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enh tables in modality agnostic files
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‎src/02-common-principles.md‎

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@@ -426,13 +426,13 @@ Note that if a field name included in the data dictionary matches a column name
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then that field MUST contain a description of the corresponding column,
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using an object containing the following fields:
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| Field name | Requirement level | Data type | Definition |
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| ----------- | ----------------- | ------------------------- | --------------------------------------------------------------------------------------------------------------- |
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| LongName | OPTIONAL | [string][] | Long (unabbreviated) name of the column. |
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| Description | RECOMMENDED | [string][] | Description of the column. |
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| Levels | RECOMMENDED | [object][] of [strings][] | For categorical variables: An object of possible values (keys) and their descriptions (values). |
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| Units | RECOMMENDED | [string][] | Measurement units. SI units in CMIXF formatting are RECOMMENDED (see [Units](./02-common-principles.md#units)). |
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| TermURL | RECOMMENDED | [string][] | URL pointing to a formal definition of this type of data in an ontology available on the web. |
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| **Key name** | **Requirement level** | **Data type** | **Description** |
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| ------------ | --------------------- | ------------------------- | --------------------------------------------------------------------------------------------------------------- |
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| LongName | OPTIONAL | [string][] | Long (unabbreviated) name of the column. |
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| Description | RECOMMENDED | [string][] | Description of the column. |
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| Levels | RECOMMENDED | [object][] of [strings][] | For categorical variables: An object of possible values (keys) and their descriptions (values). |
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| Units | RECOMMENDED | [string][] | Measurement units. SI units in CMIXF formatting are RECOMMENDED (see [Units](./02-common-principles.md#units)). |
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| TermURL | RECOMMENDED | [string][] | URL pointing to a formal definition of this type of data in an ontology available on the web. |
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Please note that while both `Units` and `Levels` are RECOMMENDED, typically only one
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of these two fields would be specified for describing a single TSV file column.

‎src/03-modality-agnostic-files.md‎

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@@ -14,20 +14,20 @@ Templates:
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The file `dataset_description.json` is a JSON file describing the dataset.
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Every dataset MUST include this file with the following fields:
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| **Field name** | **Definition** |
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| ------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
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| Name | REQUIRED. Name of the dataset. |
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| BIDSVersion | REQUIRED. The version of the BIDS standard that was used. |
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| HEDVersion | RECOMMENDED if HED tags are used. The version of the HED schema used to validate HED tags for study. |
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| DatasetType | RECOMMENDED. The interpretation of the dataset. MUST be one of `"raw"` or `"derivative"`. For backwards compatibility, the default value is `"raw"`. |
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| License | RECOMMENDED. The license for the dataset. The use of license name abbreviations is RECOMMENDED for specifying a license (see [Appendix II](./99-appendices/02-licenses.md)). The corresponding full license text MAY be specified in an additional `LICENSE` file. |
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| Authors | OPTIONAL. List of individuals who contributed to the creation/curation of the dataset. |
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| Acknowledgements | OPTIONAL. Text acknowledging contributions of individuals or institutions beyond those listed in Authors or Funding. |
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| HowToAcknowledge | OPTIONAL. 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. |
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| Funding | OPTIONAL. List of sources of funding (grant numbers). |
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| EthicsApprovals | OPTIONAL. List of ethics committee approvals of the research protocols and/or protocol identifiers. |
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| ReferencesAndLinks | OPTIONAL. List of references to publication that contain information on the dataset, or links. |
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| DatasetDOI | OPTIONAL. The Document Object Identifier of the dataset (not the corresponding paper). |
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| **Key name** | **Requirement level** | **Data type** | **Definition** |
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| ------------------ | --------------------- | ------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| Name | REQUIRED | [string][] | Name of the dataset. |
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| BIDSVersion | REQUIRED | [string][] | The version of the BIDS standard that was used. |
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| HEDVersion | RECOMMENDED | [string][] | If HED tags are used: The version of the HED schema used to validate HED tags for study. |
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| DatasetType | RECOMMENDED | [string][] | The interpretation of the dataset. MUST be one of `"raw"` or `"derivative"`. For backwards compatibility, the default value is `"raw"`. |
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| License | RECOMMENDED | [string][] | The license for the dataset. The use of license name abbreviations is RECOMMENDED for specifying a license (see [Appendix II](./99-appendices/02-licenses.md)). The corresponding full license text MAY be specified in an additional `LICENSE` file. |
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| Authors | OPTIONAL | [array][] of [strings][] | List of individuals who contributed to the creation/curation of the dataset. |
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| Acknowledgements | OPTIONAL | [string][] | Text acknowledging contributions of individuals or institutions beyond those listed in Authors or Funding. |
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| 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. |
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| Funding | OPTIONAL | [array][] of [strings][] | List of sources of funding (grant numbers). |
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| EthicsApprovals | OPTIONAL | [array][] of [strings][] | List of ethics committee approvals of the research protocols and/or protocol identifiers. |
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| ReferencesAndLinks | OPTIONAL | [array][] of [strings][] | List of references to publication that contain information on the dataset, or links. |
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| DatasetDOI | OPTIONAL | [string][] | The Document Object Identifier of the dataset (not the corresponding paper). |
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Example:
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@@ -69,21 +69,21 @@ In addition to the keys for raw BIDS datasets,
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derived BIDS datasets include the following REQUIRED and RECOMMENDED
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`dataset_description.json` keys:
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| **Key name** | **Description** |
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| -------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| GeneratedBy | REQUIRED. List of [objects][] with at least one element. |
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| SourceDatasets | RECOMMENDED. A list of [objects][] specifying the locations and relevant attributes of all source datasets. Valid fields in each object include `URL`, `DOI`, and `Version`. |
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| **Key name** | **Requirement level** | **Data type** | **Definition** |
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| -------------- | --------------------- | ------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| GeneratedBy | REQUIRED | [array][] of [objects][] | Used to specify provenance of the derived dataset. See table below for contents of each object. |
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| 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`, and `Version` with [string][] values. |
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Each object in the `GeneratedBy` list includes the following REQUIRED, RECOMMENDED
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and OPTIONAL keys:
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| **Key name** | **Description** |
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| ------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
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| Name | REQUIRED. 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. |
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| Version | RECOMMENDED. Version of the pipeline. |
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| Description | OPTIONAL. Plain-text description of the pipeline or process that generated the outputs. RECOMMENDED if `Name` is `"Manual"`. |
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| CodeURL | OPTIONAL. URL where the code used to generate the derivatives may be found. |
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| Container | OPTIONAL. [Object][] specifying the location and relevant attributes of software container image used to produce the derivative. Valid fields in this object include `Type`, `Tag` and `URI`. |
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| **Key name** | **Requirement level** | **Data type** | **Definition** |
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| ------------ | --------------------- | ------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
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| 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. |
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| Version | RECOMMENDED | [string][] | Version of the pipeline. |
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| Description | OPTIONAL | [string][] | Plain-text description of the pipeline or process that generated the outputs. RECOMMENDED if `Name` is `"Manual"`. |
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| CodeURL | OPTIONAL | [string][] | URL where the code used to generate the derivatives may be found. |
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| Container | OPTIONAL | [object][] | Used to specify the location and relevant attributes of software container image used to produce the derivative. Valid keys in this object include `Type`, `Tag` and `URI` with [string][] values. |
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Example:
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[objects]: https://www.json.org/json-en.html
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[object]: https://www.json.org/json-en.html
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[string]: https://www.w3schools.com/js/js_json_syntax.asp
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[strings]: https://www.w3schools.com/js/js_json_syntax.asp
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[array]: https://www.w3schools.com/js/js_json_arrays.asp

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