[Add Check]: age Duration range and Best Practice

[CodyCBakerPhD]

What would you like to see added to the NWBInspector?

From discussion the other day, need to formalize a Best Practice for using the age of Subject as a free-form text field to account for some additional properties.

We already recommend ISO 8601 when exact age is known. If only a range is available, this uncertainty should be indicated.

I think what we landed on was using interval notation, e.g., age="(P4W, P6W)" to indicate subject age could have been as low as 4 weeks and as high as 6 weeks old, but exact age unknown.

There was also the reference time of 'birth' or 'stage' of development, which can be added on using a separation character such as '-', for the form age="P4D - <reference point>", .e.g. age="P4D - Conception" for in utero mouse studies, or age="P1D - Adulthood" for Drosophila melanogaster studies, with global default <reference point> being "birth".

Pseudocode or other logic of the check

No response

Do you have any interest in helping implement the check function?

Yes.

Code of Conduct

• I agree to follow this project's Code of Conduct
• Have you ensured this check was not already requested?

[CodyCBakerPhD]

I think @h-mayorquin expressed interest in leading this

[bendichter]

I believe we decided to use attributes of the dataset.

• It is recommended, if known, to use ISO 8601 duration for the age field.
• If a precise age is not known, enter any string for age, e.g. "6-8 weeks".
• If exact age is not known but an age range is known, use the attributes age.lower_bound and age.upper_bound, which if used are required to be ISO 8610 duration format.
• If the age is with respect to fertilization time, set age.reference = "fertilization".

[h-mayorquin]

Commenting here for the to-do list.

[bendichter]

DANDI landed on using a slash for age range. We have already added this to the docs here and to the code here:

nwbinspector/src/nwbinspector/checks/nwbfile_metadata.py

Lines 132 to 158 in acbd678

	@register_check(importance=Importance.BEST_PRACTICE_SUGGESTION, neurodata_type=Subject)
	def check_subject_age(subject: Subject):
	"""Check if the Subject age is in ISO 8601 or our extension of it for ranges."""
	if subject.age is None:
	if subject.date_of_birth is None:
	return InspectorMessage(message="Subject is missing age and date_of_birth.")
	else:
	return
	if re.fullmatch(pattern=duration_regex, string=subject.age):
	return
	if "/" in subject.age:
	subject_lower_age_bound, subject_upper_age_bound = subject.age.split("/")
	if re.fullmatch(pattern=duration_regex, string=subject_lower_age_bound) and (
	re.fullmatch(pattern=duration_regex, string=subject_upper_age_bound) or subject_upper_age_bound == ""
	):
	return
	return InspectorMessage(
	message=(
	f"Subject age, '{subject.age}', does not follow ISO 8601 duration format, e.g. 'P2Y' for 2 years "
	"or 'P23W' for 23 weeks. You may also specify a range using a '/' separator, e.g., 'P1D/P3D' for an "
	"age range somewhere from 1 to 3 days. If you cannot specify the upper bound of the range, "
	"you may leave the right side blank, e.g., 'P90Y/' means 90 years old or older."
	)
	)

Age reference is now a field within NWB.

The only final point is one of "growth stage", which I have only ever seen come up for C. elegens, so maybe we should make a species-specific exception there

[CodyCBakerPhD]

The only final point is one of "growth stage", which I have only ever seen come up for C. elegens, so maybe we should make a species-specific exception there

Didn't fly life stages (or maybe it was also fly larvae) also follow a similar type of customized pattern?