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Add descriptions.tsv to the schema #1707

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31 changes: 20 additions & 11 deletions src/derivatives/common-data-types.md
Original file line number Diff line number Diff line change
Expand Up @@ -256,24 +256,33 @@ static volume, a `RepetitionTime` property would no longer be relevant).

## descriptions.tsv

Template:

```Text
[sub-<label>/]
[ses-<label>/]
[sub-<label>_][ses-<label>_]descriptions.tsv
[sub-<label>_][ses-<label>_]descriptions.json
```

Optional: Yes

To keep a record of processing steps applied to the data, a `descriptions.tsv` file MAY be used.
The `descriptions.tsv` file MUST contain at least the following two columns:
The `descriptions.tsv` file consists of one row for each unique `desc-<label>`
entity used in the dataset and a set of REQUIRED and OPTIONAL columns:

- `desc_id`
- `description`
<!-- This block generates a columns table.
The definitions of these fields can be found in
src/schema/rules/tabular_data/*.yaml
and a guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_columns_table("derivatives.common_derivatives.Descriptions") }}

This file MAY be located at the root of the derivative dataset,
or at the subject or session level
([Inheritance Principle](../common-principles.md#the-inheritance-principle)).

The `desc_id` column contains the labels used with the [`desc entity`](../appendices/entities.md#desc),
within the particular nesting that the `descriptions.tsv` file is placed.
For example, if the `descriptions.tsv` file is placed at the root of the derivative dataset,
its `desc_id` column SHOULD contain all labels of the [`desc entity`](../appendices/entities.md#desc)
used across the entire derivative dataset.

The `description` column contains human-readable descriptions of the processing steps.

The use of `descriptions.tsv` files together with the [`desc entity`](../appendices/entities.md#desc)
are helpful to document how files are generated, even if their use may not be sufficient
to provide full computational reproducibility.
Expand Down
21 changes: 21 additions & 0 deletions src/schema/objects/columns.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -110,6 +110,21 @@ derived_from:
for example a slice of tissue (`sample-02`) derived from a block of tissue (`sample-01`).
type: string
pattern: ^sample-[0-9a-zA-Z]+$
desc_id:
name: desc_id
display_name: Description Label
description: |
A `desc-<label>` entity present in the derivatives dataset.

The `desc_id` column contains the labels used with the
[`desc` entity](SPEC_ROOT/appendices/entities.md#desc),
within the particular nesting that the `descriptions.tsv` file is placed.

For example, if the `descriptions.tsv` file is placed at the root of the derivative dataset,
its `desc_id` column SHOULD contain all labels of the `desc` entity)
used across the entire derivative dataset.
type: string
pattern: ^desc-[0-9a-zA-Z]+$
description:
name: description
display_name: Description
Expand All @@ -122,6 +137,12 @@ description__optode:
description: |
Free-form text description of the optode, or other information of interest.
type: string
description__entities:
name: description
display_name: Description
description: |
Free-form text description of the entity's label (defined in `<entity>_id` column).
type: string
dimension:
name: dimension
display_name: Dimension
Expand Down
12 changes: 12 additions & 0 deletions src/schema/objects/suffixes.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -549,6 +549,18 @@ defacemask:
description: |
A binary mask that was used to remove facial features from an anatomical MRI
image.
descriptions:
value: descriptions
display_name: Description Entity Definitions
description: |
A TSV file describing labels found for the `desc` entity in a Derivatives dataset.

This file MAY be located at the root of the derivative dataset,
or at the subject or session level.

The use of `descriptions.tsv` files together with the desc entity are helpful to
document how files are generated,
even if their use may not be sufficient to provide full computational reproducibility.
dseg:
value: dseg
display_name: Discrete Segmentation
Expand Down
11 changes: 11 additions & 0 deletions src/schema/rules/files/deriv/tables.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
---
descriptions:
level: optional
suffixes:
- descriptions
extensions:
- .tsv
- .json
entities:
subject: optional
session: optional
Original file line number Diff line number Diff line change
Expand Up @@ -10,3 +10,19 @@ SegmentationLookup:
color: optional
mapping: optional
index_columns: [index]

Descriptions:
selectors:
- suffix == "descriptions"
- extension == ".tsv"
initial_columns:
- desc_id
- description__entities
columns:
desc_id: required
description__entities:
level: required
description_addendum: |
The corresponding label column is `desc_id`.
index_columns: [desc_id]
additional_columns: allowed