mirror of
https://github.com/p2p-ld/nwb-linkml.git
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665 lines
27 KiB
YAML
665 lines
27 KiB
YAML
name: core.nwb.file
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id: core.nwb.file
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imports:
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- core.nwb.base
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- hdmf-common.table
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- core.nwb.device
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- core.nwb.ecephys
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- core.nwb.icephys
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- core.nwb.ogen
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- core.nwb.ophys
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- core.nwb.epoch
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- core.nwb.misc
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- nwb.language
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default_prefix: core.nwb.file/
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classes:
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ScratchData:
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name: ScratchData
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description: Any one-off datasets
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is_a: NWBData
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attributes:
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name:
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name: name
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range: string
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required: true
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notes:
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name: notes
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description: Any notes the user has about the dataset being stored
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range: text
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tree_root: true
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NWBFile:
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name: NWBFile
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description: An NWB file storing cellular-based neurophysiology data from a single
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experimental session.
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is_a: NWBContainer
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attributes:
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name:
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name: name
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ifabsent: string(root)
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range: string
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required: true
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equals_string: root
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nwb_version:
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name: nwb_version
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description: File version string. Use semantic versioning, e.g. 1.2.1. This
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will be the name of the format with trailing major, minor and patch numbers.
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range: text
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file_create_date:
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name: file_create_date
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description: 'A record of the date the file was created and of subsequent
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modifications. The date is stored in UTC with local timezone offset as ISO
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8601 extended formatted strings: 2018-09-28T14:43:54.123+02:00. Dates stored
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in UTC end in "Z" with no timezone offset. Date accuracy is up to milliseconds.
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The file can be created after the experiment was run, so this may differ
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from the experiment start time. Each modification to the nwb file adds a
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new entry to the array.'
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multivalued: true
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range: isodatetime
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required: true
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identifier:
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name: identifier
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description: A unique text identifier for the file. For example, concatenated
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lab name, file creation date/time and experimentalist, or a hash of these
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and/or other values. The goal is that the string should be unique to all
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other files.
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multivalued: false
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range: text
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required: true
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session_description:
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name: session_description
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description: A description of the experimental session and data in the file.
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multivalued: false
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range: text
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required: true
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session_start_time:
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name: session_start_time
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description: 'Date and time of the experiment/session start. The date is stored
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in UTC with local timezone offset as ISO 8601 extended formatted string:
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2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in "Z" with no timezone
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offset. Date accuracy is up to milliseconds.'
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multivalued: false
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range: isodatetime
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required: true
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timestamps_reference_time:
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name: timestamps_reference_time
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description: 'Date and time corresponding to time zero of all timestamps.
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The date is stored in UTC with local timezone offset as ISO 8601 extended
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formatted string: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end
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in "Z" with no timezone offset. Date accuracy is up to milliseconds. All
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times stored in the file use this time as reference (i.e., time zero).'
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multivalued: false
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range: isodatetime
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required: true
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acquisition:
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name: acquisition
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description: Data streams recorded from the system, including ephys, ophys,
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tracking, etc. This group should be read-only after the experiment is completed
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and timestamps are corrected to a common timebase. The data stored here
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may be links to raw data stored in external NWB files. This will allow keeping
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bulky raw data out of the file while preserving the option of keeping some/all
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in the file. Acquired data includes tracking and experimental data streams
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(i.e., everything measured from the system). If bulky data is stored in
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the /acquisition group, the data can exist in a separate NWB file that is
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linked to by the file being used for processing and analysis.
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multivalued: true
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any_of:
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- range: NWBDataInterface
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- range: DynamicTable
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analysis:
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name: analysis
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description: Lab-specific and custom scientific analysis of data. There is
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no defined format for the content of this group - the format is up to the
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individual user/lab. To facilitate sharing analysis data between labs, the
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contents here should be stored in standard types (e.g., neurodata_types)
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and appropriately documented. The file can store lab-specific and custom
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data analysis without restriction on its form or schema, reducing data formatting
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restrictions on end users. Such data should be placed in the analysis group.
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The analysis data should be documented so that it could be shared with other
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labs.
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multivalued: true
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any_of:
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- range: NWBContainer
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- range: DynamicTable
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scratch:
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name: scratch
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description: A place to store one-off analysis results. Data placed here is
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not intended for sharing. By placing data here, users acknowledge that there
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is no guarantee that their data meets any standard.
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multivalued: true
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any_of:
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- range: NWBContainer
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- range: DynamicTable
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processing:
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name: processing
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description: The home for ProcessingModules. These modules perform intermediate
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analysis of data that is necessary to perform before scientific analysis.
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Examples include spike clustering, extracting position from tracking data,
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stitching together image slices. ProcessingModules can be large and express
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many data sets from relatively complex analysis (e.g., spike detection and
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clustering) or small, representing extraction of position information from
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tracking video, or even binary lick/no-lick decisions. Common software tools
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(e.g., klustakwik, MClust) are expected to read/write data here. 'Processing'
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refers to intermediate analysis of the acquired data to make it more amenable
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to scientific analysis.
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multivalued: true
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any_of:
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- range: ProcessingModule
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stimulus:
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name: stimulus
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description: Data pushed into the system (eg, video stimulus, sound, voltage,
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etc) and secondary representations of that data (eg, measurements of something
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used as a stimulus). This group should be made read-only after experiment
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complete and timestamps are corrected to common timebase. Stores both presented
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stimuli and stimulus templates, the latter in case the same stimulus is
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presented multiple times, or is pulled from an external stimulus library.
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Stimuli are here defined as any signal that is pushed into the system as
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part of the experiment (eg, sound, video, voltage, etc). Many different
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experiments can use the same stimuli, and stimuli can be re-used during
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an experiment. The stimulus group is organized so that one version of template
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stimuli can be stored and these be used multiple times. These templates
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can exist in the present file or can be linked to a remote library file.
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multivalued: false
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range: NWBFile__stimulus
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required: true
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general:
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name: general
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description: Experimental metadata, including protocol, notes and description
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of hardware device(s). The metadata stored in this section should be used
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to describe the experiment. Metadata necessary for interpreting the data
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is stored with the data. General experimental metadata, including animal
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strain, experimental protocols, experimenter, devices, etc, are stored under
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'general'. Core metadata (e.g., that required to interpret data fields)
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is stored with the data itself, and implicitly defined by the file specification
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(e.g., time is in seconds). The strategy used here for storing non-core
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metadata is to use free-form text fields, such as would appear in sentences
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or paragraphs from a Methods section. Metadata fields are text to enable
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them to be more general, for example to represent ranges instead of numerical
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values. Machine-readable metadata is stored as attributes to these free-form
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datasets. All entries in the below table are to be included when data is
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present. Unused groups (e.g., intracellular_ephys in an optophysiology experiment)
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should not be created unless there is data to store within them.
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multivalued: false
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range: NWBFile__general
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required: true
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intervals:
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name: intervals
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description: Experimental intervals, whether that be logically distinct sub-experiments
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having a particular scientific goal, trials (see trials subgroup) during
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an experiment, or epochs (see epochs subgroup) deriving from analysis of
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data.
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multivalued: false
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range: NWBFile__intervals
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required: false
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units:
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name: units
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description: Data about sorted spike units.
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multivalued: false
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range: Units
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required: false
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tree_root: true
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NWBFile__stimulus:
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name: NWBFile__stimulus
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description: Data pushed into the system (eg, video stimulus, sound, voltage,
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etc) and secondary representations of that data (eg, measurements of something
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used as a stimulus). This group should be made read-only after experiment complete
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and timestamps are corrected to common timebase. Stores both presented stimuli
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and stimulus templates, the latter in case the same stimulus is presented multiple
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times, or is pulled from an external stimulus library. Stimuli are here defined
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as any signal that is pushed into the system as part of the experiment (eg,
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sound, video, voltage, etc). Many different experiments can use the same stimuli,
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and stimuli can be re-used during an experiment. The stimulus group is organized
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so that one version of template stimuli can be stored and these be used multiple
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times. These templates can exist in the present file or can be linked to a remote
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library file.
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attributes:
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name:
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name: name
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ifabsent: string(stimulus)
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range: string
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required: true
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equals_string: stimulus
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presentation:
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name: presentation
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description: Stimuli presented during the experiment.
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multivalued: true
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any_of:
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- range: TimeSeries
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templates:
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name: templates
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description: Template stimuli. Timestamps in templates are based on stimulus
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design and are relative to the beginning of the stimulus. When templates
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are used, the stimulus instances must convert presentation times to the
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experiment`s time reference frame.
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multivalued: true
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any_of:
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- range: TimeSeries
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- range: Images
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NWBFile__general:
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name: NWBFile__general
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description: Experimental metadata, including protocol, notes and description
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of hardware device(s). The metadata stored in this section should be used to
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describe the experiment. Metadata necessary for interpreting the data is stored
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with the data. General experimental metadata, including animal strain, experimental
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protocols, experimenter, devices, etc, are stored under 'general'. Core metadata
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(e.g., that required to interpret data fields) is stored with the data itself,
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and implicitly defined by the file specification (e.g., time is in seconds).
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The strategy used here for storing non-core metadata is to use free-form text
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fields, such as would appear in sentences or paragraphs from a Methods section.
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Metadata fields are text to enable them to be more general, for example to represent
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ranges instead of numerical values. Machine-readable metadata is stored as attributes
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to these free-form datasets. All entries in the below table are to be included
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when data is present. Unused groups (e.g., intracellular_ephys in an optophysiology
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experiment) should not be created unless there is data to store within them.
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attributes:
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name:
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name: name
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ifabsent: string(general)
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range: string
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required: true
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equals_string: general
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data_collection:
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name: data_collection
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description: Notes about data collection and analysis.
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multivalued: false
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range: text
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required: false
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experiment_description:
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name: experiment_description
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description: General description of the experiment.
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multivalued: false
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range: text
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required: false
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experimenter:
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name: experimenter
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description: Name of person(s) who performed the experiment. Can also specify
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roles of different people involved.
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multivalued: true
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range: text
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required: false
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institution:
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name: institution
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description: Institution(s) where experiment was performed.
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multivalued: false
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range: text
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required: false
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keywords:
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name: keywords
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description: Terms to search over.
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multivalued: true
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range: text
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required: false
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lab:
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name: lab
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description: Laboratory where experiment was performed.
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multivalued: false
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range: text
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required: false
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notes:
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name: notes
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description: Notes about the experiment.
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multivalued: false
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range: text
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required: false
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pharmacology:
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name: pharmacology
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description: Description of drugs used, including how and when they were administered.
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Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc.
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multivalued: false
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range: text
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required: false
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protocol:
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name: protocol
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description: Experimental protocol, if applicable. e.g., include IACUC protocol
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number.
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multivalued: false
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range: text
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required: false
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related_publications:
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name: related_publications
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description: Publication information. PMID, DOI, URL, etc.
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multivalued: true
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range: text
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required: false
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session_id:
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name: session_id
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description: Lab-specific ID for the session.
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multivalued: false
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range: text
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required: false
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slices:
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name: slices
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description: Description of slices, including information about preparation
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thickness, orientation, temperature, and bath solution.
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multivalued: false
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range: text
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required: false
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source_script:
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name: source_script
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description: Script file or link to public source code used to create this
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NWB file.
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multivalued: false
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range: NWBFile__general__source_script
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required: false
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stimulus:
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name: stimulus
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description: Notes about stimuli, such as how and where they were presented.
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multivalued: false
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range: text
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required: false
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surgery:
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name: surgery
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description: Narrative description about surgery/surgeries, including date(s)
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and who performed surgery.
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multivalued: false
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range: text
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required: false
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virus:
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name: virus
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description: Information about virus(es) used in experiments, including virus
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ID, source, date made, injection location, volume, etc.
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multivalued: false
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range: text
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required: false
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lab_meta_data:
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name: lab_meta_data
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description: Place-holder than can be extended so that lab-specific meta-data
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can be placed in /general.
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multivalued: true
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range: LabMetaData
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required: false
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devices:
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name: devices
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description: Description of hardware devices used during experiment, e.g.,
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monitors, ADC boards, microscopes, etc.
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multivalued: true
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any_of:
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- range: Device
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subject:
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name: subject
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description: Information about the animal or person from which the data was
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measured.
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multivalued: false
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range: Subject
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required: false
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extracellular_ephys:
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name: extracellular_ephys
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description: Metadata related to extracellular electrophysiology.
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multivalued: false
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range: NWBFile__general__extracellular_ephys
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required: false
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intracellular_ephys:
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name: intracellular_ephys
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description: Metadata related to intracellular electrophysiology.
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multivalued: false
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range: NWBFile__general__intracellular_ephys
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required: false
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optogenetics:
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name: optogenetics
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description: Metadata describing optogenetic stimuluation.
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multivalued: true
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any_of:
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- range: OptogeneticStimulusSite
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optophysiology:
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name: optophysiology
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description: Metadata related to optophysiology.
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multivalued: true
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any_of:
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- range: ImagingPlane
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NWBFile__general__source_script:
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name: NWBFile__general__source_script
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description: Script file or link to public source code used to create this NWB
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file.
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attributes:
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name:
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name: name
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ifabsent: string(source_script)
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range: string
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required: true
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equals_string: source_script
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file_name:
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name: file_name
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description: Name of script file.
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range: text
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value:
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name: value
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range: text
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required: true
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NWBFile__general__extracellular_ephys:
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name: NWBFile__general__extracellular_ephys
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description: Metadata related to extracellular electrophysiology.
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attributes:
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name:
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name: name
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ifabsent: string(extracellular_ephys)
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range: string
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required: true
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equals_string: extracellular_ephys
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electrode_group:
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name: electrode_group
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description: Physical group of electrodes.
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multivalued: true
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range: ElectrodeGroup
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required: false
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electrodes:
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name: electrodes
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description: A table of all electrodes (i.e. channels) used for recording.
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multivalued: false
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range: DynamicTable
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required: false
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|
NWBFile__general__intracellular_ephys:
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name: NWBFile__general__intracellular_ephys
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description: Metadata related to intracellular electrophysiology.
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attributes:
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name:
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name: name
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ifabsent: string(intracellular_ephys)
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range: string
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required: true
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equals_string: intracellular_ephys
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filtering:
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name: filtering
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description: '[DEPRECATED] Use IntracellularElectrode.filtering instead. Description
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of filtering used. Includes filtering type and parameters, frequency fall-off,
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etc. If this changes between TimeSeries, filter description should be stored
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as a text attribute for each TimeSeries.'
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multivalued: false
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range: text
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required: false
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|
intracellular_electrode:
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name: intracellular_electrode
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description: An intracellular electrode.
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multivalued: true
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range: IntracellularElectrode
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required: false
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|
sweep_table:
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name: sweep_table
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description: '[DEPRECATED] Table used to group different PatchClampSeries.
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|
SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable
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|
tables. Additional SequentialRecordingsTable, RepetitionsTable and ExperimentalConditions
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|
tables provide enhanced support for experiment metadata.'
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multivalued: false
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range: SweepTable
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required: false
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|
intracellular_recordings:
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name: intracellular_recordings
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description: A table to group together a stimulus and response from a single
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electrode and a single simultaneous recording. Each row in the table represents
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a single recording consisting typically of a stimulus and a corresponding
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|
response. In some cases, however, only a stimulus or a response are recorded
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as as part of an experiment. In this case both, the stimulus and response
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will point to the same TimeSeries while the idx_start and count of the invalid
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column will be set to -1, thus, indicating that no values have been recorded
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for the stimulus or response, respectively. Note, a recording MUST contain
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at least a stimulus or a response. Typically the stimulus and response are
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PatchClampSeries. However, the use of AD/DA channels that are not associated
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to an electrode is also common in intracellular electrophysiology, in which
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|
case other TimeSeries may be used.
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multivalued: false
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range: IntracellularRecordingsTable
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required: false
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|
simultaneous_recordings:
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name: simultaneous_recordings
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description: A table for grouping different intracellular recordings from
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the IntracellularRecordingsTable table together that were recorded simultaneously
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from different electrodes
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multivalued: false
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range: SimultaneousRecordingsTable
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required: false
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|
sequential_recordings:
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name: sequential_recordings
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description: A table for grouping different sequential recordings from the
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|
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
|