Determine policies for env_local_scale

[mslarae13]

https://github.com/microbiomedata/issues/discussions/835

Criteria for completion

• Determine NMDC policy for env_local_scale
• Determine NMDC policy/ method for env_local_scale in SOIL
• Draft ADR for environment trial methods / policies

Not part of this issue:

• The ADR will change once #844 & #845 are complete.
• Finalized policy will be recorded & ADR will be updated with tasks #846
• How many env_local_scale values are not a children of material entity? (from what's in NMDC mongo or postgres or NCBI) (see other issue)
• • @sierra-moxon can review, issue coming

Policy for env_local_scale outside of the limitation of any environment is doable.

• ANY local scale (material entities - biomes - env systems that are shadow of biome - environmental materials).
• Local scale should not be quantifiable, it's countable.
• This is still a large list with this narrowing.
• From here, we have to figure out how to do it for each environment.

[sierra-moxon]

for sierra: background: https://github.com/EnvironmentOntology/envo/wiki/ENVO-annotations-for-MIxS-v5

• [ ] spin up https://github.com/microbiomedata/external-metadata-awareness development environment and run tests
• [ ] review oak usage

[turbomam]

Using ENVO with MIxS

In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen.

Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale

Less helpful than the env_broad_scale and env_medium guidance, but we should still keep it in mind

[mslarae13]

Using dynamic enumeration for submisson portal. Separate syntax. OR, decide, do we use dynamic enums in LinkML or populate enums with pre-determined static enum.

Using a dynamic enum & refreshing it, you get all new and different content according to source ontology

Evaluate Pros & Cons

What about old data? What if a term is removed? Dynamic enums is concerning when users are selecting these terms.

• In general, what will be NMDC's policy if ENVO changes, removes something, and a user can't find it?

For GOLD, we do not evaluate data in Mongo for still valid pathway, on monthly basis, the enum is re-generated to match GOLD as part of the release cycle.

• Does GOLD update its DB?
• Like with NCBI taxonomy changes, we don't change.
• Policy for if we change the existing records, out of scope?