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

name: core.nwb.file
id: core.nwb.file
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
default_prefix: core.nwb.file/
classes:
  ScratchData:
    name: ScratchData
    description: Any one-off datasets
    is_a: NWBData
    attributes:
      name:
        name: name
        range: string
        required: true
      notes:
        name: notes
        description: Any notes the user has about the dataset being stored
        range: text
    tree_root: true
  NWBFile:
    name: NWBFile
    description: An NWB file storing cellular-based neurophysiology data from a single
      experimental session.
    is_a: NWBContainer
    attributes:
      name:
        name: name
        ifabsent: string(root)
        range: string
        required: true
        equals_string: root
      nwb_version:
        name: nwb_version
        description: File version string. Use semantic versioning, e.g. 1.2.1. This
          will be the name of the format with trailing major, minor and patch numbers.
        range: text
      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
      identifier:
        name: identifier
        description: A unique text identifier for the file. For example, concatenated
          lab name, file creation date/time and experimentalist, or a hash of these
          and/or other values. The goal is that the string should be unique to all
          other files.
        multivalued: false
        range: text
        required: true
      session_description:
        name: session_description
        description: A description of the experimental session and data in the file.
        multivalued: false
        range: text
        required: true
      session_start_time:
        name: session_start_time
        description: 'Date and time of the experiment/session start. The date is stored
          in UTC with local timezone offset as ISO 8601 extended formatted string:
          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.'
        multivalued: false
        range: isodatetime
        required: true
      timestamps_reference_time:
        name: timestamps_reference_time
        description: 'Date and time corresponding to time zero of all timestamps.
          The date is stored in UTC with local timezone offset as ISO 8601 extended
          formatted string: 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. All
          times stored in the file use this time as reference (i.e., time zero).'
        multivalued: false
        range: isodatetime
        required: true
      acquisition:
        name: 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.
        multivalued: true
        any_of:
        - range: NWBDataInterface
        - range: DynamicTable
      analysis:
        name: 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.
        multivalued: true
        any_of:
        - range: NWBContainer
        - range: DynamicTable
      scratch:
        name: 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.
        multivalued: true
        any_of:
        - range: NWBContainer
        - range: DynamicTable
      processing:
        name: 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.
        multivalued: true
        any_of:
        - range: ProcessingModule
      stimulus:
        name: 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.
        multivalued: false
        range: NWBFile__stimulus
        required: true
      general:
        name: 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.
        multivalued: false
        range: NWBFile__general
        required: true
      intervals:
        name: 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.
        multivalued: false
        range: NWBFile__intervals
        required: false
      units:
        name: units
        description: Data about sorted spike units.
        multivalued: false
        range: Units
        required: false
    tree_root: true
  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
      value:
        name: value
        range: text
        required: true
  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
  LabMetaData:
    name: LabMetaData
    description: Lab-specific meta-data.
    is_a: NWBContainer
    attributes:
      name:
        name: name
        range: string
        required: true
    tree_root: true
  Subject:
    name: Subject
    description: Information about the animal or person from which the data was measured.
    is_a: NWBContainer
    attributes:
      name:
        name: name
        range: string
        required: true
      age:
        name: age
        description: Age of subject. Can be supplied instead of 'date_of_birth'.
        multivalued: false
        range: Subject__age
        required: false
      date_of_birth:
        name: date_of_birth
        description: Date of birth of subject. Can be supplied instead of 'age'.
        multivalued: false
        range: isodatetime
        required: false
      description:
        name: description
        description: Description of subject and where subject came from (e.g., breeder,
          if animal).
        multivalued: false
        range: text
        required: false
      genotype:
        name: genotype
        description: Genetic strain. If absent, assume Wild Type (WT).
        multivalued: false
        range: text
        required: false
      sex:
        name: sex
        description: Gender of subject.
        multivalued: false
        range: text
        required: false
      species:
        name: species
        description: Species of subject.
        multivalued: false
        range: text
        required: false
      strain:
        name: strain
        description: Strain of subject.
        multivalued: false
        range: text
        required: false
      subject_id:
        name: subject_id
        description: ID of animal/person used/participating in experiment (lab convention).
        multivalued: false
        range: text
        required: false
      weight:
        name: weight
        description: Weight at time of experiment, at time of surgery and at other
          important times.
        multivalued: false
        range: text
        required: false
    tree_root: true
  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
      value:
        name: value
        range: text
        required: true