Modality agnostic files

Dataset description

Templates:

dataset_description.json
README[.md|.rst|.txt]
CITATION.cff
CHANGES
LICENSE

`dataset_description.json`

The file dataset_description.json is a JSON file describing the dataset.

Every dataset MUST include this file with the following fields:

Key name	Requirement Level	Data type	Description
Name	REQUIRED	string	Name of the dataset.
BIDSVersion	REQUIRED	string	The version of the BIDS standard that was used.
HEDVersion	RECOMMENDED	string or array of strings	If HED tags are used: The version of the HED schema used to validate HED tags for study. May include a single schema or a base schema and one or more library schema.
DatasetLinks	REQUIRED if BIDS URIs are used	object of strings	Used to map a given `<dataset-name>` from a BIDS URI of the form `bids:<dataset-name>:path/within/dataset` to a local or remote location. The `<dataset-name>`: `""` (an empty string) is a reserved keyword that MUST NOT be a key in `DatasetLinks` (example: `bids::path/within/dataset`).
DatasetType	RECOMMENDED	string	The interpretation of the dataset. For backwards compatibility, the default value is `"raw"`. Must be one of: `"raw"`, `"derivative"`.
License	RECOMMENDED	string	The license for the dataset. The use of license name abbreviations is RECOMMENDED for specifying a license (see Licenses). The corresponding full license text MAY be specified in an additional `LICENSE` file.
Authors	RECOMMENDED	array of strings	List of individuals who contributed to the creation/curation of the dataset.
Acknowledgements	OPTIONAL	string	Text acknowledging contributions of individuals or institutions beyond those listed in Authors or Funding.
HowToAcknowledge	OPTIONAL	string	Text containing instructions on how researchers using this dataset should acknowledge the original authors. This field can also be used to define a publication that should be cited in publications that use the dataset.
Funding	OPTIONAL	array of strings	List of sources of funding (grant numbers).
EthicsApprovals	OPTIONAL	array of strings	List of ethics committee approvals of the research protocols and/or protocol identifiers.
ReferencesAndLinks	OPTIONAL	array of strings	List of references to publications that contain information on the dataset. A reference may be textual or a URI.
DatasetDOI	OPTIONAL	string	The Digital Object Identifier of the dataset (not the corresponding paper). DOIs SHOULD be expressed as a valid URI; bare DOIs such as `10.0.2.3/dfjj.10` are DEPRECATED.
GeneratedBy	RECOMMENDED	array of objects	Used to specify provenance of the dataset.
SourceDatasets	RECOMMENDED	array of objects	Used to specify the locations and relevant attributes of all source datasets. Valid keys in each object include `"URL"`, `"DOI"` (see URI), and `"Version"` with string values.

Each object in the GeneratedBy array includes the following REQUIRED, RECOMMENDED and OPTIONAL keys:

Key name	Requirement Level	Data type	Description
Name	REQUIRED	string	Name of the pipeline or process that generated the outputs. Use `"Manual"` to indicate the derivatives were generated by hand, or adjusted manually after an initial run of an automated pipeline.
Version	RECOMMENDED	string	Version of the pipeline
Description	OPTIONAL	string	Plain-text description of the pipeline or process that generated the outputs. RECOMMENDED if `Name` is `"Manual"`.
CodeURL	OPTIONAL	string	URL where the code used to generate the dataset may be found.
Container	OPTIONAL	object	Used to specify the location and relevant attributes of software container image used to produce the dataset. Valid keys in this object include `Type`, `Tag` and `URI` with string values.

Example:

{
  "Name": "The mother of all experiments",
  "BIDSVersion": "1.6.0",
  "DatasetType": "raw",
  "License": "CC0",
  "Authors": [
    "Paul Broca",
    "Carl Wernicke"
  ],
  "Acknowledgements": "Special thanks to Korbinian Brodmann for help in formatting this dataset in BIDS. We thank Alan Lloyd Hodgkin and Andrew Huxley for helpful comments and discussions about the experiment and manuscript; Hermann Ludwig Helmholtz for administrative support; and Claudius Galenus for providing data for the medial-to-lateral index analysis.",
  "HowToAcknowledge": "Please cite this paper: https://www.ncbi.nlm.nih.gov/pubmed/001012092119281",
  "Funding": [
    "National Institute of Neuroscience Grant F378236MFH1",
    "National Institute of Neuroscience Grant 5RMZ0023106"
  ],
  "EthicsApprovals": [
    "Army Human Research Protections Office (Protocol ARL-20098-10051, ARL 12-040, and ARL 12-041)"
  ],
  "ReferencesAndLinks": [
    "https://www.ncbi.nlm.nih.gov/pubmed/001012092119281",
    "Alzheimer A., & Kraepelin, E. (2015). Neural correlates of presenile dementia in humans. Journal of Neuroscientific Data, 2, 234001. doi:1920.8/jndata.2015.7"
  ],
  "DatasetDOI": "doi:10.0.2.3/dfjj.10",
  "HEDVersion": "8.0.0",
  "GeneratedBy": [
    {
      "Name": "reproin",
      "Version": "0.6.0",
      "Container": {
        "Type": "docker",
        "Tag": "repronim/reproin:0.6.0"
      }
    }
  ],
  "SourceDatasets": [
    {
      "URL": "s3://dicoms/studies/correlates",
      "Version": "April 11 2011"
    }
  ]
}

Derived dataset and pipeline description

As for any BIDS dataset, a dataset_description.json file MUST be found at the top level of every derived dataset: <dataset>/derivatives/<pipeline_name>/dataset_description.json.

In contrast to raw BIDS datasets, derived BIDS datasets MUST include a GeneratedBy key:

Key name	Requirement Level	Data type	Description
GeneratedBy	REQUIRED	array of objects	Used to specify provenance of the dataset.

If a derived dataset is stored as a subdirectory of the raw dataset, then the Name field of the first GeneratedBy object MUST be a substring of the derived dataset directory name. That is, in a directory <dataset>/derivatives/<pipeline>[-<variant>]/, the first GeneratedBy object should have a Name of <pipeline>.

Example:

{
  "Name": "FMRIPREP Outputs",
  "BIDSVersion": "1.6.0",
  "DatasetType": "derivative",
  "GeneratedBy": [
    {
      "Name": "fmriprep",
      "Version": "1.4.1",
      "Container": {
        "Type": "docker",
        "Tag": "poldracklab/fmriprep:1.4.1"
        }
    },
    {
      "Name": "Manual",
      "Description": "Re-added RepetitionTime metadata to bold.json files"
    }
  ],
  "SourceDatasets": [
    {
      "DOI": "doi:10.18112/openneuro.ds000114.v1.0.1",
      "URL": "https://openneuro.org/datasets/ds000114/versions/1.0.1",
      "Version": "1.0.1"
    }
  ]
}

`README`

A REQUIRED text file, README, SHOULD describe the dataset in more detail. The README file MUST be either in ASCII or UTF-8 encoding and MAY have one of the extensions: .md (Markdown), .rst (reStructuredText), or .txt. A BIDS dataset MUST NOT contain more than one README file (with or without extension) at its root directory. BIDS does not make any recommendations with regards to the Markdown flavor and does not validate the syntax of Markdown and reStructuredText. The README file SHOULD be structured such that its contents can be easily understood even if the used format is not rendered. A guideline for creating a good README file can be found in the bids-starter-kit.

`CITATION.cff`

A description of the citation information for the dataset, following the Citation File Format specification. This file permits more detailed and structured descriptions than dataset_description.json.

For most redundant fields between CITATION.cff and dataset_description.json, the CITATION.cff SHOULD take precedence. To avoid inconsistency, metadata present in CITATION.cff SHOULD NOT be be included in dataset_description.json, with the exception of Name and DatasetDOI, to ensure that CITATION.cff-unaware tools can generate references to the dataset. In particular, if CITATION.cff is present, the "Authors" field of dataset_description.json MUST be omitted, and the "HowToAcknowledge", "License" and "ReferencesAndLinks" SHOULD be omitted in favor of the CITATION.cff fields message/preferred-citation, license and references.

`CHANGES`

Version history of the dataset (describing changes, updates and corrections) MAY be provided in the form of a CHANGES text file. This file MUST follow the CPAN Changelog convention. The CHANGES file MUST be either in ASCII or UTF-8 encoding.

Example:

1.0.1 2015-08-27
  - Fixed slice timing information.

1.0.0 2015-08-17
  - Initial release.

`LICENSE`

A LICENSE file MAY be provided in addition to the short specification of the used license in the dataset_description.json "License" field. The "License" field and LICENSE file MUST correspond. The LICENSE file MUST be either in ASCII or UTF-8 encoding.

Participants file

Template:

participants.tsv
participants.json

The purpose of this RECOMMENDED file is to describe properties of participants such as age, sex, handedness, species and strain. If this file exists, it MUST contain the column participant_id, which MUST consist of sub-<label> values identifying one row for each participant, followed by a list of optional columns describing participants. Each participant MUST be described by one and only one row.

Commonly used optional columns in participants.tsv files are age, sex, handedness, strain, and strain_rrid.

The RECOMMENDED species column SHOULD be a binomial species name from the NCBI Taxonomy (for examples homo sapiens, mus musculus, rattus norvegicus). For backwards compatibility, if species is absent, the participant is assumed to be homo sapiens.

We RECOMMEND to make use of these columns, and in case that you do use them, we RECOMMEND to use the following values for them:

Column name	Requirement Level	Data type	Description
participant_id	REQUIRED	string	A participant identifier of the form `sub-<label>`, matching a participant entity found in the dataset. There MUST be exactly one row for each participant. Values in `participant_id` MUST be unique. This column must appear first in the file.
species	RECOMMENDED	string	The `species` column SHOULD be a binomial species name from the NCBI Taxonomy (for example, `homo sapiens`, `mus musculus`, `rattus norvegicus`). For backwards compatibility, if `species` is absent, the participant is assumed to be `homo sapiens`. This column may appear anywhere in the file.
age	RECOMMENDED	number	Numeric value in years (float or integer value). It is RECOMMENDED to tag participant ages that are 89 or higher as 89+, for privacy purposes. This column may appear anywhere in the file.
sex	RECOMMENDED	string	String value indicating phenotypical sex, one of "male", "female", "other". For "male", use one of these values: `male`, `m`, `M`, `MALE`, `Male`. For "female", use one of these values: `female`, `f`, `F`, `FEMALE`, `Female`. For "other", use one of these values: `other`, `o`, `O`, `OTHER`, `Other`. This column may appear anywhere in the file. For a list of valid values for this column, see the associated glossary entry.
handedness	RECOMMENDED	string	String value indicating one of "left", "right", "ambidextrous". For "left", use one of these values: `left`, `l`, `L`, `LEFT`, `Left`. For "right", use one of these values: `right`, `r`, `R`, `RIGHT`, `Right`. For "ambidextrous", use one of these values: `ambidextrous`, `a`, `A`, `AMBIDEXTROUS`, `Ambidextrous`. This column may appear anywhere in the file. For a list of valid values for this column, see the associated glossary entry.
strain	RECOMMENDED	string	For species different from `homo sapiens`, string value indicating the strain of the species, for example: `C57BL/6J`. This column may appear anywhere in the file.
strain_rrid	RECOMMENDED	string	For species different from `homo sapiens`, research resource identifier (RRID) of the strain of the species, for example: `RRID:IMSR_JAX:000664`. This column may appear anywhere in the file.
Additional Columns	OPTIONAL	`n/a`	Additional columns are allowed.

Throughout BIDS you can indicate missing values with n/a (for "not available").

participants.tsv example:

participant_id age sex handedness group
sub-01 34 M right read
sub-02 12 F right write
sub-03 33 F n/a read

It is RECOMMENDED to accompany each participants.tsv file with a sidecar participants.json file to describe the TSV column names and properties of their values (see also the section on tabular files). Such sidecar files are needed to interpret the data, especially so when optional columns are defined beyond age, sex, handedness, species, strain, and strain_rrid, such as group in this example, or when a different age unit is needed (for example, gestational weeks). If no units is provided for age, it will be assumed to be in years relative to date of birth.

participants.json example:

{
    "age": {
        "Description": "age of the participant",
        "Units": "year"
    },
    "sex": {
        "Description": "sex of the participant as reported by the participant",
        "Levels": {
            "M": "male",
            "F": "female"
        }
    },
    "handedness": {
        "Description": "handedness of the participant as reported by the participant",
        "Levels": {
            "left": "left",
            "right": "right"
        }
    },
    "group": {
        "Description": "experimental group the participant belonged to",
        "Levels": {
            "read": "participants who read an inspirational text before the experiment",
            "write": "participants who wrote an inspirational text before the experiment"
        }
    }
}

Samples file

Template:

samples.tsv
samples.json

The purpose of this file is to describe properties of samples, indicated by the sample entity. This file is REQUIRED if sample-<label> is present in any filename within the dataset. Each sample MUST be described by one and only one row.

Column name	Requirement Level	Data type	Description
sample_id	REQUIRED	string	A sample identifier of the form `sample-<label>`, matching a sample entity found in the dataset. The combination of `sample_id` and `participant_id` MUST be unique.
participant_id	REQUIRED	string	A participant identifier of the form `sub-<label>`, matching a participant entity found in the dataset. The combination of `sample_id` and `participant_id` MUST be unique.
sample_type	REQUIRED	string	Biosample type defined by ENCODE Biosample Type. Must be one of: `"cell line"`, `"in vitro differentiated cells"`, `"primary cell"`, `"cell-free sample"`, `"cloning host"`, `"tissue"`, `"whole organisms"`, `"organoid"`, `"technical sample"`.
pathology	RECOMMENDED	string	String value describing the pathology of the sample or type of control. When different from `healthy`, pathology SHOULD be specified. The pathology may be specified in either `samples.tsv` or `sessions.tsv`, depending on whether the pathology changes over time.
derived_from	RECOMMENDED	string	`sample-<label>` entity from which a sample is derived, for example a slice of tissue (`sample-02`) derived from a block of tissue (`sample-01`).
Additional Columns	OPTIONAL	`n/a`	Additional columns are allowed.

samples.tsv example:

sample_id participant_id sample_type derived_from
sample-01 sub-01 tissue n/a
sample-02 sub-01 tissue sample-01
sample-03 sub-01 tissue sample-01
sample-04 sub-02 tissue n/a
sample-05 sub-02 tissue n/a

It is RECOMMENDED to accompany each samples.tsv file with a sidecar samples.json file to describe the TSV column names and properties of their values (see also the section on tabular files).

samples.json example:

{
    "sample_type": {
        "Description": "type of sample from ENCODE Biosample Type (https://www.encodeproject.org/profiles/biosample_type)",
    },
    "derived_from": {
        "Description": "sample_id from which the sample is derived"
    }
}

Phenotypic and assessment data

Template:

phenotype/
    <measurement_tool_name>.tsv
    <measurement_tool_name>.json

Optional: Yes

If the dataset includes multiple sets of participant level measurements (for example responses from multiple questionnaires) they can be split into individual files separate from participants.tsv.

Each of the measurement files MUST be kept in a /phenotype directory placed at the root of the BIDS dataset and MUST end with the .tsv extension. Filenames SHOULD be chosen to reflect the contents of the file. For example, the "Adult ADHD Clinical Diagnostic Scale" could be saved in a file called /phenotype/acds_adult.tsv.

The files can include an arbitrary set of columns, but one of them MUST be participant_id and the entries of that column MUST correspond to the subjects in the BIDS dataset and participants.tsv file.

As with all other tabular data, the additional phenotypic information files MAY be accompanied by a JSON file describing the columns in detail (see Tabular files).

In addition to the column descriptions, the JSON file MAY contain the following fields:

Key name	Requirement Level	Data type	Description
MeasurementToolMetadata	OPTIONAL	object	A description of the measurement tool as a whole. Contains two fields: `"Description"` and `"TermURL"`. `"Description"` is a free text description of the measurement tool. `"TermURL"` is a URL to an entity in an ontology corresponding to this tool.
Derivative	OPTIONAL	boolean	Indicates that values in the corresponding column are transformations of values from other columns (for example a summary score based on a subset of items in a questionnaire). Must be one of: `"true"`, `"false"`.

As an example, consider the contents of a file called phenotype/acds_adult.json:

{
  "MeasurementToolMetadata": {
    "Description": "Adult ADHD Clinical Diagnostic Scale V1.2",
    "TermURL": "https://www.cognitiveatlas.org/task/id/trm_5586ff878155d"
  },
  "adhd_b": {
    "Description": "B. CHILDHOOD ONSET OF ADHD (PRIOR TO AGE 7)",
    "Levels": {
      "1": "YES",
      "2": "NO"
    }
  },
  "adhd_c_dx": {
    "Description": "As child met A, B, C, D, E and F diagnostic criteria",
    "Levels": {
      "1": "YES",
      "2": "NO"
    }
  }
}

Please note that in this example MeasurementToolMetadata includes information about the questionnaire and adhd_b and adhd_c_dx correspond to individual columns.

In addition to the keys available to describe columns in all tabular files (LongName, Description, Levels, Units, and TermURL) the participants.json file as well as phenotypic files can also include column descriptions with a Derivative field that, when set to true, indicates that values in the corresponding column is a transformation of values from other columns (for example a summary score based on a subset of items in a questionnaire).

Scans file

Template:

sub-<label>/
    [ses-<label>/]
        sub-<label>[_ses-<label>]_scans.tsv
        sub-<label>[_ses-<label>]_scans.json

Optional: Yes

The purpose of this file is to describe timing and other properties of each recording file within one session. In general, each of these files SHOULD be described by exactly one row.

For file formats that are based on several files of different extensions, or a directory of files with different extensions (multi-file file formats), only that file SHOULD be listed that would also be passed to analysis software for reading the data. For example for BrainVision data (.vhdr, .vmrk, .eeg), only the .vhdr SHOULD be listed; for EEGLAB data (.set, .fdt), only the .set file SHOULD be listed; and for CTF data (.ds), the whole .ds directory SHOULD be listed, and not the individual files in that directory.

Some neural recordings consist of multiple parts, that span several files, but that share the same extension. For example in entity-linked file collections, commonly used for qMRI, where recordings may be linked through entities such as echo and part (using .nii or .nii.gz extensions). For another example consider the case of large files in .fif format that are linked through the split entity (see Split files). Such recordings MUST be documented with one row per file (unlike the case of multi-file file formats described above).

Column name	Requirement Level	Data type	Description
filename	REQUIRED	string	Relative paths to files. There MUST be exactly one row for each file. Values in `filename` MUST be unique. This column must appear first in the file.
acq_time	OPTIONAL	string	Acquisition time refers to when the first data point in each run was acquired. Furthermore, if this header is provided, the acquisition times of all files from the same recording MUST be identical. Datetime format and their anonymization are described in Units. This column may appear anywhere in the file.
Additional Columns	OPTIONAL	`n/a`	Additional columns are allowed.

Additional fields can include external behavioral measures relevant to the scan. For example vigilance questionnaire score administered after a resting state scan. All such included additional fields SHOULD be documented in an accompanying _scans.json file that describes these fields in detail (see Tabular files).

Example _scans.tsv:

filename    acq_time
func/sub-control01_task-nback_bold.nii.gz   1877-06-15T13:45:30
func/sub-control01_task-motor_bold.nii.gz   1877-06-15T13:55:33
meg/sub-control01_task-rest_split-01_meg.nii.gz 1877-06-15T12:15:27
meg/sub-control01_task-rest_split-02_meg.nii.gz 1877-06-15T12:15:27

Sessions file

Template:

sub-<label>/
    sub-<label>_sessions.tsv

Optional: Yes

In case of multiple sessions there is an option of adding additional sessions.tsv files describing variables changing between sessions. In such case one file per participant SHOULD be added. These files MUST include a session_id column and describe each session by one and only one row. Column names in sessions.tsv files MUST be different from group level participant key column names in the participants.tsv file.

Column name	Requirement Level	Data type	Description
session_id	REQUIRED	string	A session identifier of the form `ses-<label>`, matching a session found in the dataset. There MUST be exactly one row for each session. Values in `session_id` MUST be unique. This column must appear first in the file.
acq_time	OPTIONAL	string	Acquisition time refers to when the first data point of the first run was acquired. Datetime format and their anonymization are described in Units. This column may appear anywhere in the file.
pathology	RECOMMENDED	string	String value describing the pathology of the sample or type of control. When different from `healthy`, pathology SHOULD be specified. The pathology may be specified in either `samples.tsv` or `sessions.tsv`, depending on whether the pathology changes over time. This column may appear anywhere in the file.
Additional Columns	OPTIONAL	`n/a`	Additional columns are allowed.

_sessions.tsv example:

session_id  acq_time    systolic_blood_pressure
ses-predrug 2009-06-15T13:45:30 120
ses-postdrug    2009-06-16T13:45:30 100
ses-followup    2009-06-17T13:45:30 110

Code

Template: code/*

Source code of scripts that were used to prepare the dataset MAY be stored here. Examples include anonymization or defacing of the data, or the conversion from the format of the source data to the BIDS format (see source vs. raw vs. derived data). Extra care should be taken to avoid including original IDs or any identifiable information with the source code. There are no limitations or recommendations on the language and/or code organization of these scripts at the moment.