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

src/schema/objects/columns.yaml

@@ -42,9 +42,27 @@ 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
+  display_name: birthdate
+  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: birthtime
+  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
@@ -89,6 +107,23 @@ 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 (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
@@ -252,6 +287,25 @@ index:
   description: |
     The label integer index.
   type: integer
+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
 low_cutoff:
   name: low_cutoff
   display_name: Low cutoff

src/schema/objects/enums.yaml

@@ -1436,3 +1436,89 @@ 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
+  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.
+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).

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, '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

src/schema/rules/dataset_metadata.yaml

@@ -57,3 +57,10 @@ genetic_info:
     TissueOrigin: optional
     BrainLocation: optional
     CellType: optional
+
+participants:
+  selectors:
+    - path == "/participants.json"
+    - '"age" in columns'
+  fields:
+    AgeReference: recommended

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