`depth` and `soil_depth` terms have same MIxS IDs

[sujaypatil96]

The depth and soil_depth terms in the terms.yaml file have the same MIxS ID i.e., MIXS:0000018.

So when rendering the new documentation pages using linkml docgen, the generator doesn't know which term to refer to to create a page for https://genomicsstandardsconsortium.github.io/mixs/0000018.

[turbomam]

please see https://github.com/GenomicsStandardsConsortium/mixs/issues/441 and changes made to the NMDC copy of the Google Sheets

[turbomam]

We should consider the MIxS IDs the primary keys for terms, not the structured comment names

[lschriml]

In the agriculture package, propose to update the term name from soil depth to depth. Note: Also update the definition to match grammar of other 'depth' terms.

[turbomam]

@lschriml , which "name" are you speaking of? Presumably Package item?

If we change the Package item or the Structured comment name, then a new ID will have to be assigned.

[lschriml]

In this case, the name should have been updated to just 'depth'.

When we edited for version 6.0, we made this update. the Agriculture MixS group began the creation of their package before we made this 'depth' term name update, thus they still were using the older term, soil depth. It is the same concept, the edit we will make is to the term name for soil depth to depth.

If they were defining ta new concept, then we would create a new ID. Agreed.

[mslarae13]

I just checked https://genomicsstandardsconsortium.github.io/mixs/term_list/

soil_depth is not present

depth is available in Agriculture : https://genomicsstandardsconsortium.github.io/mixs/0000018/

Can we close this?

[turbomam]

Closing this issue as the duplicate MIXS ID problem has been resolved.

Evidence:

• soil_depth term has been removed from src/mixs/schema/mixs.yaml (0 occurrences)
• MIXS:0000018 now appears only once in the schema, assigned to the depth term
• No duplicate ID conflict exists anymore

Verified with:

grep -c "soil_depth" src/mixs/schema/mixs.yaml  # Returns: 0
grep -c "MIXS:0000018" src/mixs/schema/mixs.yaml  # Returns: 1

The documentation page https://genomicsstandardsconsortium.github.io/mixs/0000018 should now correctly resolve to the depth term without ambiguity.