Add guidance and/or example text to soil template terms

[pvangay]

Some terms were reported by ESS attendees. This is an exhaustive list of terms in the Soil-EMSL template on the submission portal that either are missing guidance text and/or example text.

Missing guidance text and example text:

• [x] sample shipped amount
• [x] number technical replicate
• [x] history/extreme events
• [x] history/fire
• [x] history/flooding
• [x] filter method
• [x] experimental factor- other
• [x] non-microbial biomass
• [x] non-microbial biomass method
• [x] microbial biomass carbon
• [x] microbial biomass carbon method
• [x] microbial biomass nitrogen
• [x] microbial biomass nitrogen method
• [x] organic nitrogen method
• [x] other treatments
• [x] isotope exposure/addition

Missing example text:

• [x] replicate number
• [x] slope aspect
• [x] extreme_unusual_properties/Al saturation
• [x] extreme_unusual_properties/Al saturation method
• [x] mean annual precipitation
• [x] current vegetation
• [x] current vegetation method
• [x] extreme_unusual_properties/heavy metals method
• [ ] #584
• [ ] #678
• [ ] #679
• [ ] soil_taxonomic/local classification (https://github.com/microbiomedata/nmdc-schema/issues/585)
• [ ] #585
• [x] history/previous land use method
• [x] history/previous land use
• [x] mean seasonal precipitation
• [x] slope gradient
• [ ] #680
• [ ] soil texture method
• [ ] soil type method (https://github.com/microbiomedata/nmdc-schema/issues/585)
• [x] water content
• [x] water content method
• [x] pH method
• [x] microbial biomass
• [x] microbial biomass method
• [x] total carbon
• [x] total nitrogen content
• [x] total nitrogen content method
• [x] total organic carbon
• [x] total organic carbon method
• [x] salinity method
• [x] composite design/sieving
• [x] #586
• [x] gaseous environment
• [x] watering regimen

Note that @mslarae13 will need to help with content for all of these terms, then coordinate with @turbomam to update appropriately. FYI @ssarrafan

[turbomam]

Wow! That's a lot! Adding annotations to those slots will make the schema much better!

Many of those slots come from MIxS. Ideally any annotations that are prepared for them would go straight to the GSC. If there's a concern that the turn around time would be too slow, I recommend that @mslarae13 or any other contributors make a copy of the MIxS 6 term updates Google Sheets and enter their annotations there. It will be easy to do a diff between our version ans their version. If they decide to accept them, then it will already be in a suitable format. If they reject them or if the process starts dragging on too long, it will be easy to feed the annotations into sheets-for-nmdc-submission-schema, the input for our submission portal schema.

Here's some notes about the LinkML slots that currently appear in the DH help dialogs, which include the catch-all "Guidance" section.

[mslarae13]

See also https://github.com/microbiomedata/nmdc-schema/issues/374

[ssarrafan]

Related to https://github.com/microbiomedata/nmdc-schema/issues/373

[ssarrafan]

@mslarae13 do you want this issue in the next sprint? Next sprint is very short due to the retreat.

[ssarrafan]

@mslarae13 I'm removing this one from the sprint until there is a plan to work on it.

[mslarae13]

@ssarrafan can you add this to the sprint starting Monday?

[mslarae13]

I'm using "comments" in LinkML to capture what should be in "guidance" on the submission portal

[mslarae13]

Progress / commit tracking

Missing guidance text and example text: 2022-12-08 PR: https://github.com/microbiomedata/nmdc-schema/pull/571

• [x] sample shipped amount
• [x] number technical replicate
• [x] history/fire
• [x] history/flooding

2022-12-08 PR: https://github.com/microbiomedata/nmdc-schema/pull/545

• [x] history/extreme events

2022-12-23 PR: https://github.com/microbiomedata/nmdc-schema/pull/571 mixs_inspired.yaml edited directly

• [x] filter method
• [x] experimental factor- other
• [x] non-microbial biomass
• [x] non-microbial biomass method
• [x] microbial biomass carbon
• [x] microbial biomass carbon method
• [x] microbial biomass nitrogen
• [x] microbial biomass nitrogen method
• [x] organic nitrogen method
• [x] other treatments
• [x] isotope exposure/addition

Missing example text: 2022-12-30

• [x] experimental factor- other
• [x] replicate number
• [x] slope aspect (changed description to remove example)
• [x] extreme_unusual_properties/Al saturation
• [x] extreme_unusual_properties/Al saturation method
• [x] mean annual precipitation
• [x] current vegetation
• [x] current vegetation method
• [x] extreme_unusual_properties/heavy metals method
• [x] extreme_unusual_properties/heavy metals
• [x] mean seasonal precipitation
• [x] slope gradient
• [x] pH method
• [x] microbial biomass
• [x] microbial biomass method (no longer using MIxS biomass. updated MIxS inspired terms)
• [x] total carbon
• [x] total nitrogen content
• [x] total nitrogen content method
• [x] total organic carbon
• [x] total organic carbon method
• [x] salinity method
• [x] composite design/sieving
• [x] gaseous environment
• [x] watering regimen

Skip until discussion

• [ ] horizon method
• [ ] soil_taxonomic/local classification method
• [ ] soil_taxonomic/local classification
• [ ] soil type method
• [ ] soil_taxonomic/FAO classification
• [ ] link to classification information
• [ ] link to climate information
• [x] water content
• [x] water content method
• [ ] climate environment (I don't know how to write this according to the structure. Would like to see some completed exampels)

Commented out? (How are these commented out but still in the submission portal if the submission portal schema is made from these files?

• [ ] history/previous land use method
• [ ] history/previous land use
• [ ] horizon method
• [ ] soil texture measurement
• [ ] soil texture method

[mslarae13]

Submit a GSC ticket for the following when PR approved

• [ ] history/extreme events
• [ ] history/fire
• [ ] history/flooding
• [ ] extreme_unusual_properties/Al saturation (update title and description)
• [ ] tot_nitro vs tot_nitro_content .. content vs concentration... tot_nitro is water specific. Otherwise seems the same. Why does water need a separate slot?

[mslarae13]

For experimental_factor_other , from Mark Instead of "this is open text" I would recommend "This column (or field) accepts open-ended text about your sample. We recommend using key:value pairs. Then your keys will be considered for inclusion as future slots/terms in this data collection template."

then some examples could be

value: "sound: oink" value: "flavor: orange; calories: 100"

[mslarae13]

@turbomam Do you know why horizon and horizon method are commented out in nmdc.yaml

and horizon is commented out of mixs.yam https://github.com/microbiomedata/nmdc-schema/blob/c097bfdbf5feae5b1895deb3079f4d2b27e02edf/src/schema/mixs.yaml#L6437

[mslarae13]

Is adding an example where one does not exists count as changing the slot & it "no longer being the same IRI"? Per the conversation at the metadata sync : https://docs.google.com/document/d/1CDLw4zwD4Z_0dNHyT8nQGey6fDvVd0zQd4cDqG_ulqg/edit?usp=sharing

@turbomam , @cmungall , @sujaypatil96 thoughts?

[mslarae13]

@ssarrafan overdue, please add to January 2023 sprint

[ssarrafan]

@ssarrafan overdue, please add to January 2023 sprint

@mslarae13 Are these still in review status? I will move to the next sprint but let me know if it should go to the backlog instead.

[mslarae13]

PR has been merged. Any outstanding slots to update have individual issues assigned. Closing this one.