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

[ree-gupta]

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

This is open for discussion.

Related issues:

• [ENH] microelectrode electrophysiology specification (BEP032) #1705
• Formalize participants' age to clarify the reference point #1634
• Clarify that age Units could be overriden + that type is number OR "89+" string #1791

@bids-standard/bep032

[bendichter]

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

[yarikoptic]

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.

[yarikoptic]

slight tune ups

[yarikoptic]

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

@lzehl says "No!"

[yarikoptic]

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.

[lzehl]

@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).

[ree-gupta]

@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?

[lzehl]

@ree-gupta https://openminds-documentation.readthedocs.io/en/latest/instance_libraries/terminologies/ageCategory.html for looking up the ones we use in openMINDS (sometimes we refined definitions compared to the ontology). We focused on the UBERON ontology for life cycle stage. Note that gestational stage is missing from this ontology (we could request to add it).

For life cycle temporal boundaries we can refer to some of UBERON, but we will have to contribute to complete this (or just define them ourselves as terminology). These terms should potentially be grouped under age_reference or age_temporal_boundary. This group would include for example: start of neonate stage (synonym: birth), start of embryo stage (synonym: fertilization), start of gestational stage, end of life cycle (synonym: death), etc.