From eebdb15e103acc4895e2cd924530ad2e742d9781 Mon Sep 17 00:00:00 2001 From: Reema Gupta Date: Mon, 27 May 2024 14:01:16 +0200 Subject: [PATCH 01/46] 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 02/46] [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 03/46] 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 04/46] 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 05/46] 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 From 8612a980f10a205a2cfb4fb0c9d7a8c7170e04ab Mon Sep 17 00:00:00 2001 From: Reema Gupta <59512969+ree-gupta@users.noreply.github.com> Date: Mon, 17 Mar 2025 07:39:50 +0100 Subject: [PATCH 06/46] Applied changes to column definitions and their requirement levels Co-authored-by: Lyuba Zehl --- src/schema/objects/columns.yaml | 22 +++++++++---------- .../rules/tabular_data/modality_agnostic.yaml | 6 ++--- 2 files changed, 13 insertions(+), 15 deletions(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index beb7b69188..4665d3fdbc 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -42,18 +42,17 @@ age: for privacy purposes. type: number unit: year -age_category: - name: age_category - display_name: Age category +life_cycle_stage: + name: life cycle stage + display_name: life cycle stage description: | - 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. + A non-numeric life cycle stage (e.g., 'adult stage'), inspired by the [UBERON life cycle stage](http://purl.obolibrary.org/obo/UBERON_0000105). type: string -age_type: - name: age_type - display_name: Age type +age_reference: + name: age reference + display_name: age reference description: | - Type of age measurement (e.g. `postnatal`, `fetal`, `gestational`). If not specified, `postnatal` is assumed. + Non-numeric life cycle point of an organism that serves as reference for the numeric age information. type: string enum: - $ref: objects.enums.postnatal.value @@ -61,10 +60,9 @@ age_type: - $ref: objects.enums.gestational.value birthdate: name: birthdate - display_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). + Date of birth (start point of the neonate stage) of the subject. Datetime format. Should not be provided or anonymized for human subjects. type: string format: datetime cardiac: diff --git a/src/schema/rules/tabular_data/modality_agnostic.yaml b/src/schema/rules/tabular_data/modality_agnostic.yaml index cd6579d281..2c8907e6d1 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 - birthdate: recommended - age_category: recommended - age_type: optional + birthdate: optional + life_cycle_stage: recommended + age_reference: recommended index_columns: [participant_id] additional_columns: allowed From cfca31d14557be2a79d9d72526ab49145aef1048 Mon Sep 17 00:00:00 2001 From: Reema Gupta Date: Mon, 17 Mar 2025 08:22:57 +0100 Subject: [PATCH 07/46] Added enum listings for participant age specification --- src/schema/objects/enums.yaml | 106 +++++++++++++++++++++++++++------- 1 file changed, 85 insertions(+), 21 deletions(-) diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml index 6dc330be47..5801e727e5 100644 --- a/src/schema/objects/enums.yaml +++ b/src/schema/objects/enums.yaml @@ -1405,24 +1405,88 @@ 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. +start_of_embryo_stage: + value: start of embryo stage + display_name: start of embryo stage + description: | + The beginning of the embryo stage, which is also commonly referred as the "conception". +start_of_gestational_stage: + value: start of gestational stage + display_name: start of gestational stage + description: | + The beginning of the gestational stage, which is also commonly referred as the + "first day of the mother's last menstrual period". +start_of_neonate_stage: + value: start of neonatal stage + display_name: start of neonatal stage + description: | + The beginning of the neonatal stage, which is also commonky referred as the "birth". +end_of_adult_stage: + value: end of adult stage + display_name: end of adult stage + description: | + The end of the adult stage, which is also commonly referred as the "death". +adolescent: + value: adolescent + display_name: adolescent + description: | + The transitional life cycle stage of growth and development between childhood and adulthood, + often described as ‘puberty’. +adult: + value: adult + display_name: adult + description: | + The life cycle stage of an animal or human that reached sexual maturity. + The UBERON term for this stage is 'post-juvenile adult stage' - http://purl.obolibrary.org/obo/UBERON_0000113. +embryo: + value: embryo + display_name: embryo + description: | + The life cycle stage of an animal or human that starts with fertilitzation + and ends with the fully formed embryo. The UBERON term for this stage is + 'embryo stage' - http://purl.obolibrary.org/obo/UBERON_0000068. +infant: + value: infant + display_name: infant + description: | + The life cycle stage of mammals (animal or human) that follows the neonate stage and ends at weaning. + The UBERON term for this stage is 'infant stage' - http://purl.obolibrary.org/obo/UBERON_0034920. +juveline: + value: juveline + display_name: juveline + description: | + The life cycle stage of an animal or human that starts with the independence of the nest and/or + caregivers and ends with sexual maturity. The UBERON term for this stage is + 'juvenile stage' - http://purl.obolibrary.org/obo/UBERON_0034919. +late_adult: + value: late adult + display_name: late adult + description: | + The life cycle stage of an animal or human that follows the prime adult stage. + The UBERON term for this stage is 'late adult stage' - http://purl.obolibrary.org/obo/UBERON_0007222. +neonate: + value: neonate + display_name: neonate + description: + The life cycle stage of an animal or human that immediately follows birth. + The UBERON term for this stage is 'neonate stage' - http://purl.obolibrary.org/obo/UBERON_0007221. +perinatal: + value: perinatal + display_name: perinatal + description: | + The life cycle stage of an animal or human that starts right before birth + and ends right after birth. The UBERON term for this stage + is 'perinatal stage' - http://purl.obolibrary.org/obo/UBERON_0012101. +prime_adult: + value: prime adult + display_name: prime adult + description: | + The life cycle stage of an animal or human that starts at the onset of sexual maturity or + the cessation of growth, whichever comes last, and ends before senescence. + The UBERON term for this stage is 'prime adult stage' - http://purl.obolibrary.org/obo/UBERON_0018241. +young_adult: + value: young adult + display_name: young adult + description: | + the early adult stage of an animal or human when sexual maturity has been reached, + but not the cessation of growth. From c558d50df16964a3413bd0b18ced624c409b52e7 Mon Sep 17 00:00:00 2001 From: Reema Gupta Date: Mon, 17 Mar 2025 08:31:29 +0100 Subject: [PATCH 08/46] Added enums to columns object for age and lifecycle_stage --- src/schema/objects/columns.yaml | 27 +++++++++++++++++++++------ 1 file changed, 21 insertions(+), 6 deletions(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 4665d3fdbc..020ac34bf3 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -46,23 +46,38 @@ life_cycle_stage: name: life cycle stage display_name: life cycle stage description: | - A non-numeric life cycle stage (e.g., 'adult stage'), inspired by the [UBERON life cycle stage](http://purl.obolibrary.org/obo/UBERON_0000105). + A non-numeric life cycle stage (e.g., 'adult stage'), inspired by the + [UBERON life cycle stage](http://purl.obolibrary.org/obo/UBERON_0000105). type: string + enum: + - $ref: objects.enums.adolescent.value + - $ref: objects.enums.adult.value + - $ref: objects.enums.embryo.value + - $ref: objects.enums.infant.value + - $ref: objects.enums.juvenile.value + - $ref: objects.enums.late_adult.value + - $ref: objects.enums.neonate.value + - $ref: objects.enums.perinatal.value + - $ref: objects.enums.prime_adult.value + - $ref: objects.enums.young_adult.value age_reference: name: age reference display_name: age reference description: | - Non-numeric life cycle point of an organism that serves as reference for the numeric age information. + Non-numeric life cycle point of an organism that serves as reference for + the numeric age information. type: string enum: - - $ref: objects.enums.postnatal.value - - $ref: objects.enums.fetal.value - - $ref: objects.enums.gestational.value + - $ref: objects.enums.start_of_embryo_stage.value + - $ref: objects.enums.start_of_gestational_stage.value + - $ref: objects.enums.start_of_neonate_stage.value + - $ref: objects.enums.end_of_adult_stage.value birthdate: name: birthdate display_name: birthdate description: | - Date of birth (start point of the neonate stage) of the subject. Datetime format. Should not be provided or anonymized for human subjects. + Date of birth (start point of the neonate stage) of the subject. Datetime format. + Should not be provided or anonymized for human subjects. type: string format: datetime cardiac: From ae2ecab0f041fbe31e38bfb54e8506c081a7c625 Mon Sep 17 00:00:00 2001 From: Reema Gupta <59512969+ree-gupta@users.noreply.github.com> Date: Tue, 18 Mar 2025 10:59:09 +0100 Subject: [PATCH 09/46] Apply suggestions from description review Co-authored-by: Lyuba Zehl --- src/schema/objects/columns.yaml | 9 +++-- src/schema/objects/enums.yaml | 69 ++++++++++++++++++--------------- 2 files changed, 43 insertions(+), 35 deletions(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 020ac34bf3..917d0fbce4 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -46,7 +46,8 @@ life_cycle_stage: name: life cycle stage display_name: life cycle stage description: | - A non-numeric life cycle stage (e.g., 'adult stage'), inspired by the + A non-numeric term for a subject's life cycle stage (e.g., 'adult stage'). + Inspired by the [UBERON life cycle stage](http://purl.obolibrary.org/obo/UBERON_0000105). type: string enum: @@ -64,8 +65,8 @@ age_reference: name: age reference display_name: age reference description: | - Non-numeric life cycle point of an organism that serves as reference for - the numeric age information. + Non-numeric term of for a time point in a subject's life cycle that serves + as reference for the numeric age information (e.g., 'start of embryo stage'). type: string enum: - $ref: objects.enums.start_of_embryo_stage.value @@ -76,7 +77,7 @@ birthdate: name: birthdate display_name: birthdate description: | - Date of birth (start point of the neonate stage) of the subject. Datetime format. + Date of the start of a subject's neonate stage. Datetime format. Should not be provided or anonymized for human subjects. type: string format: datetime diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml index 5801e727e5..dac4295edc 100644 --- a/src/schema/objects/enums.yaml +++ b/src/schema/objects/enums.yaml @@ -1409,84 +1409,91 @@ start_of_embryo_stage: value: start of embryo stage display_name: start of embryo stage description: | - The beginning of the embryo stage, which is also commonly referred as the "conception". + Point of fertilization marking the beginning of the subject's embryo + stage. start_of_gestational_stage: value: start of gestational stage display_name: start of gestational stage description: | - The beginning of the gestational stage, which is also commonly referred as the - "first day of the mother's last menstrual period". + Point of gestation defined as the first day of the mother's last menstrual period. + Marks the beginning of the subject's gestational stage. Used as reference when + time point of fertilization is unknown. start_of_neonate_stage: value: start of neonatal stage display_name: start of neonatal stage description: | - The beginning of the neonatal stage, which is also commonky referred as the "birth". -end_of_adult_stage: - value: end of adult stage - display_name: end of adult stage + Point of birth marking the beginning of a subject's neonatal stage. Often assumed + as default age reference if not otherwise specified. +start_of_death_stage: + value: start of death stage + display_name: start of death stage description: | - The end of the adult stage, which is also commonly referred as the "death". + Point of death marking the beginning of a subject's death stage. adolescent: value: adolescent display_name: adolescent description: | - The transitional life cycle stage of growth and development between childhood and adulthood, - often described as ‘puberty’. + Life cycle stage of a subject loosely defined by the transitional growth + and development between childhood and adulthood, often described as ‘puberty’. adult: value: adult display_name: adult description: | - The life cycle stage of an animal or human that reached sexual maturity. - The UBERON term for this stage is 'post-juvenile adult stage' - http://purl.obolibrary.org/obo/UBERON_0000113. + Life cycle stage of a subject that starts with sexual maturity and ends with + death. Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0000113. embryo: value: embryo display_name: embryo description: | - The life cycle stage of an animal or human that starts with fertilitzation - and ends with the fully formed embryo. The UBERON term for this stage is - 'embryo stage' - http://purl.obolibrary.org/obo/UBERON_0000068. + Life cycle stage of a subject that starts with fertilization and ends with the + fully formed embryo. Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0000068. +death: + value: death + display_name: death + description: | + Life cycle stage of a subject that starts with death and ends with full + decomposition of the subject's body. Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0000071. infant: value: infant display_name: infant description: | - The life cycle stage of mammals (animal or human) that follows the neonate stage and ends at weaning. - The UBERON term for this stage is 'infant stage' - http://purl.obolibrary.org/obo/UBERON_0034920. + Life cycle stage of subjects (mammals) that follows the neonate stage and ends at + weaning. Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0034920. juveline: value: juveline display_name: juveline description: | - The life cycle stage of an animal or human that starts with the independence of the nest and/or - caregivers and ends with sexual maturity. The UBERON term for this stage is - 'juvenile stage' - http://purl.obolibrary.org/obo/UBERON_0034919. + Life cycle stage of a subject that starts with the independence of the nest + and/or caregivers and ends with sexual maturity. Adapted from + UBERON - http://purl.obolibrary.org/obo/UBERON_0034919. late_adult: value: late adult display_name: late adult description: | - The life cycle stage of an animal or human that follows the prime adult stage. - The UBERON term for this stage is 'late adult stage' - http://purl.obolibrary.org/obo/UBERON_0007222. + Life cycle stage of a subject that follows the prime adult stage and ends with + death. Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0007222. neonate: value: neonate display_name: neonate description: - The life cycle stage of an animal or human that immediately follows birth. - The UBERON term for this stage is 'neonate stage' - http://purl.obolibrary.org/obo/UBERON_0007221. + Life cycle stage of a subject that immediately follows birth. + Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0007221. perinatal: value: perinatal display_name: perinatal description: | - The life cycle stage of an animal or human that starts right before birth - and ends right after birth. The UBERON term for this stage - is 'perinatal stage' - http://purl.obolibrary.org/obo/UBERON_0012101. + Life cycle stage of a subject that starts right before and ends right after birth. + Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0012101. prime_adult: value: prime adult display_name: prime adult description: | - The life cycle stage of an animal or human that starts at the onset of sexual maturity or + Life cycle stage of a subject that starts with sexual maturity or the cessation of growth, whichever comes last, and ends before senescence. - The UBERON term for this stage is 'prime adult stage' - http://purl.obolibrary.org/obo/UBERON_0018241. + Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0018241. young_adult: value: young adult display_name: young adult description: | - the early adult stage of an animal or human when sexual maturity has been reached, - but not the cessation of growth. + Life cycle stage of a subject that starts with sexual maturity and ends with the + cessation of growth (if this is reached after sexual maturity). From 5135dd4ea42a2373ca40bfee3d4d7245efbe0249 Mon Sep 17 00:00:00 2001 From: Reema Gupta <59512969+ree-gupta@users.noreply.github.com> Date: Wed, 19 Mar 2025 15:51:17 +0100 Subject: [PATCH 10/46] Apply suggestions from code review Co-authored-by: Lyuba Zehl --- src/schema/objects/columns.yaml | 5 +++-- src/schema/objects/enums.yaml | 6 +++--- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 917d0fbce4..0bda141184 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -53,12 +53,13 @@ life_cycle_stage: enum: - $ref: objects.enums.adolescent.value - $ref: objects.enums.adult.value + - $ref: objects.enums.death.value - $ref: objects.enums.embryo.value - $ref: objects.enums.infant.value - $ref: objects.enums.juvenile.value - $ref: objects.enums.late_adult.value - $ref: objects.enums.neonate.value - - $ref: objects.enums.perinatal.value + - $ref: objects.enums.perinate.value - $ref: objects.enums.prime_adult.value - $ref: objects.enums.young_adult.value age_reference: @@ -72,7 +73,7 @@ age_reference: - $ref: objects.enums.start_of_embryo_stage.value - $ref: objects.enums.start_of_gestational_stage.value - $ref: objects.enums.start_of_neonate_stage.value - - $ref: objects.enums.end_of_adult_stage.value + - $ref: objects.enums.start_of_death_stage.value birthdate: name: birthdate display_name: birthdate diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml index dac4295edc..4649b96d01 100644 --- a/src/schema/objects/enums.yaml +++ b/src/schema/objects/enums.yaml @@ -1478,9 +1478,9 @@ neonate: description: Life cycle stage of a subject that immediately follows birth. Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0007221. -perinatal: - value: perinatal - display_name: perinatal +perinate: + value: perinate + display_name: perinate description: | Life cycle stage of a subject that starts right before and ends right after birth. Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0012101. From edbd4b5bae2b35ebba46286e884285173dfd6f76 Mon Sep 17 00:00:00 2001 From: Reema Gupta Date: Mon, 14 Apr 2025 14:53:20 +0200 Subject: [PATCH 11/46] Move age_reference from columns definition to metadata definition --- src/schema/objects/metadata.yaml | 12 ++++++++++++ src/schema/rules/tabular_data/modality_agnostic.yaml | 1 - 2 files changed, 12 insertions(+), 1 deletion(-) diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml index 1b13a6a614..d9dc637839 100644 --- a/src/schema/objects/metadata.yaml +++ b/src/schema/objects/metadata.yaml @@ -49,6 +49,18 @@ AcquisitionVoxelSize: type: number exclusiveMinimum: 0 unit: mm +AgeReference: + name: AgeReference + display_name: Age Reference + description: | + Non-numeric term of for a time point in a subject's life cycle that serves + as reference for the numeric age information (e.g., 'start of embryo stage'). + type: string + enum: + - $ref: objects.enums.start_of_embryo_stage.value + - $ref: objects.enums.start_of_gestational_stage.value + - $ref: objects.enums.start_of_neonate_stage.value + - $ref: objects.enums.start_of_death_stage.value Anaesthesia: name: Anaesthesia display_name: Anaesthesia diff --git a/src/schema/rules/tabular_data/modality_agnostic.yaml b/src/schema/rules/tabular_data/modality_agnostic.yaml index 2c8907e6d1..7b790ccb00 100644 --- a/src/schema/rules/tabular_data/modality_agnostic.yaml +++ b/src/schema/rules/tabular_data/modality_agnostic.yaml @@ -17,7 +17,6 @@ Participants: strain_rrid: recommended birthdate: optional life_cycle_stage: recommended - age_reference: recommended index_columns: [participant_id] additional_columns: allowed From f9e5f6862ca3faba231223b088db7f850e8f907e Mon Sep 17 00:00:00 2001 From: Reema Gupta Date: Mon, 14 Apr 2025 15:00:54 +0200 Subject: [PATCH 12/46] Add rule for AgeReference in participants.json --- src/schema/rules/dataset_metadata.yaml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml index d0a92081a0..f4e663128f 100644 --- a/src/schema/rules/dataset_metadata.yaml +++ b/src/schema/rules/dataset_metadata.yaml @@ -48,3 +48,9 @@ genetic_info: TissueOrigin: optional BrainLocation: optional CellType: optional + +participants: + selectors: + - path == "/participants.json" + fields: + AgeReference: recommended From 33895b0c86181b217a462eb59c75899a3eb0c7bb Mon Sep 17 00:00:00 2001 From: "Yaroslav O. Halchenko" Date: Wed, 21 May 2025 11:16:25 -0400 Subject: [PATCH 13/46] RF: move life_cycle_staget in alphabetical order --- src/schema/objects/columns.yaml | 40 ++++++++++++++++----------------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 94b081cbcf..0b5fd85a58 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -45,26 +45,6 @@ age: "Description": "Subject age in postnatal years", "Units": "year", } -life_cycle_stage: - name: life cycle stage - display_name: life cycle stage - description: | - A non-numeric term for a subject's life cycle stage (e.g., 'adult stage'). - Inspired by the - [UBERON life cycle stage](http://purl.obolibrary.org/obo/UBERON_0000105). - type: string - enum: - - $ref: objects.enums.adolescent.value - - $ref: objects.enums.adult.value - - $ref: objects.enums.death.value - - $ref: objects.enums.embryo.value - - $ref: objects.enums.infant.value - - $ref: objects.enums.juvenile.value - - $ref: objects.enums.late_adult.value - - $ref: objects.enums.neonate.value - - $ref: objects.enums.perinate.value - - $ref: objects.enums.prime_adult.value - - $ref: objects.enums.young_adult.value age_reference: name: age reference display_name: age reference @@ -292,6 +272,26 @@ index: description: | The label integer index. type: integer +life_cycle_stage: + name: life cycle stage + display_name: life cycle stage + description: | + A non-numeric term for a subject's life cycle stage (e.g., 'adult stage'). + Inspired by the + [UBERON life cycle stage](http://purl.obolibrary.org/obo/UBERON_0000105). + type: string + enum: + - $ref: objects.enums.adolescent.value + - $ref: objects.enums.adult.value + - $ref: objects.enums.death.value + - $ref: objects.enums.embryo.value + - $ref: objects.enums.infant.value + - $ref: objects.enums.juvenile.value + - $ref: objects.enums.late_adult.value + - $ref: objects.enums.neonate.value + - $ref: objects.enums.perinate.value + - $ref: objects.enums.prime_adult.value + - $ref: objects.enums.young_adult.value low_cutoff: name: low_cutoff display_name: Low cutoff From 30f6ec0bac059409973e69579efcf5a5f2cf405d Mon Sep 17 00:00:00 2001 From: "Yaroslav O. Halchenko" Date: Wed, 21 May 2025 11:20:22 -0400 Subject: [PATCH 14/46] ENH: add conditioning recommended by @effigies for AgeReference --- src/schema/rules/dataset_metadata.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml index e6e7bf9ae7..e66e74bc08 100644 --- a/src/schema/rules/dataset_metadata.yaml +++ b/src/schema/rules/dataset_metadata.yaml @@ -61,5 +61,6 @@ genetic_info: participants: selectors: - path == "/participants.json" + - '"age" in columns' fields: AgeReference: recommended From 86ffb22d23a2196972f61237da8ca62d5f210985 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Wed, 21 May 2025 11:26:14 -0400 Subject: [PATCH 15/46] Remove start_of_death_stage from AgeReference etc + typo fix Co-authored-by: Lyuba Zehl Co-authored-by: Thomas Wachtler --- src/schema/objects/columns.yaml | 1 - src/schema/objects/enums.yaml | 11 +++-------- src/schema/objects/metadata.yaml | 1 - 3 files changed, 3 insertions(+), 10 deletions(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 0b5fd85a58..7800d4b332 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -56,7 +56,6 @@ age_reference: - $ref: objects.enums.start_of_embryo_stage.value - $ref: objects.enums.start_of_gestational_stage.value - $ref: objects.enums.start_of_neonate_stage.value - - $ref: objects.enums.start_of_death_stage.value birthdate: name: birthdate display_name: birthdate diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml index f5d6a47c28..32525c483e 100644 --- a/src/schema/objects/enums.yaml +++ b/src/schema/objects/enums.yaml @@ -1455,11 +1455,6 @@ start_of_neonate_stage: description: | Point of birth marking the beginning of a subject's neonatal stage. Often assumed as default age reference if not otherwise specified. -start_of_death_stage: - value: start of death stage - display_name: start of death stage - description: | - Point of death marking the beginning of a subject's death stage. adolescent: value: adolescent display_name: adolescent @@ -1490,9 +1485,9 @@ infant: description: | Life cycle stage of subjects (mammals) that follows the neonate stage and ends at weaning. Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0034920. -juveline: - value: juveline - display_name: juveline +juvenile: + value: juvenile + display_name: juvenile description: | Life cycle stage of a subject that starts with the independence of the nest and/or caregivers and ends with sexual maturity. Adapted from diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml index 547d51fd89..6906166849 100644 --- a/src/schema/objects/metadata.yaml +++ b/src/schema/objects/metadata.yaml @@ -60,7 +60,6 @@ AgeReference: - $ref: objects.enums.start_of_embryo_stage.value - $ref: objects.enums.start_of_gestational_stage.value - $ref: objects.enums.start_of_neonate_stage.value - - $ref: objects.enums.start_of_death_stage.value Anaesthesia: name: Anaesthesia display_name: Anaesthesia From e7c02b2c943a71b32fabe7b284257672ecc72f79 Mon Sep 17 00:00:00 2001 From: "Yaroslav O. Halchenko" Date: Wed, 21 May 2025 11:30:04 -0400 Subject: [PATCH 16/46] Replace bad latin "e.g." --- src/schema/objects/columns.yaml | 4 ++-- src/schema/objects/metadata.yaml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 7800d4b332..51b5c4b353 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -50,7 +50,7 @@ age_reference: display_name: age reference description: | Non-numeric term of for a time point in a subject's life cycle that serves - as reference for the numeric age information (e.g., 'start of embryo stage'). + as reference for the numeric age information (for instance, 'start of embryo stage'). type: string enum: - $ref: objects.enums.start_of_embryo_stage.value @@ -275,7 +275,7 @@ life_cycle_stage: name: life cycle stage display_name: life cycle stage description: | - A non-numeric term for a subject's life cycle stage (e.g., 'adult stage'). + A non-numeric term for a subject's life cycle stage (for instance, 'adult stage'). Inspired by the [UBERON life cycle stage](http://purl.obolibrary.org/obo/UBERON_0000105). type: string diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml index 6906166849..cb5da6808e 100644 --- a/src/schema/objects/metadata.yaml +++ b/src/schema/objects/metadata.yaml @@ -54,7 +54,7 @@ AgeReference: display_name: Age Reference description: | Non-numeric term of for a time point in a subject's life cycle that serves - as reference for the numeric age information (e.g., 'start of embryo stage'). + as reference for the numeric age information (for instance, 'start of embryo stage'). type: string enum: - $ref: objects.enums.start_of_embryo_stage.value From 9aedef1fc6a9d042c7732961dd117f28288e7ecc Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Thu, 12 Jun 2025 05:17:21 -0400 Subject: [PATCH 17/46] Update src/schema/objects/columns.yaml Co-authored-by: Lyuba Zehl --- src/schema/objects/columns.yaml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 51b5c4b353..72085b9953 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -63,7 +63,15 @@ birthdate: Date of the start of a subject's neonate stage. Datetime format. Should not be provided or anonymized for human subjects. type: string - format: datetime + format: date +birthtime: + name: birthtime + display_name: birthtime + description: | + Time of the start of a subject's neonate stage. Time format (hh:mm:ssZ) + Should not be provided or anonymized for human subjects. + type: string + format: time cardiac: name: cardiac display_name: Cardiac measurement From 761dd5da1370acda930485af19155173de906ce8 Mon Sep 17 00:00:00 2001 From: Lyuba Zehl Date: Thu, 12 Jun 2025 11:27:46 +0200 Subject: [PATCH 18/46] Update columns.yaml --- src/schema/objects/columns.yaml | 26 +++++++++++++++++++++----- 1 file changed, 21 insertions(+), 5 deletions(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 72085b9953..6bb6d8c3ec 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -53,14 +53,15 @@ age_reference: as reference for the numeric age information (for instance, 'start of embryo stage'). type: string enum: - - $ref: objects.enums.start_of_embryo_stage.value - - $ref: objects.enums.start_of_gestational_stage.value - - $ref: objects.enums.start_of_neonate_stage.value + - $ref: objects.enums.fertilization.value + - $ref: objects.enums.gestation.value + - $ref: objects.enums.birth.value + - $ref: objects.enums.death.value birthdate: name: birthdate display_name: birthdate description: | - Date of the start of a subject's neonate stage. Datetime format. + Date of the start of a subject's neonate stage. Date format (YYYY:MM:DD). Should not be provided or anonymized for human subjects. type: string format: date @@ -116,6 +117,22 @@ component: - $ref: objects.enums.quat_y.value - $ref: objects.enums.quat_z.value - $ref: objects.enums.quat_w.value +deathdate: + name: deathdate + display_name: deathdate + description: | + Date of the end of a subject's life cycle. Date format (YYYY:MM:DD). + Should not be provided or anonymized for human subjects. + type: string + format: date +deathtime: + name: deathtime + display_name: deathtime + description: | + Time of the end of a subject's life cycle. Time format (hh:mm:ssZ) + Should not be provided or anonymized for human subjects. + type: string + format: time detector__channels: name: detector display_name: Detector Name @@ -290,7 +307,6 @@ life_cycle_stage: enum: - $ref: objects.enums.adolescent.value - $ref: objects.enums.adult.value - - $ref: objects.enums.death.value - $ref: objects.enums.embryo.value - $ref: objects.enums.infant.value - $ref: objects.enums.juvenile.value From 46cdce4ca6b1a839834598b82b0b1b18392345c6 Mon Sep 17 00:00:00 2001 From: Lyuba Zehl Date: Thu, 12 Jun 2025 11:44:38 +0200 Subject: [PATCH 19/46] Update enums.yaml --- src/schema/objects/enums.yaml | 47 +++++++++++++++++------------------ 1 file changed, 23 insertions(+), 24 deletions(-) diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml index 32525c483e..efd496cfc0 100644 --- a/src/schema/objects/enums.yaml +++ b/src/schema/objects/enums.yaml @@ -1436,25 +1436,30 @@ microvascular: display_name: microvascular description: | The origin of a tissue: microvascular -start_of_embryo_stage: - value: start of embryo stage - display_name: start of embryo stage - description: | - Point of fertilization marking the beginning of the subject's embryo - stage. -start_of_gestational_stage: - value: start of gestational stage - display_name: start of gestational stage - description: | - Point of gestation defined as the first day of the mother's last menstrual period. - Marks the beginning of the subject's gestational stage. Used as reference when +birth: + value: birth + display_name: birth + description: | + A life cycle temporal boundary that is defined as the emergence of a + neonate from the body of its mother. Assumed to be the default age + reference if not otherwise specified. + It marks the beginning of a subject's neonatal stage + ([UBERON_0035946](http://purl.obolibrary.org/obo/UBERON_0035946)). +fertilization: + value: fertilization + display_name: fertilization + description: | + A life cycle temporal boundary that is defined as the union of gametes of + opposite sexes during the process of sexual reproduction to form a zygote + ([GO_0009566](http://purl.obolibrary.org/obo/GO_0009566)). + It marks the beginning of the subject's embryonic stage. +gestation: + value: gestation + display_name: gestation + description: | + First day of the mother's last menstrual period. Used as reference when time point of fertilization is unknown. -start_of_neonate_stage: - value: start of neonatal stage - display_name: start of neonatal stage - description: | - Point of birth marking the beginning of a subject's neonatal stage. Often assumed - as default age reference if not otherwise specified. + It marks the beginning of the subject's gestational stage. adolescent: value: adolescent display_name: adolescent @@ -1473,12 +1478,6 @@ embryo: description: | Life cycle stage of a subject that starts with fertilization and ends with the fully formed embryo. Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0000068. -death: - value: death - display_name: death - description: | - Life cycle stage of a subject that starts with death and ends with full - decomposition of the subject's body. Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0000071. infant: value: infant display_name: infant From 31a72fca57fe307b75e52c4e0e8d18dd42df4be6 Mon Sep 17 00:00:00 2001 From: Lyuba Zehl Date: Thu, 12 Jun 2025 11:46:31 +0200 Subject: [PATCH 20/46] Update metadata.yaml --- src/schema/objects/metadata.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml index cb5da6808e..5f7e68bab9 100644 --- a/src/schema/objects/metadata.yaml +++ b/src/schema/objects/metadata.yaml @@ -57,9 +57,9 @@ AgeReference: as reference for the numeric age information (for instance, 'start of embryo stage'). type: string enum: - - $ref: objects.enums.start_of_embryo_stage.value - - $ref: objects.enums.start_of_gestational_stage.value - - $ref: objects.enums.start_of_neonate_stage.value + - $ref: objects.enums.fertilization.value + - $ref: objects.enums.gestation.value + - $ref: objects.enums.birth.value Anaesthesia: name: Anaesthesia display_name: Anaesthesia From 13bbb47a1e059df632ae056f50d974ff14c9a73b Mon Sep 17 00:00:00 2001 From: Lyuba Zehl Date: Thu, 12 Jun 2025 11:47:05 +0200 Subject: [PATCH 21/46] Update columns.yaml --- src/schema/objects/columns.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 6bb6d8c3ec..12a39bf97c 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -56,7 +56,6 @@ age_reference: - $ref: objects.enums.fertilization.value - $ref: objects.enums.gestation.value - $ref: objects.enums.birth.value - - $ref: objects.enums.death.value birthdate: name: birthdate display_name: birthdate From b7cbbb9503073ba9a9b91d19cee45e98936bab26 Mon Sep 17 00:00:00 2001 From: Lyuba Zehl Date: Thu, 12 Jun 2025 11:53:10 +0200 Subject: [PATCH 22/46] Update columns.yaml --- src/schema/objects/columns.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 12a39bf97c..d9d2a57030 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -49,8 +49,8 @@ age_reference: name: age reference display_name: age reference description: | - Non-numeric term of for a time point in a subject's life cycle that serves - as reference for the numeric age information (for instance, 'start of embryo stage'). + Non-numeric term of a temporal boundary in a subject's life cycle that serves + as reference for the numeric age information (for instance, 'birth'). type: string enum: - $ref: objects.enums.fertilization.value @@ -299,7 +299,7 @@ life_cycle_stage: name: life cycle stage display_name: life cycle stage description: | - A non-numeric term for a subject's life cycle stage (for instance, 'adult stage'). + A non-numeric term for a subject's life cycle stage (for instance, 'adult'). Inspired by the [UBERON life cycle stage](http://purl.obolibrary.org/obo/UBERON_0000105). type: string From 66b6db0f14a86ee306012864b595e75940ad7e6b Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 12 Jun 2025 10:18:21 +0000 Subject: [PATCH 23/46] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- src/schema/objects/enums.yaml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml index efd496cfc0..57c474d13f 100644 --- a/src/schema/objects/enums.yaml +++ b/src/schema/objects/enums.yaml @@ -1440,18 +1440,18 @@ birth: value: birth display_name: birth description: | - A life cycle temporal boundary that is defined as the emergence of a - neonate from the body of its mother. Assumed to be the default age + A life cycle temporal boundary that is defined as the emergence of a + neonate from the body of its mother. Assumed to be the default age reference if not otherwise specified. - It marks the beginning of a subject's neonatal stage - ([UBERON_0035946](http://purl.obolibrary.org/obo/UBERON_0035946)). + It marks the beginning of a subject's neonatal stage + ([UBERON_0035946](http://purl.obolibrary.org/obo/UBERON_0035946)). fertilization: value: fertilization display_name: fertilization description: | - A life cycle temporal boundary that is defined as the union of gametes of - opposite sexes during the process of sexual reproduction to form a zygote - ([GO_0009566](http://purl.obolibrary.org/obo/GO_0009566)). + A life cycle temporal boundary that is defined as the union of gametes of + opposite sexes during the process of sexual reproduction to form a zygote + ([GO_0009566](http://purl.obolibrary.org/obo/GO_0009566)). It marks the beginning of the subject's embryonic stage. gestation: value: gestation @@ -1459,7 +1459,7 @@ gestation: description: | First day of the mother's last menstrual period. Used as reference when time point of fertilization is unknown. - It marks the beginning of the subject's gestational stage. + It marks the beginning of the subject's gestational stage. adolescent: value: adolescent display_name: adolescent From 0954ee5691b0b797e14a75d2667eb11757356177 Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Thu, 12 Jun 2025 06:20:45 -0400 Subject: [PATCH 24/46] Update src/schema/objects/columns.yaml fix date format --- 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 d9d2a57030..6afd4e844e 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -60,7 +60,7 @@ birthdate: name: birthdate display_name: birthdate description: | - Date of the start of a subject's neonate stage. Date format (YYYY:MM:DD). + Date of the start of a subject's neonate stage. Date format (YYYY-MM-DD). Should not be provided or anonymized for human subjects. type: string format: date From b80dbbb06f9ca16b54cbe4497edbe1ce19d6229f Mon Sep 17 00:00:00 2001 From: Lyuba Zehl Date: Thu, 12 Jun 2025 12:26:27 +0200 Subject: [PATCH 25/46] Update src/schema/objects/columns.yaml Co-authored-by: Ben Dichter --- 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 6afd4e844e..8f51db58ef 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -68,7 +68,7 @@ birthtime: name: birthtime display_name: birthtime description: | - Time of the start of a subject's neonate stage. Time format (hh:mm:ssZ) + Time of birth. Time format (hh:mm:ssZ). Typically, this field will be combined with birthdate. Should not be provided or anonymized for human subjects. type: string format: time From 193d4981d77b8ff1f0a81bbcff747174689e809c Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Thu, 12 Jun 2025 06:38:28 -0400 Subject: [PATCH 26/46] Update src/schema/objects/columns.yaml clarify age reference --- src/schema/objects/columns.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 8f51db58ef..8c9e052c46 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -49,8 +49,7 @@ age_reference: name: age reference display_name: age reference description: | - Non-numeric term of a temporal boundary in a subject's life cycle that serves - as reference for the numeric age information (for instance, 'birth'). + The reference for the numeric age. If not provided, 'birth' is assumed to be the default reference. type: string enum: - $ref: objects.enums.fertilization.value From 6a3d382fc117e0131fdcb405b585e87fbcd84c61 Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Thu, 12 Jun 2025 06:39:14 -0400 Subject: [PATCH 27/46] Update src/schema/objects/columns.yaml fix deathdate format --- 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 8c9e052c46..ed20608e7c 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -119,7 +119,7 @@ deathdate: name: deathdate display_name: deathdate description: | - Date of the end of a subject's life cycle. Date format (YYYY:MM:DD). + Date of the end of a subject's life cycle. Date format (YYYY-MM-DD). Should not be provided or anonymized for human subjects. type: string format: date From f6c46482b0fdc81ccb5d40a738ea291b08750f63 Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Thu, 12 Jun 2025 06:51:00 -0400 Subject: [PATCH 28/46] Update src/schema/rules/tabular_data/modality_agnostic.yaml Co-authored-by: Lyuba Zehl --- src/schema/rules/tabular_data/modality_agnostic.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/rules/tabular_data/modality_agnostic.yaml b/src/schema/rules/tabular_data/modality_agnostic.yaml index 1fbc3a3c86..13d3f800fd 100644 --- a/src/schema/rules/tabular_data/modality_agnostic.yaml +++ b/src/schema/rules/tabular_data/modality_agnostic.yaml @@ -17,7 +17,7 @@ Participants: strain: recommended strain_rrid: recommended birthdate: optional - life_cycle_stage: recommended + age_category: recommended HED: optional index_columns: [participant_id] additional_columns: allowed From d3a22a7c33160d26a02277251fb290c5cf48f1e3 Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Thu, 12 Jun 2025 06:54:06 -0400 Subject: [PATCH 29/46] Update src/schema/objects/columns.yaml Co-authored-by: Lyuba Zehl --- src/schema/objects/columns.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index ed20608e7c..06711e7c18 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -127,7 +127,8 @@ deathtime: name: deathtime display_name: deathtime description: | - Time of the end of a subject's life cycle. Time format (hh:mm:ssZ) + Time of death. Time format (hh:mm:ssZ). Typically, this field will be + combined with deathdate. Should not be provided or anonymized for human subjects. type: string format: time From fc20dafc129675145fe1eba6c6b54e7f84bd096e Mon Sep 17 00:00:00 2001 From: Lyuba Zehl Date: Thu, 12 Jun 2025 12:54:55 +0200 Subject: [PATCH 30/46] Update src/schema/objects/columns.yaml Co-authored-by: Ben Dichter --- src/schema/objects/columns.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 06711e7c18..33c0a321e5 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -295,9 +295,9 @@ index: description: | The label integer index. type: integer -life_cycle_stage: - name: life cycle stage - display_name: life cycle stage +age_category: + name: age category + display_name: age category description: | A non-numeric term for a subject's life cycle stage (for instance, 'adult'). Inspired by the From e7845898847e530870ce08f73a0786e6680a7861 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 12 Jun 2025 10:56:55 +0000 Subject: [PATCH 31/46] [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 33c0a321e5..d23916751e 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -127,7 +127,7 @@ deathtime: name: deathtime display_name: deathtime description: | - Time of death. Time format (hh:mm:ssZ). Typically, this field will be + Time of death. Time format (hh:mm:ssZ). Typically, this field will be combined with deathdate. Should not be provided or anonymized for human subjects. type: string From e3e034930fd012ceaf1bc3d182a69f43142ae0a4 Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Thu, 12 Jun 2025 06:57:13 -0400 Subject: [PATCH 32/46] Update src/schema/rules/tabular_data/modality_agnostic.yaml --- src/schema/rules/tabular_data/modality_agnostic.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/schema/rules/tabular_data/modality_agnostic.yaml b/src/schema/rules/tabular_data/modality_agnostic.yaml index 13d3f800fd..390a1c38dd 100644 --- a/src/schema/rules/tabular_data/modality_agnostic.yaml +++ b/src/schema/rules/tabular_data/modality_agnostic.yaml @@ -17,6 +17,9 @@ Participants: strain: recommended strain_rrid: recommended birthdate: optional + birthtime: optional + deathdate: optional + deathtime: optional age_category: recommended HED: optional index_columns: [participant_id] From 31a9cfb25570e73b12270230104caba1923d826c Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Thu, 12 Jun 2025 06:57:20 -0400 Subject: [PATCH 33/46] Update src/schema/rules/tabular_data/modality_agnostic.yaml --- src/schema/rules/tabular_data/modality_agnostic.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/rules/tabular_data/modality_agnostic.yaml b/src/schema/rules/tabular_data/modality_agnostic.yaml index 390a1c38dd..606a5e9dfa 100644 --- a/src/schema/rules/tabular_data/modality_agnostic.yaml +++ b/src/schema/rules/tabular_data/modality_agnostic.yaml @@ -11,7 +11,7 @@ Participants: There MUST be exactly one row for each participant. species: recommended age: recommended - age_reference: recommended + age_reference: optional sex: recommended handedness: recommended strain: recommended From 9efd17cf71643076a72283e42a1439d5972e5104 Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Thu, 12 Jun 2025 06:57:27 -0400 Subject: [PATCH 34/46] Update src/schema/rules/tabular_data/modality_agnostic.yaml --- src/schema/rules/tabular_data/modality_agnostic.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/rules/tabular_data/modality_agnostic.yaml b/src/schema/rules/tabular_data/modality_agnostic.yaml index 606a5e9dfa..f6bd003c18 100644 --- a/src/schema/rules/tabular_data/modality_agnostic.yaml +++ b/src/schema/rules/tabular_data/modality_agnostic.yaml @@ -20,7 +20,7 @@ Participants: birthtime: optional deathdate: optional deathtime: optional - age_category: recommended + age_category: optional HED: optional index_columns: [participant_id] additional_columns: allowed From fdc1cc7f4b8d85ee3c785735394c197e93c5cb35 Mon Sep 17 00:00:00 2001 From: Lyuba Zehl Date: Thu, 12 Jun 2025 13:01:08 +0200 Subject: [PATCH 35/46] Update src/schema/objects/columns.yaml Co-authored-by: Ben Dichter --- src/schema/objects/columns.yaml | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index d23916751e..12b2670ff0 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -45,16 +45,6 @@ age: "Description": "Subject age in postnatal years", "Units": "year", } -age_reference: - name: age reference - display_name: age reference - description: | - The reference for the numeric age. If not provided, 'birth' is assumed to be the default reference. - type: string - enum: - - $ref: objects.enums.fertilization.value - - $ref: objects.enums.gestation.value - - $ref: objects.enums.birth.value birthdate: name: birthdate display_name: birthdate From 1e775def78122f6cff4385d02cd04f54ff9ca5cc Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Thu, 12 Jun 2025 07:01:27 -0400 Subject: [PATCH 36/46] Update src/schema/rules/tabular_data/modality_agnostic.yaml --- src/schema/rules/tabular_data/modality_agnostic.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/src/schema/rules/tabular_data/modality_agnostic.yaml b/src/schema/rules/tabular_data/modality_agnostic.yaml index f6bd003c18..b25d2bff55 100644 --- a/src/schema/rules/tabular_data/modality_agnostic.yaml +++ b/src/schema/rules/tabular_data/modality_agnostic.yaml @@ -11,7 +11,6 @@ Participants: There MUST be exactly one row for each participant. species: recommended age: recommended - age_reference: optional sex: recommended handedness: recommended strain: recommended From 28a064f3d52c93b7e64d9c8a179ada1b7b0438f9 Mon Sep 17 00:00:00 2001 From: Lyuba Zehl Date: Wed, 3 Sep 2025 14:53:26 +0200 Subject: [PATCH 37/46] Update columns.yaml --- src/schema/objects/columns.yaml | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index 12b2670ff0..0e30b574f1 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -42,8 +42,9 @@ age: for privacy purposes. definition: { "LongName": "Subject age", - "Description": "Subject age in postnatal years", - "Units": "year", + "Description": "Subject age in postnatal years.", + "Reference": "birth", + "Units": "year" } birthdate: name: birthdate @@ -57,7 +58,8 @@ birthtime: name: birthtime display_name: birthtime description: | - Time of birth. Time format (hh:mm:ssZ). Typically, this field will be combined with birthdate. + Time (or estimated time) of birth. Time format (hh:mm:ssZ). + Typically, this field will be combined with birthdate. Should not be provided or anonymized for human subjects. type: string format: time @@ -117,8 +119,8 @@ deathtime: name: deathtime display_name: deathtime description: | - Time of death. Time format (hh:mm:ssZ). Typically, this field will be - combined with deathdate. + Time (or estimated time) of death. Time format (hh:mm:ssZ). + Typically, this field will be combined with deathdate. Should not be provided or anonymized for human subjects. type: string format: time From 7437e04a6666d994fd070d7a8fee1e8deb5bd312 Mon Sep 17 00:00:00 2001 From: Lyuba Zehl Date: Wed, 3 Sep 2025 14:59:36 +0200 Subject: [PATCH 38/46] Update enums.yaml --- src/schema/objects/enums.yaml | 24 ------------------------ 1 file changed, 24 deletions(-) diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml index 57c474d13f..012cb9a47c 100644 --- a/src/schema/objects/enums.yaml +++ b/src/schema/objects/enums.yaml @@ -1436,30 +1436,6 @@ microvascular: display_name: microvascular description: | The origin of a tissue: microvascular -birth: - value: birth - display_name: birth - description: | - A life cycle temporal boundary that is defined as the emergence of a - neonate from the body of its mother. Assumed to be the default age - reference if not otherwise specified. - It marks the beginning of a subject's neonatal stage - ([UBERON_0035946](http://purl.obolibrary.org/obo/UBERON_0035946)). -fertilization: - value: fertilization - display_name: fertilization - description: | - A life cycle temporal boundary that is defined as the union of gametes of - opposite sexes during the process of sexual reproduction to form a zygote - ([GO_0009566](http://purl.obolibrary.org/obo/GO_0009566)). - It marks the beginning of the subject's embryonic stage. -gestation: - value: gestation - display_name: gestation - description: | - First day of the mother's last menstrual period. Used as reference when - time point of fertilization is unknown. - It marks the beginning of the subject's gestational stage. adolescent: value: adolescent display_name: adolescent From 5610b3d35ed93195e5558187d76d2c72811c2481 Mon Sep 17 00:00:00 2001 From: Lyuba Zehl Date: Wed, 3 Sep 2025 15:02:17 +0200 Subject: [PATCH 39/46] Update metadata.yaml --- src/schema/objects/metadata.yaml | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml index f1a094d348..acb7fa4447 100644 --- a/src/schema/objects/metadata.yaml +++ b/src/schema/objects/metadata.yaml @@ -49,17 +49,6 @@ AcquisitionVoxelSize: type: number exclusiveMinimum: 0 unit: mm -AgeReference: - name: AgeReference - display_name: Age Reference - description: | - Non-numeric term of for a time point in a subject's life cycle that serves - as reference for the numeric age information (for instance, 'start of embryo stage'). - type: string - enum: - - $ref: objects.enums.fertilization.value - - $ref: objects.enums.gestation.value - - $ref: objects.enums.birth.value Anaesthesia: name: Anaesthesia display_name: Anaesthesia From d39b191361f5d0b8d826c81eb767cda7744e714e Mon Sep 17 00:00:00 2001 From: Lyuba Zehl Date: Wed, 3 Sep 2025 15:53:28 +0200 Subject: [PATCH 40/46] Update metadata.yaml --- src/schema/objects/metadata.yaml | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml index acb7fa4447..1512809117 100644 --- a/src/schema/objects/metadata.yaml +++ b/src/schema/objects/metadata.yaml @@ -49,6 +49,17 @@ AcquisitionVoxelSize: type: number exclusiveMinimum: 0 unit: mm +AgeReference: + name: AgeReference + display_name: Age Reference + description: | + Non-numeric term of for a time point in a subject's life cycle that serves + as reference for the numeric age information (for instance, 'birth'). + type: string + enum: + - $ref: objects.enums.fertilization.value + - $ref: objects.enums.gestation.value + - $ref: objects.enums.birth.value Anaesthesia: name: Anaesthesia display_name: Anaesthesia From e0aea957c2205fa25c36209c607f34b24520df59 Mon Sep 17 00:00:00 2001 From: Lyuba Zehl Date: Wed, 3 Sep 2025 15:58:12 +0200 Subject: [PATCH 41/46] Update enums.yaml --- src/schema/objects/enums.yaml | 27 ++++++++++++++++++++++++++- 1 file changed, 26 insertions(+), 1 deletion(-) diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml index 012cb9a47c..0f8d59ac02 100644 --- a/src/schema/objects/enums.yaml +++ b/src/schema/objects/enums.yaml @@ -1436,6 +1436,30 @@ microvascular: display_name: microvascular description: | The origin of a tissue: microvascular +birth: + value: birth + display_name: birth + description: | + A life cycle temporal boundary that is defined as the emergence of a + neonate from the body of its mother. Assumed to be the default age + reference if not otherwise specified. + It marks the beginning of a subject's neonatal stage + ([UBERON_0035946](http://purl.obolibrary.org/obo/UBERON_0035946)). +fertilization: + value: fertilization + display_name: fertilization + description: | + A life cycle temporal boundary that is defined as the union of gametes of + opposite sexes during the process of sexual reproduction to form a zygote + ([GO_0009566](http://purl.obolibrary.org/obo/GO_0009566)). + It marks the beginning of the subject's embryonic stage. +LMP_startdate: + value: gestation + display_name: gestation + description: | + First day of the mother's last menstrual period (LMP). Used as reference when + time point of fertilization is unknown. + It marks the beginning of the subject's gestational stage. adolescent: value: adolescent display_name: adolescent @@ -1453,7 +1477,8 @@ embryo: display_name: embryo description: | Life cycle stage of a subject that starts with fertilization and ends with the - fully formed embryo. Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0000068. + fully formed embryo. If fertilization is unknown the LMP startdate is assumed. + Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0000068. infant: value: infant display_name: infant From 478ccc71ff2bc8435ca50fadb9d254bfac32753e Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Thu, 4 Sep 2025 15:54:29 +0000 Subject: [PATCH 42/46] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- src/schema/objects/columns.yaml | 4 ++-- src/schema/objects/enums.yaml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index a07c4d1ab5..9f4975cf16 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -60,7 +60,7 @@ birthtime: name: birthtime display_name: birthtime description: | - Time (or estimated time) of birth. Time format (hh:mm:ssZ). + Time (or estimated time) of birth. Time format (hh:mm:ssZ). Typically, this field will be combined with birthdate. Should not be provided or anonymized for human subjects. type: string @@ -122,7 +122,7 @@ deathtime: name: deathtime display_name: deathtime description: | - Time (or estimated time) of death. Time format (hh:mm:ssZ). + Time (or estimated time) of death. Time format (hh:mm:ssZ). Typically, this field will be combined with deathdate. Should not be provided or anonymized for human subjects. type: string diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml index 9fa3992cab..424ed70ae8 100644 --- a/src/schema/objects/enums.yaml +++ b/src/schema/objects/enums.yaml @@ -1483,7 +1483,7 @@ embryo: display_name: embryo description: | Life cycle stage of a subject that starts with fertilization and ends with the - fully formed embryo. If fertilization is unknown the LMP startdate is assumed. + fully formed embryo. If fertilization is unknown the LMP startdate is assumed. Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0000068. infant: value: infant From bb3513c5e4a39d8a6cbcae7a6ea6a2ddd27d8cd3 Mon Sep 17 00:00:00 2001 From: Reema Gupta Date: Wed, 1 Oct 2025 15:21:08 +0200 Subject: [PATCH 43/46] Make the defintion of age have a more specific attribute AgeReference --- 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 9f4975cf16..e7e449dbee 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -43,7 +43,7 @@ age: definition: { "LongName": "Subject age", "Description": "Subject age in postnatal years.", - "Reference": "birth", + "AgeReference": "birth", "Format": "number", "Units": "year", "Maximum": 89, From b6a5b375f2cb69dedcd7d4518ceba88acb34d086 Mon Sep 17 00:00:00 2001 From: Reema Gupta Date: Wed, 1 Oct 2025 15:23:11 +0200 Subject: [PATCH 44/46] Switch from a time period term gestation to temporal boundary term LMP_startdate --- src/schema/objects/enums.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml index 340de06986..0ed49262c0 100644 --- a/src/schema/objects/enums.yaml +++ b/src/schema/objects/enums.yaml @@ -1470,10 +1470,11 @@ fertilization: ([GO_0009566](http://purl.obolibrary.org/obo/GO_0009566)). It marks the beginning of the subject's embryonic stage. LMP_startdate: - value: gestation - display_name: gestation + value: LMP_startdate + display_name: LMP start date description: | - First day of the mother's last menstrual period (LMP). Used as reference when + A life cycle temporal boundary that is defined as the first day of the mother's + last menstrual period (LMP). Used as reference when time point of fertilization is unknown. It marks the beginning of the subject's gestational stage. adolescent: From c73990452838bbd4dcfd3336efe1885ecf1273d6 Mon Sep 17 00:00:00 2001 From: Reema Gupta Date: Wed, 1 Oct 2025 15:24:13 +0200 Subject: [PATCH 45/46] Update AgeReference enum to include LMP_Startdate --- src/schema/objects/metadata.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml index 62b2306d4d..58ec95ed4c 100644 --- a/src/schema/objects/metadata.yaml +++ b/src/schema/objects/metadata.yaml @@ -57,7 +57,7 @@ AgeReference: type: string enum: - $ref: objects.enums.fertilization.value - - $ref: objects.enums.gestation.value + - $ref: objects.enums.LMP_startdate.value - $ref: objects.enums.birth.value Anaesthesia: name: Anaesthesia From 43c52fcc4b5d2930d9534c52ff187c70d192d81a Mon Sep 17 00:00:00 2001 From: Reema Gupta Date: Wed, 1 Oct 2025 15:48:06 +0200 Subject: [PATCH 46/46] Modify the value and display_name to match convention --- src/schema/objects/columns.yaml | 12 ++++++------ src/schema/objects/enums.yaml | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index e7e449dbee..43fdabea0a 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -50,7 +50,7 @@ age: } birthdate: name: birthdate - display_name: birthdate + display_name: Birth date description: | Date of the start of a subject's neonate stage. Date format (YYYY-MM-DD). Should not be provided or anonymized for human subjects. @@ -58,7 +58,7 @@ birthdate: format: date birthtime: name: birthtime - display_name: birthtime + display_name: Birth time description: | Time (or estimated time) of birth. Time format (hh:mm:ssZ). Typically, this field will be combined with birthdate. @@ -112,7 +112,7 @@ component: - $ref: objects.enums.quat_w.value deathdate: name: deathdate - display_name: deathdate + display_name: Death date description: | Date of the end of a subject's life cycle. Date format (YYYY-MM-DD). Should not be provided or anonymized for human subjects. @@ -120,7 +120,7 @@ deathdate: format: date deathtime: name: deathtime - display_name: deathtime + display_name: Death time description: | Time (or estimated time) of death. Time format (hh:mm:ssZ). Typically, this field will be combined with deathdate. @@ -289,8 +289,8 @@ index: The label integer index. type: integer age_category: - name: age category - display_name: age category + name: age_category + display_name: Age category description: | A non-numeric term for a subject's life cycle stage (for instance, 'adult'). Inspired by the diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml index 0ed49262c0..b3186b2697 100644 --- a/src/schema/objects/enums.yaml +++ b/src/schema/objects/enums.yaml @@ -1470,7 +1470,7 @@ fertilization: ([GO_0009566](http://purl.obolibrary.org/obo/GO_0009566)). It marks the beginning of the subject's embryonic stage. LMP_startdate: - value: LMP_startdate + value: LMP start date display_name: LMP start date description: | A life cycle temporal boundary that is defined as the first day of the mother's