Re-visit the ENVO drop downs for the soil package.

[ssarrafan]

2/3 terms that were entered for the SPRUCE data on the data portal aren’t in the drop downs

[turbomam]

This issue is about making it easier for NMDC curators to build environment-specific lists of EnvO terms that are suitable for env_broad_scale, env_local_scale and env_medium

Will bootstrap from a combination of the branch of EnvO specified by MIxS (theoretical) repaired findings from the INSDC SQLite database (empirical), and previous curations

Principal tool: ontology access kit

Output: three spreadsheets, with EnvO terms as rows and enviroment packages as columns. Curators will just have to tick off the compatible combinations.

[turbomam]

@mslarae13 @pvangay or others: where can I find the original Google Sheets in which NMDC colleagues recorded the term/enviroment curations?

[turbomam]

relevant artifacts

• MIxS and EnvO encourage using subclasses of ENVO:00000428 'biome' for env_braod_scales. See https://github.com/microbiomedata/sheets_and_friends/blob/main/artifacts/suggested_broad_scales.txt
• What's the primary source of NMDC's suggested per-enviroment curations EnvO terms for env_broad_scale, env_local_scale and env_medium? https://github.com/microbiomedata/sheets_and_friends/blob/main/artifacts/gapfilled_curated_soil_ebs_tree.txt is intended to illustrate some of the curations, but I can't remember where I got my input for it
• https://github.com/microbiomedata/sheets_and_friends/blob/main/artifacts/soil_broad_scales_annotated.tsv shows env_braod_scale values from the INSDC biosample SQLite database from samples whose lower-cased env_package matches /.*soil.*/, after submitting to Bioportal for annotation. Still needs curation.

[turbomam]

@ssarrafan @mslarae13 Moved discussion of this issue to dh_testing, especially the README.md. We have many issues and documents addressing this topic, and I will be adding links to those in the dh_testing README.md.