From 13b4c835a53eee6d90bf364fdf4b39e92750c6a7 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Fri, 4 Jun 2021 13:44:46 -0400
Subject: [PATCH 1/5] Add recommended and optional columns to participants.tsv
 in src/03-modality-agnostic-files.md

---
 src/03-modality-agnostic-files.md | 29 +++++++++++++++++++++--------
 1 file changed, 21 insertions(+), 8 deletions(-)

diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index 2da10f03cd..56887f88f3 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -162,16 +162,20 @@ 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, strain, strain_rrid, diagnosis.
 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:
+When different from `homo sapiens`, `participants.tsv` SHOULD include a `species`
+column, and the value MUST be the string of the binomial species name from
+[NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi).
+
+Commonly used *optional* columns in `participants.tsv` files are `age`, `sex`,
+`handedness`, `strain`, `strain_rrid` and `diagnosis`. 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)
 
@@ -197,6 +201,15 @@ for them:
     -   for "ambidextrous", use one of these values: `ambidextrous`, `a`, `A`,
         `AMBIDEXTROUS`, `Ambidextrous`
 
+-   `strain`: string value indicating the strain of the species
+
+-   `strain_rrid`: research resource identifier ([RRID](https://scicrunch.org/resources/Organisms/search))
+    of the strain of the species
+
+-   `diagnosis`: string value describing the diagnosis of the participant.
+    The diagnosis MAY instead be specified in [Sessions files](06-longitudinal-and-multi-site-studies.md#sessions-file)
+    in case it changes over time.
+
 Throughout BIDS you can indicate missing values with `n/a` (for "not
 available").
 
@@ -213,9 +226,9 @@ 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`,
+`strain_rrid` and `diagnosis`, 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.
 

From 8b411375784a16e3ae59dda231ff9c5e69b03550 Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Fri, 16 Jul 2021 10:07:54 -0400
Subject: [PATCH 2/5] Modify species as recommended and add examples

---
 src/03-modality-agnostic-files.md | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index 56887f88f3..6d5dd2de59 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -168,9 +168,11 @@ which MUST consist of `sub-<label>` values identifying one row for each particip
 followed by a list of optional columns describing participants.
 Each participant MUST be described by one and only one row.
 
-When different from `homo sapiens`, `participants.tsv` SHOULD include a `species`
-column, and the value MUST be the string of the binomial species name from
-[NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi).
+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`, `strain_rrid` and `diagnosis`. We RECOMMEND to make use

From 71461445a00705bd8aa5031b361e3c52482d175a Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Fri, 16 Jul 2021 10:13:03 -0400
Subject: [PATCH 3/5] Remove diagnosis column (out of scope for animal
 properties)

---
 src/03-modality-agnostic-files.md | 10 +++-------
 1 file changed, 3 insertions(+), 7 deletions(-)

diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index 6d5dd2de59..097c7e5b25 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -162,7 +162,7 @@ participants.json
 ```
 
 The purpose of this RECOMMENDED file is to describe properties of participants
-such as age, sex, handedness, species, strain, strain_rrid, diagnosis.
+such as age, sex, handedness, species, strain, strain_rrid.
 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.
@@ -175,7 +175,7 @@ For backwards compatibility, if `species` is absent, the participant is assumed
 `homo sapiens`.
 
 Commonly used *optional* columns in `participants.tsv` files are `age`, `sex`,
-`handedness`, `strain`, `strain_rrid` and `diagnosis`. We RECOMMEND to make use
+`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:
 
@@ -208,10 +208,6 @@ following values for them:
 -   `strain_rrid`: research resource identifier ([RRID](https://scicrunch.org/resources/Organisms/search))
     of the strain of the species
 
--   `diagnosis`: string value describing the diagnosis of the participant.
-    The diagnosis MAY instead be specified in [Sessions files](06-longitudinal-and-multi-site-studies.md#sessions-file)
-    in case it changes over time.
-
 Throughout BIDS you can indicate missing values with `n/a` (for "not
 available").
 
@@ -229,7 +225,7 @@ It is RECOMMENDED to accompany each `participants.tsv` file with a sidecar
 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`, `handedness`, `species`, `strain`,
-`strain_rrid` and `diagnosis`, such as `group` in this example, or when a different
+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.

From b451671e84d9f004e36ae6d4e3299f682a721dff Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Fri, 16 Jul 2021 10:59:04 -0400
Subject: [PATCH 4/5] Add example to strain ans strain_rrid

---
 src/03-modality-agnostic-files.md | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index 097c7e5b25..7ba94c372b 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -162,7 +162,7 @@ participants.json
 ```
 
 The purpose of this RECOMMENDED file is to describe properties of participants
-such as age, sex, handedness, species, strain, strain_rrid.
+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.
@@ -203,10 +203,12 @@ following values for them:
     -   for "ambidextrous", use one of these values: `ambidextrous`, `a`, `A`,
         `AMBIDEXTROUS`, `Ambidextrous`
 
--   `strain`: string value indicating the strain of the species
+-   `strain`: for species different from `homo sapiens`, string value indicating
+    the strain of the species, for example: `C57BL/6J`.
 
--   `strain_rrid`: research resource identifier ([RRID](https://scicrunch.org/resources/Organisms/search))
-    of the strain of the species
+-   `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 examples: `RRID:IMSR_JAX:000664`.
 
 Throughout BIDS you can indicate missing values with `n/a` (for "not
 available").

From 4822ed0d30e81f030b468eacc60075135df0d97a Mon Sep 17 00:00:00 2001
From: Marie-Helene Bourget <bourgetmarieh@gmail.com>
Date: Tue, 31 Aug 2021 18:34:18 -0400
Subject: [PATCH 5/5] Fix typo

---
 src/03-modality-agnostic-files.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/03-modality-agnostic-files.md b/src/03-modality-agnostic-files.md
index 6381f074bc..c592f4ca5e 100644
--- a/src/03-modality-agnostic-files.md
+++ b/src/03-modality-agnostic-files.md
@@ -212,7 +212,7 @@ following values for them:
 
 -   `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 examples: `RRID:IMSR_JAX:000664`.
+    for example: `RRID:IMSR_JAX:000664`.
 
 Throughout BIDS you can indicate missing values with `n/a` (for "not
 available").