Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[ENH] Additional age related columns for participants.tsv file to cover animal data #1839

Open
wants to merge 6 commits into
base: master
Choose a base branch
from
Open
Show file tree
Hide file tree
Changes from 4 commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
25 changes: 25 additions & 0 deletions src/schema/objects/columns.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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.
ree-gupta marked this conversation as resolved.
Show resolved Hide resolved
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.
Copy link
Collaborator

@yarikoptic yarikoptic Jul 17, 2024

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

is there some ontology or controlled vocab to reference here as well by any chance?

@lzehl says "No!"

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

if age_reference, some time points to consider:

  • fertilization
  • birth
  • gestation
  • ...

it seems we are boiling down to establishing a list of Enums with clear definitions and possibly adding TermURLs for some of them where there is a clear association.

TODO also to formalize such "TermURL" like linking at the level of schema which seems to lack it ATM.

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
Expand Down
21 changes: 21 additions & 0 deletions src/schema/objects/enums.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -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”.
ree-gupta marked this conversation as resolved.
Show resolved Hide resolved
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.
3 changes: 3 additions & 0 deletions src/schema/rules/tabular_data/modality_agnostic.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,9 @@ Participants:
handedness: recommended
strain: recommended
strain_rrid: recommended
birthdate: recommended
age_category: recommended
age_type: optional
index_columns: [participant_id]
additional_columns: allowed

Expand Down
Loading