mirror of
https://github.com/p2p-ld/nwb-linkml.git
synced 2024-09-19 23:44:28 +00:00
277 lines
12 KiB
YAML
277 lines
12 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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- core.nwb.file.include
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- core.nwb.file
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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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LabMetaData:
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name: LabMetaData
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description: Lab-specific meta-data.
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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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range: string
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required: true
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tree_root: true
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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 measured.
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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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range: string
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required: true
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age:
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name: age
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description: Age of subject. Can be supplied instead of 'date_of_birth'.
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multivalued: false
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range: Subject__age
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required: false
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date_of_birth:
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name: date_of_birth
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description: Date of birth of subject. Can be supplied instead of 'age'.
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multivalued: false
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range: isodatetime
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required: false
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description:
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name: description
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description: Description of subject and where subject came from (e.g., breeder,
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if animal).
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multivalued: false
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range: text
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required: false
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genotype:
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name: genotype
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description: Genetic strain. If absent, assume Wild Type (WT).
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multivalued: false
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range: text
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required: false
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sex:
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name: sex
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description: Gender of subject.
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multivalued: false
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range: text
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required: false
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species:
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name: species
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description: Species of subject.
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multivalued: false
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range: text
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required: false
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strain:
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name: strain
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description: Strain of subject.
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multivalued: false
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range: text
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required: false
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subject_id:
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name: subject_id
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description: ID of animal/person used/participating in experiment (lab convention).
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multivalued: false
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range: text
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required: false
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weight:
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name: weight
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description: Weight at time of experiment, at time of surgery and at other
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important times.
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multivalued: false
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range: text
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required: false
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tree_root: true
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