NeurodataWithoutBorders / nwbinspector

Tool to help inspect NWB files for compliance with NWB Best Practices
https://nwbinspector.readthedocs.io/
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[Documentation]: Clarify convention of brain region ontologies #340

Open CodyCBakerPhD opened 1 year ago

CodyCBakerPhD commented 1 year ago

What would you like changed or added to the documentation and why?

While working on the IBL conversion, a question has come up regarding our best practice convention for brain region references on the electrodes and units tables

The best practice now: https://nwbinspector.readthedocs.io/en/dev/best_practices/ecephys.html#ontologies

It is preferable to use established ontologies instead of lab conventions for indicating anatomical region. We recommend the Allen Brain Atlas terms for mice, and you may use either the full name or the abbreviation (do not make up your own terms).

and while the IBL uses Allen as the default, they have two separate conventions when using it: lateralized and non-lateralized

As I interpret their approach, non-lateralized is essentially just wrapping the brain along the midline so that referring to a brain region does not reflect which hemisphere it belongs to

As I understand our best practice (and consistency with the x/y/z section below it), I would lean towards the lateralized interpretation for NWB, and should therefore add some clarification of that in the Best Practice section

Curious what the rest of you think, though @bendichter @rly @oruebel @alejoe91

Do you have any interest in helping write or edit the documentation?

Yes.

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CodyCBakerPhD commented 1 year ago

Although, looking deeper, it seems as if the Allen Brain Atlas itself does not lateralize region references (annotated symmetrically)...

In which case we would have to further clarify how we intend left vs. right hemispheres to be differentiated for symmetric ontologies

Here are some suggestions for how we could distinguish this, using MDm (Mediodorsal nucleus of the thalamus, medial part) as an example...

a) left-MDm/right-MDm b) MDm-left/MDm-right c) MDm-lh/MDm-rh d) lhMDm/rhMDm e) lMDm/rMDm - note the prefix 'l' is hard to distinguish from an I there

Or if anyone knows of any more official way of handling this according to the Allen folks or other experts on this topic?