[ENH] Additional age related columns for participants.tsv file to cover animal data

src/schema/objects/columns.yaml

@@ -42,6 +42,46 @@ age:
     for privacy purposes.
   type: number
   unit: 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
+  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
+birthdate:
+  name: birthdate
+  display_name: birthdate
+  description: |
+    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
 cardiac:
   name: cardiac
   display_name: Cardiac measurement

src/schema/objects/enums.yaml

@@ -1405,3 +1405,95 @@ 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 
+    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.
+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
+  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. 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: |
+    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: |
+    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).

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

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

src/schema/rules/tabular_data/modality_agnostic.yaml

@@ -15,6 +15,8 @@ Participants:
     handedness: recommended
     strain: recommended
     strain_rrid: recommended
+    birthdate: optional
+    life_cycle_stage: recommended
   index_columns: [participant_id]
   additional_columns: allowed