(NEW) Fix range of slot compound on SolutionComponent

[mslarae13]

Discovered while writing ADR

Refer to

• draft ADR for schema refactor NMDC_documentation#36 (comment)

• draft ADR for schema refactor NMDC_documentation#36 (comment)

• draft ADR for schema refactor NMDC_documentation#36 (comment)

• https://microbiomedata.github.io/berkeley-schema-fy24/SolutionComponent/

• Class:Solution has slot:has_solution_components with Range:Class:SolutionComponent where slot:compound has Range:Class:ProteolyticEnzymeEnum.

  • currently, it's string

[JamesTessmer]

Here is a branch for the issue
https://github.com/microbiomedata/berkeley-schema-fy24/tree/Fix-compound-range

[JamesTessmer]

Update: The enums are being enforced which I confirmed by adding an invalid data file and testing the valid ones with different values. The issue seems to be with the generated documentation saying the range is a string (which is technically true) but it doesn't show the enums being used to enforce the values.

[mslarae13]

@sujaypatil96 can you help sort out why the generated documentation is wrong? https://microbiomedata.github.io/berkeley-schema-fy24/SolutionComponent/

[ssarrafan]

@sujaypatil96 can you help sort out why the generated documentation is wrong? https://microbiomedata.github.io/berkeley-schema-fy24/SolutionComponent/

Should this issue be re-assigned to @sujaypatil96? @mslarae13

[ssarrafan]

I'm going to remove this issue from the sprint and add the backlog label to it. If it should be active in the next sprint let me know. If it should be re-assigned to
@Sujay Patil
let me know.

[sujaypatil96]

@mslarae13 @JamesTessmer this appears to be a schema issue?

The definition for SolutionComponent has the slot compound asserted on it, but it’s range needs to be modified to ProteolyticEnzymeEnum in a slot_usage statement underneath slots.

[turbomam]

I would like for us to review the overall modeling of solutions and reagents. The range slot_usages for compound sound relatively safe to me.

[turbomam]

see also (eventually!):

• capture ideas about proteolytic cleavage from 2024-01-29 OBI call #1741

[anastasiyaprymolenna]

The documentation generation will be resolved with the release of LinkML version 1.7.6, until then the issue will remain open

[mslarae13]

@anastasiyaprymolenna does this have relevance for the re-working of ChemicalConversionProcess?

[turbomam]

I'm working on a refactoring of everything solution related for Wednesday

[turbomam]

compound has been replaced by substances_used