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

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@ree-gupta ree-gupta commented May 27, 2024

The PR adds columns for age_category, age_type, birthdate as discussed and suggested by @yarikoptic in #1826

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@bids-standard/bep032

@ree-gupta ree-gupta marked this pull request as ready for review July 17, 2024 14:13
@bendichter
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What would be the best way to indicate that these fields are recommended for non-humans, but not recommended for humans?

@yarikoptic
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What would be the best way to indicate that these fields are recommended for non-humans, but not recommended for humans?

Besides birthday I think we can entirely avoid species-specificity here, but I liked phrasing to refer to units section on anonymization. I was looking at the stages and if someone annotates that it is late adult stage - it might help finding subjects of such interest. It is more of a question to me of duplicity of metadata, thus possibly leading to incongruities.

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slight tune ups

src/schema/objects/columns.yaml Outdated Show resolved Hide resolved
src/schema/objects/enums.yaml Outdated Show resolved Hide resolved
name: age_type
display_name: Age type
description: |
Type of age measurement (e.g. `postnatal`, `fetal`, `gestational`). If not specified, `postnatal` is assumed.
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@yarikoptic yarikoptic Jul 17, 2024

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

@lzehl says "No!"

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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.

ree-gupta and others added 2 commits September 18, 2024 14:20
Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>
Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>
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lzehl commented Oct 16, 2024

@bendichter @yarikoptic I agree that only birth_date causes issues with humans due to GDPR.
For the age_category we use in openMINDS:
https://openminds-documentation.readthedocs.io/en/latest/instance_libraries/terminologies/ageCategory.html

This list is derived from the UBERON ontology where possible with small additions were needed. Note that openMINDS did not yet integrate all UBERON life cycle stages:
https://www.ebi.ac.uk/ols4/ontologies/uberon/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FUBERON_0000104?lang=en

age_type in addition to define the reference point of the age value is a good idea. I'm not sure if the ontology https://bioportal.bioontology.org/ontologies/FMA/?p=classes&conceptid=http://purl.org/sig/ont/fma/fma312872 suggested by @satra in #1634 is species independent defined (definitions are also very sparse in this ontology).

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@lzehl @yarikoptic @bids-standard/bep032 As discussed in our last meeting, one of my TODOs was to add enums for age_caegory. Could one of you please remind me if we decided which ontology/list to use from the ones listed in the comment above?

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4 participants