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
prefixes:
  core.nwb.file:
    prefix_prefix: core.nwb.file
    prefix_reference: https://example.com/core.nwb.file/
default_prefix: core.nwb.file
classes:
  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:
      name:
        name: name
        ifabsent: string(stimulus)
        range: string
        required: true
        equals_string: stimulus
      presentation:
        name: presentation
        description: Stimuli presented during the experiment.
        multivalued: true
        any_of:
        - range: TimeSeries
      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: true
        any_of:
        - range: TimeSeries
        - range: Images
  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:
      name:
        name: name
        ifabsent: string(general)
        range: string
        required: true
        equals_string: general
      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: true
        range: text
        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: true
        range: text
        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: true
        range: text
        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
      lab_meta_data:
        name: lab_meta_data
        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: true
        any_of:
        - range: Device
      subject:
        name: subject
        description: Information about the animal or person from which the data was
          measured.
        multivalued: false
        range: 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: true
        any_of:
        - range: OptogeneticStimulusSite
      optophysiology:
        name: optophysiology
        description: Metadata related to optophysiology.
        multivalued: true
        any_of:
        - range: ImagingPlane
  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:
      name:
        name: name
        ifabsent: string(source_script)
        range: string
        required: true
        equals_string: source_script
      file_name:
        name: file_name
        description: Name of script file.
        range: text
  NWBFile__general__extracellular_ephys:
    name: NWBFile__general__extracellular_ephys
    description: Metadata related to extracellular electrophysiology.
    attributes:
      name:
        name: name
        ifabsent: string(extracellular_ephys)
        range: string
        required: true
        equals_string: extracellular_ephys
      electrode_group:
        name: electrode_group
        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: DynamicTable
        required: false
  NWBFile__general__intracellular_ephys:
    name: NWBFile__general__intracellular_ephys
    description: Metadata related to intracellular electrophysiology.
    attributes:
      name:
        name: name
        ifabsent: string(intracellular_ephys)
        range: string
        required: true
        equals_string: intracellular_ephys
      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
      intracellular_electrode:
        name: intracellular_electrode
        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: SweepTable
        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: IntracellularRecordingsTable
        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: SimultaneousRecordingsTable
        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: SequentialRecordingsTable
        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: RepetitionsTable
        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: ExperimentalConditionsTable
        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:
      name:
        name: name
        ifabsent: string(intervals)
        range: string
        required: true
        equals_string: intervals
      epochs:
        name: epochs
        description: Divisions in time marking experimental stages or sub-divisions
          of a single recording session.
        multivalued: false
        range: TimeIntervals
        required: false
      trials:
        name: trials
        description: Repeated experimental events that have a logical grouping.
        multivalued: false
        range: TimeIntervals
        required: false
      invalid_times:
        name: invalid_times
        description: Time intervals that should be removed from analysis.
        multivalued: false
        range: TimeIntervals
        required: false
      time_intervals:
        name: time_intervals
        description: Optional additional table(s) for describing other experimental
          time intervals.
        multivalued: true
        range: TimeIntervals
        required: false
  Subject__age:
    name: Subject__age
    description: Age of subject. Can be supplied instead of 'date_of_birth'.
    attributes:
      name:
        name: name
        ifabsent: string(age)
        range: string
        required: true
        equals_string: age
      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