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Brain Imaging Data Structure (BIDS) Specification
https://bids-specification.readthedocs.io/
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Formalize participants' age to clarify the reference point #1634

Open yarikoptic opened 1 year ago

yarikoptic commented 1 year ago

A satellite issue to

ATM age column is assumed to be "since birth" but in some experiments, animal or human (fetal MRI) or some organoids, it would not really be "since birth". To acknowledge the possibility of such different reference points e.g. in dandischema we defined AgeReferenceType and ATM we just use BirthReference but allow for GestationalReference happen we hit such a dataset.

I think it would be valuable for us to think in BIDS about such annotations and how we could handle them. Since somewhat of a "niche" issue really, a simple workaround solution could potentially be to rely on TermURL side car field to point to specific ontology defining gestational age, e.g. http://www.ebi.ac.uk/efo/EFO_0005112 (attn @satra -- should we use this or some other ontology right away in dandischema?). That would allow to disambiguate.

satra commented 1 year ago

the animal/cell world is more complicated including notions of stages and not age, and often characterized in relation to species. here is an ontology of age that defines postgestation and postnatal as terms: https://bioportal.bioontology.org/ontologies/FMA/?p=classes&conceptid=http://purl.org/sig/ont/fma/fma312872

satra commented 1 year ago

it may also be helpful to separate out age concepts versus age related data elements. for example age_at_death from EFO can be useful for ex vivo datasets of structure and cannot be captured by age as a keyword alone.

lzehl commented 2 weeks ago

@satra this ontology is not species independent defined correct? definitions are a bit sparse... I wondered if we could rather try to add the terms we need to the the UBERON life cycle ontology (or see if we can adapt to what they already provide): https://www.ebi.ac.uk/ols4/ontologies/uberon/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FUBERON_0000000?lang=en

satra commented 1 week ago

@lzehl - i don't know all the stage concepts well enough, but if they are there in uberon, we should just use it or add to it.

i think in the context of the original issue, for age specifically we do need a reference and how the reference is defined/measured. in humans it's different from animals.

stage can, and perhaps should, be added as an additional data element for certain species (e.g., c elegans) where the community defines them as relevant to scientific communication.