From eebdb15e103acc4895e2cd924530ad2e742d9781 Mon Sep 17 00:00:00 2001 From: Reema Gupta Date: Mon, 27 May 2024 14:01:16 +0200 Subject: [PATCH 1/5] Additional columns for participants.tsv file to cover animal data --- src/schema/objects/columns.yaml | 25 +++++++++++++++++++ src/schema/objects/enums.yaml | 21 ++++++++++++++++ .../rules/tabular_data/modality_agnostic.yaml | 3 +++ 3 files changed, 49 insertions(+) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 5ca387a007..eca2694ab8 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -42,6 +42,31 @@ age: for privacy purposes. type: number unit: year +age_category: + name: age_category + display_name: Age category + description: | + For non-numeric description of the age (e.g. developmental stage) a string can be provided. + We RECOMMEND to use the [UBERON life cycle stage](http://purl.obolibrary.org/obo/UBERON_0000105) to specify it. + type: string +age_type: + name: age_type + display_name: Age type + description: | + Type of age measurement (e.g. `postnatal`, `fetal`, `gestational`). If not specified, `postnatal` is assumed. + type: string + enum: + - $ref: objects.enums.postnatal.value + - $ref: objects.enums.fetal.value + - $ref: objects.enums.gestational.value +birthdate: + name: birthdate + display_name: Birthdate + description: | + Day of birth of the participant. Datetime format and their anonymization are described + in [Units](SPEC_ROOT/common-principles.md#units). + type: string + format: datetime cardiac: name: cardiac display_name: Cardiac measurement diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml index f01d16cdc6..6f430e17e4 100644 --- a/src/schema/objects/enums.yaml +++ b/src/schema/objects/enums.yaml @@ -1405,3 +1405,24 @@ microvascular: display_name: microvascular description: | The origin of a tissue: microvascular +postnatal: + value: postnatal + display_name: postnatal + description: | + This is the actual time that has passed since a subject's birth, + also known as “chronological age”. + If age_type is omitted, age is assumed to be this type. +fetal: + value: fetal + display_name: fetal + description: | + Also known as "embryonic age," this measures the age of a + fetus or embryo from the time of conception. It's typically about two weeks + less than the gestational age. +gestational: + value: gestational + display_name: gestational + description: | + This measures the duration of pregnancy from the first day of the + mother's last menstrual period to the current date. This should be included + for experiments where some subjects have not been born. diff --git a/src/schema/rules/tabular_data/modality_agnostic.yaml b/src/schema/rules/tabular_data/modality_agnostic.yaml index fcaa4b32d4..db2d44c286 100644 --- a/src/schema/rules/tabular_data/modality_agnostic.yaml +++ b/src/schema/rules/tabular_data/modality_agnostic.yaml @@ -15,6 +15,9 @@ Participants: handedness: recommended strain: recommended strain_rrid: recommended + age_category: recommended + age_type: recommended + birthdate: recommended index_columns: [participant_id] additional_columns: allowed From e6f432581402e26b072dc72caff97ec564f1287b Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 27 May 2024 12:07:57 +0000 Subject: [PATCH 2/5] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- src/schema/objects/columns.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index eca2694ab8..5a08086356 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -63,7 +63,7 @@ birthdate: name: birthdate display_name: Birthdate description: | - Day of birth of the participant. Datetime format and their anonymization are described + Day of birth of the participant. Datetime format and their anonymization are described in [Units](SPEC_ROOT/common-principles.md#units). type: string format: datetime From 793a6d8a0a50fca512c77fed74de346e58d1a827 Mon Sep 17 00:00:00 2001 From: Reema Gupta Date: Mon, 27 May 2024 14:15:39 +0200 Subject: [PATCH 3/5] Modified age_type requirement level and rearranged columns --- src/schema/rules/tabular_data/modality_agnostic.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/schema/rules/tabular_data/modality_agnostic.yaml b/src/schema/rules/tabular_data/modality_agnostic.yaml index db2d44c286..cd6579d281 100644 --- a/src/schema/rules/tabular_data/modality_agnostic.yaml +++ b/src/schema/rules/tabular_data/modality_agnostic.yaml @@ -15,9 +15,9 @@ Participants: handedness: recommended strain: recommended strain_rrid: recommended - age_category: recommended - age_type: recommended birthdate: recommended + age_category: recommended + age_type: optional index_columns: [participant_id] additional_columns: allowed From 2f6531bc6331e5bf7f6993aad32e6b4febad66e6 Mon Sep 17 00:00:00 2001 From: Reema Gupta <59512969+ree-gupta@users.noreply.github.com> Date: Wed, 18 Sep 2024 14:20:34 +0200 Subject: [PATCH 4/5] Update src/schema/objects/columns.yaml Co-authored-by: Yaroslav Halchenko --- src/schema/objects/columns.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 5a08086356..beb7b69188 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -46,7 +46,7 @@ age_category: name: age_category display_name: Age category description: | - For non-numeric description of the age (e.g. developmental stage) a string can be provided. + For non-numeric description of the age (e.g. `prime adult stage`) a string can be provided. We RECOMMEND to use the [UBERON life cycle stage](http://purl.obolibrary.org/obo/UBERON_0000105) to specify it. type: string age_type: From bb04dc40a2cac1d8548fc1cc5c713f78c8769bef Mon Sep 17 00:00:00 2001 From: Reema Gupta <59512969+ree-gupta@users.noreply.github.com> Date: Wed, 18 Sep 2024 14:20:47 +0200 Subject: [PATCH 5/5] Update src/schema/objects/enums.yaml Co-authored-by: Yaroslav Halchenko --- src/schema/objects/enums.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml index 6f430e17e4..6dc330be47 100644 --- a/src/schema/objects/enums.yaml +++ b/src/schema/objects/enums.yaml @@ -1410,7 +1410,7 @@ postnatal: display_name: postnatal description: | This is the actual time that has passed since a subject's birth, - also known as “chronological age”. + also known as "chronological age". If age_type is omitted, age is assumed to be this type. fetal: value: fetal