Consolidate "oxygenation status of sample" and "relationship to oxygen"

[pvangay]

from ESS attendees:

"oxygenation status of sample" and "relationship to oxygen" are very similar terms. There is currently no drop down selection enabled on "oxygenation status of sample".

@mslarae13 indicated that a decision was made during the GSC meeting this week to remove one term. This issue is for Montana to determine which one to remove then coordinate with @turbomam as needed.

[turbomam]

See also GenomicsStandardsConsortium/mixs#440

[mslarae13]

Looks like GSC came to a different resolution. See Ramona's comment: GenomicsStandardsConsortium/mixs#440 (comment)

oxy_stat_samp is appropriate for some packages like soil, and it describes the (non-organismal) sample.

rel_to_oxygen can be used in certain checklists (e.g., MIGS, MIMARKS), but it is not mandatory in any of them. Just because something is in core, does not meet it has to be in everything (or even anything).

If I'm understanding that correctly. We should remove rel_to_oxygen as it's checklist specific, and we're focusing more on the sample. @cmungall , @turbomam , thoughts?

[turbomam]

I'm going to type this out in my own words, based on looking at MIxS 6 term updates,

oxy_stat_samp is paired with several packages on the MIxS6 packages - Final_clean tab. rel_to_oxygen is not mentioned on that tab.

oxy_stat_samp's permissible values are [aerobic|anaerobic|other]

MIxS6 Core- Final_clean follows the opposite pattern: rel_to_oxygen is paired with several checklists , but oxy_stat_samp isn't mentioned.

rel_to_oxygen has the permissible values [aerobe|anaerobe|facultative|microaerophilic|microanaerobe|obligate aerobe|obligate anaerobe]

I have no objection to removing rel_to_oxygen from our templates and only using oxy_stat_samp to express the apparently shared phenomenon.

Do we feel like the permissible values for oxy_stat_samp are expressive enough?

[mslarae13]

@turbomam

Those permissible values remind me why I also couldn't decide which to remove... rel_to_oxygen has more and better values.. but oxy_stat_sample being package specific makes more sense to keep.

I am curious if we can query the 2 values and see which is used more often & how it's used... are the other permissible values needed?

[mslarae13]

@ssarrafan overdue, please add to January 2023 sprint

[ssarrafan]

@mslarae13 moving to the next sprint, let me know if you don't plan to work on it in the next few weeks please

[mslarae13]

#689