Skip to content

Commit

Permalink
[ENH] BEP031 - New columns to participants.tsv file (#816)
Browse files Browse the repository at this point in the history
* Add recommended and optional columns to participants.tsv in
src/03-modality-agnostic-files.md

* Modify species as recommended and add examples

* Remove diagnosis column (out of scope for animal properties)

* Add example to strain ans strain_rrid

* Fix typo
  • Loading branch information
mariehbourget authored Oct 13, 2021
1 parent d323a9f commit aae6274
Showing 1 changed file with 21 additions and 8 deletions.
29 changes: 21 additions & 8 deletions src/03-modality-agnostic-files.md
Original file line number Diff line number Diff line change
Expand Up @@ -166,16 +166,22 @@ participants.json
```

The purpose of this RECOMMENDED file is to describe properties of participants
such as age, sex, handedness.
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 `participant.tsv` files are `age`, `sex`,
and `handedness`. 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:
The RECOMMENDED `species` column SHOULD be a binomial species name from the
[NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi)
(for examples `homo sapiens`, `mus musculus`, `rattus norvegicus`).
For backwards compatibility, if `species` is absent, the participant is assumed to be
`homo sapiens`.

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

- `age`: numeric value in years (float or integer value)

Expand All @@ -201,6 +207,13 @@ for them:
- for "ambidextrous", use one of these values: `ambidextrous`, `a`, `A`,
`AMBIDEXTROUS`, `Ambidextrous`

- `strain`: for species different from `homo sapiens`, string value indicating
the strain of the species, for example: `C57BL/6J`.

- `strain_rrid`: for species different from `homo sapiens`, research resource identifier
([RRID](https://scicrunch.org/resources/Organisms/search)) of the strain of the species,
for example: `RRID:IMSR_JAX:000664`.

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

Expand All @@ -217,9 +230,9 @@ 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](02-common-principles.md#tabular-files)).
Such sidecar files are needed to interpret the data, especially so when
optional columns are defined beyond `age`, `sex`, and `handedness`, such as
`group` in this example, or when a different age unit is needed
(for example, gestational weeks).
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.

Expand Down

0 comments on commit aae6274

Please sign in to comment.