NEON soil metagenome story

[turbomam]

@aclum your example data and schema files were extremely helpful.

So far, I have copied and pasted, instead of merging. Then I have applied some modifications. Let me know how you want to reconcile what I have done to get good semantics, reuse, etc. vs what you need for the science.

[aclum]

Notes from the squad meeting

• Either new class Protocol or generic slots for protocol information (name and url )
• make extraction more generic and add to enum for valid values for extraction_type (DNA, RNA, metabolite, protein)
• figure out what to do with has_input/has_inputs and has_output/has_outputs for Classes (Pooling,Extraction, LIbraryPreparation). has_inputs and has_outputs inherits from class PlannedProcess so it is confusing to also allow slots has_input and/or has_output. Proposal: use has_inputs and has_outputs and specify cardinality explicitly for a class. Make these slots required, otherwise we'll have orphaned records.

[aclum]

@turbomam I believe we are still missing syntax patterns for the new classes where we'll need to mint IDs
-ProcessedSample
-Pooling
-Extraction
-LibraryConstruction

[turbomam]

OK, I created a new issue for the identifier patterns and will complete it by mid day Monday.

• create id patterns for new classes in support of NEON #936

[ssarrafan]

@turbomam @aclum can this issue be closed? All checkboxes are complete and there is a new issue #936

[aclum]

Up to @turbomam but I'd prefer to leave this open since there are changes in the corresponding branch, https://github.com/microbiomedata/nmdc-schema/tree/issue-917-neon-story, which still need to be merged in related to slots for analytical samples as well as date slots for Class ProcessedSamples. This branch contains the example valid data for #936 and #908, #906

[aclum]

Dependencies are resolved.