset. Date accuracy is up to milliseconds.
          The file can be created after the experiment was run, so this may differ
          from the experiment start time. Each modification to the nwb file adds a
          new entry to the array.'
        multivalued: true
        range: isodatetime
        required: true
  NWBFile__acquisition:
    name: NWBFile__acquisition
    description: Data streams recorded from the system, including ephys, ophys, tracking,
      etc. This group should be read-only after the experiment is completed and timestamps
      are corrected to a common timebase. The data stored here may be links to raw
      data stored in external NWB files. This will allow keeping bulky raw data out
      of the file while preserving the option of keeping some/all in the file. Acquired
      data includes tracking and experimental data streams (i.e., everything measured
      from the system). If bulky data is stored in the /acquisition group, the data
      can exist in a separate NWB file that is linked to by the file being used for
      processing and analysis.
    attributes:
      NWBDataInterface:
        name: NWBDataInterface
        description: Acquired, raw data.
        multivalued: true
        range: NWBDataInterface
        required: false
      DynamicTable:
        name: DynamicTable
        description: Tabular data that is relevant to acquisition
        multivalued: true
        range: DynamicTable
        required: false
  NWBFile__analysis:
    name: NWBFile__analysis
    description: Lab-specific and custom scientific analysis of data. There is no
      defined format for the content of this group - the format is up to the individual
      user/lab. To facilitate sharing analysis data between labs, the contents here
      should be stored in standard types (e.g., neurodata_types) and appropriately
      documented. The file can store lab-specific and custom data analysis without
      restriction on its form or schema, reducing data formatting restrictions on
      end users. Such data should be placed in the analysis group. The analysis data
      should be documented so that it could be shared with other labs.
    attributes:
      NWBContainer:
        name: NWBContainer
        description: Custom analysis results.
        multivalued: true
        range: NWBContainer
        required: false
      DynamicTable:
        name: DynamicTable
        description: Tabular data that is relevant to data stored in analysis
        multivalued: true
        range: DynamicTable
        required: false
  NWBFile__scratch:
    name: NWBFile__scratch
    description: A place to store one-off analysis results. Data placed here is not
      intended for sharing. By placing data here, users acknowledge that there is
      no guarantee that their data meets any standard.
    attributes:
      ScratchData:
        name: ScratchData
        description: Any one-off datasets
        multivalued: true
        range: ScratchData
        required: false
      NWBContainer:
        name: NWBContainer
        description: Any one-off containers
        multivalued: true
        range: NWBContainer
        required: false
      DynamicTable:
        name: DynamicTable
        description: Any one-off tables
        multivalued: true
        range: DynamicTable
        required: false
  NWBFile__processing:
    name: NWBFile__processing
    description: The home for ProcessingModules. These modules perform intermediate
      analysis of data that is necessary to perform before scientific analysis. Examples
      include spike clustering, extracting position from tracking data, stitching
      together image slices. ProcessingModules can be large and express many data
      sets from relatively complex analysis (e.g., spike detection and clustering)
      or small, representing extraction of position information from tracking video,
      or even binary lick/no-lick decisions. Common software tools (e.g., klustakwik,
      MClust) are expected to read/write data here.  'Processing' refers to intermediate
      analysis of the acquired data to make it more amenable to scientific analysis.
    attributes:
      ProcessingModule:
        name: ProcessingModule
        description: Intermediate analysis of acquired data.
        multivalued: true
        range: ProcessingModule
        required: false
  NWBFile__stimulus:
    name: NWBFile__stimulus
    description: Data pushed into the system (eg, video stimulus, sound, voltage,
      etc) and secondary representations of that data (eg, measurements of something
      used as a stimulus). This group should be made read-only after experiment complete
      and timestamps are corrected to common timebase. Stores both presented stimuli
      and stimulus templates, the latter in case the same stimulus is presented multiple
      times, or is pulled from an external stimulus library. Stimuli are here defined
      as any signal that is pushed into the system as part of the experiment (eg,
      sound, video, voltage, etc). Many different experiments can use the same stimuli,
      and stimuli can be re-used during an experiment. The stimulus group is organized
      so that one version of template stimuli can be stored and these be used multiple
      times. These templates can exist in the present file or can be linked to a remote
      library file.
    attributes:
      presentation:
        name: presentation
        description: Stimuli presented during the experiment.
        multivalued: false
        range: NWBFile__stimulus__presentation
        required: true
      templates:
        name: templates
        description: Template stimuli. Timestamps in templates are based on stimulus
          design and are relative to the beginning of the stimulus. When templates
          are used, the stimulus instances must convert presentation times to the
          experiment`s time reference frame.
        multivalued: false
        range: NWBFile__stimulus__templates
        required: true
  NWBFile__stimulus__presentation:
    name: NWBFile__stimulus__presentation
    description: Stimuli presented during the experiment.
    attributes:
      TimeSeries:
        name: TimeSeries
        description: TimeSeries objects containing data of presented stimuli.
        multivalued: true
        range: TimeSeries
        required: false
  NWBFile__stimulus__templates:
    name: NWBFile__stimulus__templates
    description: Template stimuli. Timestamps in templates are based on stimulus design
      and are relative to the beginning of the stimulus. When templates are used,
      the stimulus instances must convert presentation times to the experiment`s time
      reference frame.
    attributes:
      TimeSeries:
        name: TimeSeries
        description: TimeSeries objects containing template data of presented stimuli.
        multivalued: true
        range: TimeSeries
        required: false
      Images:
        name: Images
        description: Images objects containing images of presented stimuli.
        multivalued: true
        range: Images
        required: false
  NWBFile__general:
    name: NWBFile__general
    description: Experimental metadata, including protocol, notes and description
      of hardware device(s).  The metadata stored in this section should be used to
      describe the experiment. Metadata necessary for interpreting the data is stored
      with the data. General experimental metadata, including animal strain, experimental
      protocols, experimenter, devices, etc, are stored under 'general'. Core metadata
      (e.g., that required to interpret data fields) is stored with the data itself,
      and implicitly defined by the file specification (e.g., time is in seconds).
      The strategy used here for storing non-core metadata is to use free-form text
      fields, such as would appear in sentences or paragraphs from a Methods section.
      Metadata fields are text to enable them to be more general, for example to represent
      ranges instead of numerical values. Machine-readable metadata is stored as attributes
      to these free-form datasets. All entries in the below table are to be included
      when data is present. Unused groups (e.g., intracellular_ephys in an optophysiology
      experiment) should not be created unless there is data to store within them.
    attributes:
      data_collection:
        name: data_collection
        description: Notes about data collection and analysis.
        multivalued: false
        range: text
        required: false
      experiment_description:
        name: experiment_description
        description: General description of the experiment.
        multivalued: false
        range: text
        required: false
      experimenter:
        name: experimenter
        description: Name of person(s) who performed the experiment. Can also specify
          roles of different people involved.
        multivalued: false
        range: NWBFile__general__experimenter
        required: false
      institution:
        name: institution
        description: Institution(s) where experiment was performed.
        multivalued: false
        range: text
        required: false
      keywords:
        name: keywords
        description: Terms to search over.
        multivalued: false
        range: NWBFile__general__keywords
        required: false
      lab:
        name: lab
        description: Laboratory where experiment was performed.
        multivalued: false
        range: text
        required: false
      notes:
        name: notes
        description: Notes about the experiment.
        multivalued: false
        range: text
        required: false
      pharmacology:
        name: pharmacology
        description: Description of drugs used, including how and when they were administered.
          Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc.
        multivalued: false
        range: text
        required: false
      protocol:
        name: protocol
        description: Experimental protocol, if applicable. e.g., include IACUC protocol
          number.
        multivalued: false
        range: text
        required: false
      related_publications:
        name: related_publications
        description: Publication information. PMID, DOI, URL, etc.
        multivalued: false
        range: NWBFile__general__related_publications
        required: false
      session_id:
        name: session_id
        description: Lab-specific ID for the session.
        multivalued: false
        range: text
        required: false
      slices:
        name: slices
        description: Description of slices, including information about preparation
          thickness, orientation, temperature, and bath solution.
        multivalued: false
        range: text
        required: false
      source_script:
        name: source_script
        description: Script file or link to public source code used to create this
          NWB file.
        multivalued: false
        range: NWBFile__general__source_script
        required: false
      stimulus:
        name: stimulus
        description: Notes about stimuli, such as how and where they were presented.
        multivalued: false
        range: text
        required: false
      surgery:
        name: surgery
        description: Narrative description about surgery/surgeries, including date(s)
          and who performed surgery.
        multivalued: false
        range: text
        required: false
      virus:
        name: virus
        description: Information about virus(es) used in experiments, including virus
          ID, source, date made, injection location, volume, etc.
        multivalued: false
        range: text
        required: false
      LabMetaData:
        name: LabMetaData
        description: Place-holder than can be extended so that lab-specific meta-data
          can be placed in /general.
        multivalued: true
        range: LabMetaData
        required: false
      devices:
        name: devices
        description: Description of hardware devices used during experiment, e.g.,
          monitors, ADC boards, microscopes, etc.
        multivalued: false
        range: NWBFile__general__devices
        required: false
      subject:
        name: subject
        description: Information about the animal or person from which the data was
          measured.
        multivalued: false
        range: NWBFile__general__subject
        required: false
      extracellular_ephys:
        name: extracellular_ephys
        description: Metadata related to extracellular electrophysiology.
        multivalued: false
        range: NWBFile__general__extracellular_ephys
        required: false
      intracellular_ephys:
        name: intracellular_ephys
        description: Metadata related to intracellular electrophysiology.
        multivalued: false
        range: NWBFile__general__intracellular_ephys
        required: false
      optogenetics:
        name: optogenetics
        description: Metadata describing optogenetic stimuluation.
        multivalued: false
        range: NWBFile__general__optogenetics
        required: false
      optophysiology:
        name: optophysiology
        description: Metadata related to optophysiology.
        multivalued: false
        range: NWBFile__general__optophysiology
        required: false
  NWBFile__general__experimenter:
    name: NWBFile__general__experimenter
    description: Name of person(s) who performed the experiment. Can also specify
      roles of different people involved.
    attributes:
      experimenter:
        name: experimenter
        description: Name of person(s) who performed the experiment. Can also specify
          roles of different people involved.
        multivalued: true
        range: text
        required: false
  NWBFile__general__keywords:
    name: NWBFile__general__keywords
    description: Terms to search over.
    attributes:
      keywords:
        name: keywords
        description: Terms to search over.
        multivalued: true
        range: text
        required: false
  NWBFile__general__related_publications:
    name: NWBFile__general__related_publications
    description: Publication information. PMID, DOI, URL, etc.
    attributes:
      related_publications:
        name: related_publications
        description: Publication information. PMID, DOI, URL, etc.
        multivalued: true
        range: text
        required: false
  NWBFile__general__source_script:
    name: NWBFile__general__source_script
    description: Script file or link to public source code used to create this NWB
      file.
    attributes:
      file_name:
        name: file_name
        description: Name of script file.
        range: text
  NWBFile__general__devices:
    name: NWBFile__general__devices
    description: Description of hardware devices used during experiment, e.g., monitors,
      ADC boards, microscopes, etc.
    attributes:
      Device:
        name: Device
        description: Data acquisition devices.
        multivalued: true
        range: Device
        required: false
  NWBFile__general__subject:
    name: NWBFile__general__subject
    description: Information about the animal or person from which the data was measured.
    is_a: Subject
  NWBFile__general__extracellular_ephys:
    name: NWBFile__general__extracellular_ephys
    description: Metadata related to extracellular electrophysiology.
    attributes:
      ElectrodeGroup:
        name: ElectrodeGroup
        description: Physical group of electrodes.
        multivalued: true
        range: ElectrodeGroup
        required: false
      electrodes:
        name: electrodes
        description: A table of all electrodes (i.e. channels) used for recording.
        multivalued: false
        range: NWBFile__general__extracellular_ephys__electrodes
        required: false
  NWBFile__general__extracellular_ephys__electrodes:
    name: NWBFile__general__extracellular_ephys__electrodes
    description: A table of all electrodes (i.e. channels) used for recording.
    is_a: DynamicTable
    attributes:
      x:
        name: x
        description: x coordinate of the channel location in the brain (+x is posterior).
        multivalued: true
        range: float32
      y:
        name: y
        description: y coordinate of the channel location in the brain (+y is inferior).
        multivalued: true
        range: float32
      z:
        name: z
        description: z coordinate of the channel location in the brain (+z is right).
        multivalued: true
        range: float32
      imp:
        name: imp
        description: Impedance of the channel, in ohms.
        multivalued: true
        range: float32
      location:
        name: location
        description: Location of the electrode (channel). Specify the area, layer,
          comments on estimation of area/layer, stereotaxic coordinates if in vivo,
          etc. Use standard atlas names for anatomical regions when possible.
        multivalued: true
        range: text
      filtering:
        name: filtering
        description: Description of hardware filtering, including the filter name
          and frequency cutoffs.
        multivalued: true
        range: text
      group:
        name: group
        description: Reference to the ElectrodeGroup this electrode is a part of.
        multivalued: true
        range: ElectrodeGroup
      group_name:
        name: group_name
        description: Name of the ElectrodeGroup this electrode is a part of.
        multivalued: true
        range: text
      rel_x:
        name: rel_x
        description: x coordinate in electrode group
        multivalued: true
        range: float32
      rel_y:
        name: rel_y
        description: y coordinate in electrode group
        multivalued: true
        range: float32
      rel_z:
        name: rel_z
        description: z coordinate in electrode group
        multivalued: true
        range: float32
      reference:
        name: reference
        description: Description of the reference electrode and/or reference scheme
          used for this electrode, e.g., "stainless steel skull screw" or "online
          common average referencing".
        multivalued: true
        range: text
  NWBFile__general__intracellular_ephys:
    name: NWBFile__general__intracellular_ephys
    description: Metadata related to intracellular electrophysiology.
    attributes:
      filtering:
        name: filtering
        description: '[DEPRECATED] Use IntracellularElectrode.filtering instead. Description
          of filtering used. Includes filtering type and parameters, frequency fall-off,
          etc. If this changes between TimeSeries, filter description should be stored
          as a text attribute for each TimeSeries.'
        multivalued: false
        range: text
        required: false
      IntracellularElectrode:
        name: IntracellularElectrode
        description: An intracellular electrode.
        multivalued: true
        range: IntracellularElectrode
        required: false
      sweep_table:
        name: sweep_table
        description: '[DEPRECATED] Table used to group different PatchClampSeries.
          SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable
          tables. Additional SequentialRecordingsTable, RepetitionsTable and ExperimentalConditions
          tables provide enhanced support for experiment metadata.'
        multivalued: false
        range: NWBFile__general__intracellular_ephys__sweep_table
        required: false
      intracellular_recordings:
        name: intracellular_recordings
        description: A table to group together a stimulus and response from a single
          electrode and a single simultaneous recording. Each row in the table represents
          a single recording consisting typically of a stimulus and a corresponding
          response. In some cases, however, only a stimulus or a response are recorded
          as as part of an experiment. In this case both, the stimulus and response
          will point to the same TimeSeries while the idx_start and count of the invalid
          column will be set to -1, thus, indicating that no values have been recorded
          for the stimulus or response, respectively. Note, a recording MUST contain
          at least a stimulus or a response. Typically the stimulus and response are
          PatchClampSeries. However, the use of AD/DA channels that are not associated
          to an electrode is also common in intracellular electrophysiology, in which
          case other TimeSeries may be used.
        multivalued: false
        range: NWBFile__general__intracellular_ephys__intracellular_recordings
        required: false
      simultaneous_recordings:
        name: simultaneous_recordings
        description: A table for grouping different intracellular recordings from
          the IntracellularRecordingsTable table together that were recorded simultaneously
          from different electrodes
        multivalued: false
        range: NWBFile__general__intracellular_ephys__simultaneous_recordings
        required: false
      sequential_recordings:
        name: sequential_recordings
        description: A table for grouping different sequential recordings from the
          SimultaneousRecordingsTable table together. This is typically used to group
          together sequential recordings where the a sequence of stimuli of the same
          type with varying parameters have been presented in a sequence.
        multivalued: false
        range: NWBFile__general__intracellular_ephys__sequential_recordings
        required: false
      repetitions:
        name: repetitions
        description: A table for grouping different sequential intracellular recordings
          together. With each SequentialRecording typically representing a particular
          type of stimulus, the RepetitionsTable table is typically used to group
          sets of stimuli applied in sequence.
        multivalued: false
        range: NWBFile__general__intracellular_ephys__repetitions
        required: false
      experimental_conditions:
        name: experimental_conditions
        description: A table for grouping different intracellular recording repetitions
          together that belong to the same experimental experimental_conditions.
        multivalued: false
        range: NWBFile__general__intracellular_ephys__experimental_conditions
        required: false
  NWBFile__general__intracellular_ephys__sweep_table:
    name: NWBFile__general__intracellular_ephys__sweep_table
    description: '[DEPRECATED] Table used to group different PatchClampSeries. SweepTable
      is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable
      tables. Additional SequentialRecordingsTable, RepetitionsTable and ExperimentalConditions
      tables provide enhanced support for experiment metadata.'
    is_a: SweepTable
  NWBFile__general__intracellular_ephys__intracellular_recordings:
    name: NWBFile__general__intracellular_ephys__intracellular_recordings
    description: A table to group together a stimulus and response from a single electrode
      and a single simultaneous recording. Each row in the table represents a single
      recording consisting typically of a stimulus and a corresponding response. In
      some cases, however, only a stimulus or a response are recorded as as part of
      an experiment. In this case both, the stimulus and response will point to the
      same TimeSeries while the idx_start and count of the invalid column will be
      set to -1, thus, indicating that no values have been recorded for the stimulus
      or response, respectively. Note, a recording MUST contain at least a stimulus
      or a response. Typically the stimulus and response are PatchClampSeries. However,
      the use of AD/DA channels that are not associated to an electrode is also common
      in intracellular electrophysiology, in which case other TimeSeries may be used.
    is_a: IntracellularRecordingsTable
  NWBFile__general__intracellular_ephys__simultaneous_recordings:
    name: NWBFile__general__intracellular_ephys__simultaneous_recordings
    description: A table for grouping different intracellular recordings from the
      IntracellularRecordingsTable table together that were recorded simultaneously
      from different electrodes
    is_a: SimultaneousRecordingsTable
  NWBFile__general__intracellular_ephys__sequential_recordings:
    name: NWBFile__general__intracellular_ephys__sequential_recordings
    description: A table for grouping different sequential recordings from the SimultaneousRecordingsTable
      table together. This is typically used to group together sequential recordings
      where the a sequence of stimuli of the same type with varying parameters have
      been presented in a sequence.
    is_a: SequentialRecordingsTable
  NWBFile__general__intracellular_ephys__repetitions:
    name: NWBFile__general__intracellular_ephys__repetitions
    description: A table for grouping different sequential intracellular recordings
      together. With each SequentialRecording typically representing a particular
      type of stimulus, the RepetitionsTable table is typically used to group sets
      of stimuli applied in sequence.
    is_a: RepetitionsTable
  NWBFile__general__intracellular_ephys__experimental_conditions:
    name: NWBFile__general__intracellular_ephys__experimental_conditions
    description: A table for grouping different intracellular recording repetitions
      together that belong to the same experimental experimental_conditions.
    is_a: ExperimentalConditionsTable
  NWBFile__general__optogenetics:
    name: NWBFile__general__optogenetics
    description: Metadata describing optogenetic stimuluation.
    attributes:
      OptogeneticStimulusSite:
        name: OptogeneticStimulusSite
        description: An optogenetic stimulation site.
        multivalued: true
        range: OptogeneticStimulusSite
        required: false
  NWBFile__general__optophysiology:
    name: NWBFile__general__optophysiology
    description: Metadata related to optophysiology.
    attributes:
      ImagingPlane:
        name: ImagingPlane
        description: An imaging plane.
        multivalued: true
        range: ImagingPlane
        required: false
  NWBFile__intervals:
    name: NWBFile__intervals
    description: Experimental intervals, whether that be logically distinct sub-experiments
      having a particular scientific goal, trials (see trials subgroup) during an
      experiment, or epochs (see epochs subgroup) deriving from analysis of data.
    attributes:
      epochs:
        name: epochs
        description: Divisions in time marking experimental stages or sub-divisions
          of a single recording session.
        multivalued: false
        range: NWBFile__intervals__epochs
        required: false
      trials:
        name: trials
        description: Repeated experimental events that have a logical grouping.
        multivalued: false
        range: NWBFile__intervals__trials
        required: false
      invalid_times:
        name: invalid_times
        description: Time intervals that should be removed from analysis.
        multivalued: false
        range: NWBFile__intervals__invalid_times
        required: false
      TimeIntervals:
        name: TimeIntervals
        description: Optional additional table(s) for describing other experimental
          time intervals.
        multivalued: true
        range: TimeIntervals
        required: false
  NWBFile__intervals__epochs:
    name: NWBFile__intervals__epochs
    description: Divisions in time marking experimental stages or sub-divisions of
      a single recording session.
    is_a: TimeIntervals
  NWBFile__intervals__trials:
    name: NWBFile__intervals__trials
    description: Repeated experimental events that have a logical grouping.
    is_a: TimeIntervals
  NWBFile__intervals__invalid_times:
    name: NWBFile__intervals__invalid_times
    description: Time intervals that should be removed from analysis.
    is_a: TimeIntervals
  NWBFile__units:
    name: NWBFile__units
    description: Data about sorted spike units.
    is_a: Units
  Subject__age:
    name: Subject__age
    description: Age of subject. Can be supplied instead of 'date_of_birth'.
    attributes:
      reference:
        name: reference
        description: Age is with reference to this event. Can be 'birth' or 'gestational'.
          If reference is omitted, 'birth' is implied.
        range: text