diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml index e216094579..c2ca61f302 100644 --- a/src/schema/objects/columns.yaml +++ b/src/schema/objects/columns.yaml @@ -47,6 +47,42 @@ age: "Units": "year", "Maximum": 89, } +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 + [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.perinate.value + - $ref: objects.enums.prime_adult.value + - $ref: objects.enums.young_adult.value +birthdate: + 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. + type: string + format: date +birthtime: + 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. + Should not be provided or anonymized for human subjects. + type: string + format: time cardiac: name: cardiac display_name: Cardiac measurement @@ -99,6 +135,23 @@ coordinate_system: Name of the coordinate system defined in `coordsystem.json` in which the electrode's `x`, `y`, and (optionally) `z` coordinates are given. type: string +deathdate: + 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. + type: string + format: date +deathtime: + 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. + Should not be provided or anonymized for human subjects. + type: string + format: time detector__channels: name: detector display_name: Detector Name diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml index be12f2f624..f65bd42131 100644 --- a/src/schema/objects/enums.yaml +++ b/src/schema/objects/enums.yaml @@ -1481,3 +1481,67 @@ PhysioTypeEyetrack: display_name: Eye-tracking recording description: | A specific physiological recording type: eye-tracking. +# Life cycle stages for age_category +adolescent: + value: adolescent + display_name: Adolescent + description: | + 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: | + 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: | + 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. + Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0000068. +infant: + value: infant + display_name: 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. +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 + UBERON - http://purl.obolibrary.org/obo/UBERON_0034919. +late_adult: + value: late adult + display_name: Late adult + description: | + 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: | + Life cycle stage of a subject that immediately follows birth. + Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0007221. +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. +prime_adult: + value: prime adult + display_name: Prime adult + description: | + Life cycle stage of a subject that starts with sexual maturity or + the cessation of growth, whichever comes last, and ends before senescence. + Adapted from UBERON - http://purl.obolibrary.org/obo/UBERON_0018241. +young_adult: + value: young adult + display_name: Young adult + description: | + 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). diff --git a/src/schema/rules/tabular_data/modality_agnostic.yaml b/src/schema/rules/tabular_data/modality_agnostic.yaml index 83fd7e14f4..b25d2bff55 100644 --- a/src/schema/rules/tabular_data/modality_agnostic.yaml +++ b/src/schema/rules/tabular_data/modality_agnostic.yaml @@ -15,6 +15,11 @@ Participants: handedness: recommended strain: recommended strain_rrid: recommended + birthdate: optional + birthtime: optional + deathdate: optional + deathtime: optional + age_category: optional HED: optional index_columns: [participant_id] additional_columns: allowed