mirror of
https://github.com/p2p-ld/nwb-linkml.git
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502 lines
21 KiB
YAML
502 lines
21 KiB
YAML
groups:
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- neurodata_type_def: NWBFile
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neurodata_type_inc: NWBContainer
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name: root
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doc: An NWB file storing cellular-based neurophysiology data from a single
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experimental session.
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attributes:
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- name: nwb_version
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dtype: text
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value: "2.6.0"
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doc: File version string. Use semantic versioning, e.g. 1.2.1. This will be the
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name of the format with trailing major, minor and patch numbers.
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datasets:
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- name: file_create_date
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dtype: isodatetime
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dims:
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- num_modifications
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shape:
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- null
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doc: 'A record of the date the file was created and of subsequent modifications.
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The date is stored in UTC with local timezone offset as ISO 8601
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extended formatted strings: 2018-09-28T14:43:54.123+02:00. Dates stored in
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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 from
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the experiment start time. Each modification to the nwb file adds a new entry
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to the array.'
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- name: identifier
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dtype: text
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doc: A unique text identifier for the file. For example, concatenated lab name,
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file creation date/time and experimentalist, or a hash of these and/or other
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values. The goal is that the string should be unique to all other files.
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- name: session_description
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dtype: text
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doc: A description of the experimental session and data in the file.
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- name: session_start_time
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dtype: isodatetime
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doc: '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.
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Dates stored in UTC end in "Z" with no timezone offset. Date accuracy is
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up to milliseconds.'
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- name: timestamps_reference_time
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dtype: isodatetime
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doc: 'Date and time corresponding to time zero of all timestamps. The
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date is stored in UTC with local timezone offset as ISO 8601 extended formatted
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string: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in "Z" with
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no timezone offset. Date accuracy is up to milliseconds. All times stored
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in the file use this time as reference (i.e., time zero).'
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groups:
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- name: acquisition
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doc: Data streams recorded from the system, including ephys, ophys, tracking,
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etc. This group should be read-only after the experiment is completed and
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timestamps are corrected to a common timebase. The data stored here may be links
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to raw data stored in external NWB files. This will allow keeping bulky raw
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data out of the file while preserving the option of keeping some/all in the
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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 the /acquisition
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group, the data can exist in a separate NWB file that is linked to by the file
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being used for processing and analysis.
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groups:
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- neurodata_type_inc: NWBDataInterface
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doc: Acquired, raw data.
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quantity: '*'
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- neurodata_type_inc: DynamicTable
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doc: Tabular data that is relevant to acquisition
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quantity: '*'
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- name: analysis
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doc: Lab-specific and custom scientific analysis of data. There is no defined
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format for the content of this group - the format is up to the individual user/lab.
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To facilitate sharing analysis data between labs, the contents here
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should be stored in standard types (e.g., neurodata_types) and appropriately documented.
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The file can store lab-specific and custom data analysis without
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restriction on its form or schema, reducing data formatting restrictions on
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end users. Such data should be placed in the analysis group. The analysis data
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should be documented so that it could be shared with other labs.
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groups:
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- neurodata_type_inc: NWBContainer
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doc: Custom analysis results.
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quantity: '*'
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- neurodata_type_inc: DynamicTable
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doc: Tabular data that is relevant to data stored in analysis
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quantity: '*'
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- name: scratch
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doc: 'A place to store one-off analysis results. Data placed here is not intended for
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sharing. By placing data here, users acknowledge that there is no guarantee that
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their data meets any standard.'
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quantity: '?'
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groups:
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- neurodata_type_inc: NWBContainer
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doc: Any one-off containers
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quantity: '*'
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- neurodata_type_inc: DynamicTable
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doc: Any one-off tables
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quantity: '*'
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datasets:
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- neurodata_type_inc: ScratchData
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doc: Any one-off datasets
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quantity: '*'
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- name: processing
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doc: "The home for ProcessingModules. These modules perform intermediate analysis\
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\ of data that is necessary to perform before scientific analysis. Examples\
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\ include spike clustering, extracting position from tracking data, stitching\
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\ together image slices. ProcessingModules can be large\
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\ and express many data sets from relatively complex analysis (e.g., spike detection\
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\ and clustering) or small, representing extraction of position information\
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\ from tracking video, or even binary lick/no-lick decisions. Common software\
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\ tools (e.g., klustakwik, MClust) are expected to read/write data here. \
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\ 'Processing' refers to intermediate analysis of the acquired data to make\
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\ it more amenable to scientific analysis."
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groups:
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- neurodata_type_inc: ProcessingModule
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doc: Intermediate analysis of acquired data.
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quantity: '*'
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- name: stimulus
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doc: 'Data pushed into the system (eg, video stimulus, sound, voltage, etc) and
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secondary representations of that data (eg, measurements of something used as
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a stimulus). This group should be made read-only after experiment complete and timestamps
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are corrected to common timebase. Stores both presented stimuli and stimulus
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templates, the latter in case the same stimulus is presented multiple times,
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or is pulled from an external stimulus library. Stimuli are here
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defined as any signal that is pushed into the system as part of the experiment
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(eg, sound, video, voltage, etc). Many different experiments can use the same
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stimuli, and stimuli can be re-used during an experiment. The stimulus group
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is organized so that one version of template stimuli can be stored and these
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be used multiple times. These templates can exist in the present file or can
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be linked to a remote library file.'
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groups:
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- name: presentation
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doc: Stimuli presented during the experiment.
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groups:
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- neurodata_type_inc: TimeSeries
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doc: TimeSeries objects containing data of presented stimuli.
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quantity: '*'
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- name: templates
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doc: '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 are
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used, the stimulus instances must convert presentation times to the experiment`s
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time reference frame.'
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groups:
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- neurodata_type_inc: TimeSeries
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doc: TimeSeries objects containing template data of presented stimuli.
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quantity: '*'
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- neurodata_type_inc: Images
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doc: Images objects containing images of presented stimuli.
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quantity: '*'
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- name: general
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doc: "Experimental metadata, including protocol, notes and description of hardware\
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\ 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\
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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) is\
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\ 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 metadata\
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\ is to use free-form text fields, such as would appear in sentences or paragraphs\
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\ from a Methods section. Metadata fields are text to enable them to be more\
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\ general, for example to represent ranges instead of numerical values. Machine-readable\
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\ metadata is stored as attributes to these free-form datasets. All entries\
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\ in the below table are to be included when data is present. Unused groups\
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\ (e.g., intracellular_ephys in an optophysiology experiment) should not be\
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\ created unless there is data to store within them."
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datasets:
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- name: data_collection
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dtype: text
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doc: Notes about data collection and analysis.
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quantity: '?'
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- name: experiment_description
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dtype: text
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doc: General description of the experiment.
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quantity: '?'
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- name: experimenter
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dtype: text
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doc: Name of person(s) who performed the experiment. Can also specify roles
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of different people involved.
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quantity: '?'
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dims:
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- num_experimenters
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shape:
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- null
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- name: institution
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dtype: text
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doc: Institution(s) where experiment was performed.
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quantity: '?'
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- name: keywords
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dtype: text
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dims:
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- num_keywords
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shape:
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- null
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doc: Terms to search over.
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quantity: '?'
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- name: lab
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dtype: text
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doc: Laboratory where experiment was performed.
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quantity: '?'
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- name: notes
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dtype: text
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doc: Notes about the experiment.
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quantity: '?'
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- name: pharmacology
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dtype: text
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doc: 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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quantity: '?'
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- name: protocol
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dtype: text
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doc: Experimental protocol, if applicable. e.g., include IACUC protocol number.
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quantity: '?'
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- name: related_publications
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dtype: text
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doc: Publication information. PMID, DOI, URL, etc.
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dims:
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- num_publications
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shape:
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- null
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quantity: '?'
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- name: session_id
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dtype: text
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doc: Lab-specific ID for the session.
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quantity: '?'
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- name: slices
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dtype: text
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doc: Description of slices, including information about preparation thickness,
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orientation, temperature, and bath solution.
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quantity: '?'
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- name: source_script
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dtype: text
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doc: Script file or link to public source code used to create this NWB file.
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quantity: '?'
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attributes:
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- name: file_name
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dtype: text
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doc: Name of script file.
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- name: stimulus
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dtype: text
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doc: Notes about stimuli, such as how and where they were presented.
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quantity: '?'
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- name: surgery
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dtype: text
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doc: Narrative description about surgery/surgeries, including date(s) and who
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performed surgery.
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quantity: '?'
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- name: virus
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dtype: text
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doc: Information about virus(es) used in experiments, including virus ID, source,
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date made, injection location, volume, etc.
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quantity: '?'
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groups:
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- neurodata_type_inc: LabMetaData
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doc: Place-holder than can be extended so that lab-specific meta-data can be
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placed in /general.
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quantity: '*'
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- name: devices
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doc: Description of hardware devices used during experiment, e.g., monitors,
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ADC boards, microscopes, etc.
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quantity: '?'
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groups:
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- neurodata_type_inc: Device
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doc: Data acquisition devices.
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quantity: '*'
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- name: subject
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neurodata_type_inc: Subject
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doc: Information about the animal or person from which the data was measured.
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quantity: '?'
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- name: extracellular_ephys
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doc: Metadata related to extracellular electrophysiology.
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quantity: '?'
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groups:
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- neurodata_type_inc: ElectrodeGroup
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doc: Physical group of electrodes.
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quantity: '*'
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- name: electrodes
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neurodata_type_inc: DynamicTable
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doc: A table of all electrodes (i.e. channels) used for recording.
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quantity: '?'
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datasets:
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- name: x
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neurodata_type_inc: VectorData
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dtype: float32
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doc: x coordinate of the channel location in the brain (+x is posterior).
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quantity: '?'
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- name: y
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neurodata_type_inc: VectorData
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dtype: float32
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doc: y coordinate of the channel location in the brain (+y is inferior).
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quantity: '?'
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- name: z
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neurodata_type_inc: VectorData
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dtype: float32
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doc: z coordinate of the channel location in the brain (+z is right).
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quantity: '?'
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- name: imp
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neurodata_type_inc: VectorData
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dtype: float32
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doc: Impedance of the channel, in ohms.
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quantity: '?'
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- name: location
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neurodata_type_inc: VectorData
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dtype: text
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doc: Location of the electrode (channel). Specify the area, layer, comments
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on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use
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standard atlas names for anatomical regions when possible.
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- name: filtering
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neurodata_type_inc: VectorData
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dtype: text
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doc: Description of hardware filtering, including the filter name and frequency cutoffs.
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quantity: '?'
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- name: group
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neurodata_type_inc: VectorData
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dtype:
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target_type: ElectrodeGroup
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reftype: object
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doc: Reference to the ElectrodeGroup this electrode is a part of.
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- name: group_name
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neurodata_type_inc: VectorData
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dtype: text
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doc: Name of the ElectrodeGroup this electrode is a part of.
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- name: rel_x
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neurodata_type_inc: VectorData
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dtype: float32
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doc: x coordinate in electrode group
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quantity: '?'
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- name: rel_y
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neurodata_type_inc: VectorData
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dtype: float32
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doc: y coordinate in electrode group
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quantity: '?'
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- name: rel_z
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neurodata_type_inc: VectorData
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dtype: float32
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doc: z coordinate in electrode group
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quantity: '?'
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- name: reference
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neurodata_type_inc: VectorData
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dtype: text
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doc: Description of the reference electrode and/or reference scheme used for this electrode, e.g.,
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"stainless steel skull screw" or "online common average referencing".
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quantity: '?'
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- name: intracellular_ephys
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doc: Metadata related to intracellular electrophysiology.
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quantity: '?'
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datasets:
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- name: filtering
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dtype: text
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doc: '[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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quantity: '?'
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groups:
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- neurodata_type_inc: IntracellularElectrode
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doc: An intracellular electrode.
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quantity: '*'
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- name: sweep_table
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neurodata_type_inc: SweepTable
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doc: '[DEPRECATED] Table used to group different PatchClampSeries. SweepTable
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is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable
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tables. Additional SequentialRecordingsTable, RepetitionsTable and
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ExperimentalConditions tables provide enhanced support for experiment metadata.'
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quantity: '?'
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- name: intracellular_recordings
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neurodata_type_inc: IntracellularRecordingsTable
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doc: A table to group together a stimulus and response from a single electrode
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and a single simultaneous recording. Each row in the table represents a
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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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quantity: '?'
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- name: simultaneous_recordings
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neurodata_type_inc: SimultaneousRecordingsTable
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doc: A table for grouping different intracellular recordings from the IntracellularRecordingsTable
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table together that were recorded simultaneously from different electrodes
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quantity: '?'
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- name: sequential_recordings
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neurodata_type_inc: SequentialRecordingsTable
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doc: A table for grouping different sequential recordings from the SimultaneousRecordingsTable
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table together. This is typically used to group together sequential recordings
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where the a sequence of stimuli of the same type with varying parameters
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have been presented in a sequence.
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quantity: '?'
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- name: repetitions
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neurodata_type_inc: RepetitionsTable
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doc: A table for grouping different sequential intracellular recordings together.
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With each SequentialRecording typically representing a particular type of
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stimulus, the RepetitionsTable table is typically used to group sets of
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stimuli applied in sequence.
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quantity: '?'
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- name: experimental_conditions
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neurodata_type_inc: ExperimentalConditionsTable
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doc: A table for grouping different intracellular recording repetitions together
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that belong to the same experimental experimental_conditions.
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quantity: '?'
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- name: optogenetics
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doc: Metadata describing optogenetic stimuluation.
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quantity: '?'
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groups:
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- neurodata_type_inc: OptogeneticStimulusSite
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doc: An optogenetic stimulation site.
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quantity: '*'
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- name: optophysiology
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doc: Metadata related to optophysiology.
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quantity: '?'
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groups:
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- neurodata_type_inc: ImagingPlane
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doc: An imaging plane.
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quantity: '*'
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- name: intervals
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doc: Experimental intervals, whether that be logically distinct sub-experiments
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having a particular scientific goal, trials (see trials subgroup) during an
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experiment, or epochs (see epochs subgroup) deriving from analysis of data.
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quantity: '?'
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groups:
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- name: epochs
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neurodata_type_inc: TimeIntervals
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doc: Divisions in time marking experimental stages or sub-divisions of a single
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recording session.
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quantity: '?'
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- name: trials
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neurodata_type_inc: TimeIntervals
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doc: Repeated experimental events that have a logical grouping.
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quantity: '?'
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- name: invalid_times
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neurodata_type_inc: TimeIntervals
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doc: Time intervals that should be removed from analysis.
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quantity: '?'
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- neurodata_type_inc: TimeIntervals
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doc: Optional additional table(s) for describing other experimental time intervals.
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quantity: '*'
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- name: units
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neurodata_type_inc: Units
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doc: Data about sorted spike units.
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quantity: '?'
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- neurodata_type_def: LabMetaData
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neurodata_type_inc: NWBContainer
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doc: Lab-specific meta-data.
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- neurodata_type_def: Subject
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neurodata_type_inc: NWBContainer
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doc: Information about the animal or person from which the data was measured.
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datasets:
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- name: age
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dtype: text
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doc: Age of subject. Can be supplied instead of 'date_of_birth'.
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quantity: '?'
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attributes:
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- name: reference
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doc: "Age is with reference to this event. Can be 'birth' or
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'gestational'. If reference is omitted, 'birth' is implied."
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dtype: text
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required: false
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default_value: birth
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- name: date_of_birth
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dtype: isodatetime
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doc: Date of birth of subject. Can be supplied instead of 'age'.
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quantity: '?'
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- name: description
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dtype: text
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doc: Description of subject and where subject came from (e.g., breeder, if
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animal).
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quantity: '?'
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- name: genotype
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dtype: text
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doc: Genetic strain. If absent, assume Wild Type (WT).
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quantity: '?'
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- name: sex
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dtype: text
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doc: Gender of subject.
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quantity: '?'
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- name: species
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dtype: text
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doc: Species of subject.
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quantity: '?'
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- name: strain
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dtype: text
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doc: Strain of subject.
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quantity: '?'
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- name: subject_id
|
|
dtype: text
|
|
doc: ID of animal/person used/participating in experiment (lab convention).
|
|
quantity: '?'
|
|
- name: weight
|
|
dtype: text
|
|
doc: Weight at time of experiment, at time of surgery and at other important
|
|
times.
|
|
quantity: '?'
|
|
|
|
datasets:
|
|
- neurodata_type_def: ScratchData
|
|
neurodata_type_inc: NWBData
|
|
doc: Any one-off datasets
|
|
attributes:
|
|
- name: notes
|
|
doc: 'Any notes the user has about the dataset being stored'
|
|
dtype: text
|