Use EnvO subsets for pull-downs in triad columns

[turbomam]

@sujaypatil96 here's another one we could work on together

Right now, the MIxS environmental triad columns in the MIXS:environment field section of the NMDC Data Harmonizer accept free text (xs:token), but are validated against .* \[ENVO:\d+\]. An appropriate response for the environmental broad scale might be 'ocean [ENVO:00000015]', but the user would have to type all of that in.

Problems

• First of all, eventually we will want to accept terms form ontologies other than EnvO, like UBERON for anatomical sites like colon [UBERON:0001155]
• also, these columns could use pull-down menus, but they would be unmanageable with all terms from EnvO, much less other ontologies
  • @mslarae13 was involved in determining reasonable subsets of EnvO terms for various MIxS packages (soil, water, etc.) x each of the environmental triad columns. We could build enumerations into the LinkML that precedes the DataHarmonizer interface, which would then appear as pull-down menus.

@mslarae13 can you please remind me where to find the curated subsets?

@sujaypatil96 I can walk you though more of this if you can budget some time for this.

Triad columns

term id	description
MIXS:0000012	broad-scale environmental context
MIXS:0000013	local environmental context
MIXS:0000014	environmental medium

CC @cmungall

[turbomam]

EnvO_triad_terms_MIxS_soil_package_review_05182021

related? Mapping_GOLD_EcoPaths_MIxS_Packages_03222021

[turbomam]

First interactive pass: filter EnvO_triad_terms_MIxS_soil_package_review_05182021 on rows where MIxS Env Package - Consensus_Decision contains 'soil'