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

src/schema/objects/columns.yaml

@@ -42,6 +42,44 @@ age:
     for privacy purposes.
   type: number
   unit: year
+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).
+  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.
+  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.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.
+  type: string
+  format: datetime
 cardiac:
   name: cardiac
   display_name: Cardiac measurement

src/schema/objects/enums.yaml

@@ -1405,3 +1405,88 @@ 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: |
+    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.

src/schema/rules/tabular_data/modality_agnostic.yaml

@@ -15,6 +15,9 @@ Participants:
     handedness: recommended
     strain: recommended
     strain_rrid: recommended
+    birthdate: optional
+    life_cycle_stage: recommended
+    age_reference: recommended
   index_columns: [participant_id]
   additional_columns: allowed