Comments (6)
OK. The permissible values for the enumeration should be very succinct, preferably a single word or something_snake_cased.
Class PermissibleValue takes most of the annotations as other LinkML meta classes
If we can find OBO foundry terms for those concepts, we should assign the term CURIEs to the meaning
slot.
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Low priority. Mark can add this enum. Will need review.
If not completed next sprint will not be included in berk roll out.
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@aclum I just rewrote your title like a cowboy, but then thought oops maybe I don't really know what you want.
Can we just add permissible values to the existing LibraryTypeEnum
, or do you really feel like a new slot is required? I see that you are suggesting a new slot called rna_seq_type
. Does that mean that you would want to have something like this?
id: nmdc:libprp-99-abc123
type: nmdc:LibraryPreparation
library_type: RNA
rna_seq_type: stranded_rnaseq_r1f_r2r
There aren't any library_type
values other than 'DNA' in the metadata I put into GraphDB a week or two ago, so eliminating the 'RNA' value wouldn't require a migration.
Is there any circumstance you would want to say that the library_type
is 'RNA' without asserting a rna_seq_type
?
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I would prefer this as a separate slot since we may not have this information or we'll have to infer it from a combination of institution+processing date.
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@turbomam do you have time work on this ticket this sprint? @kaijli and I are reviewing the workflow and will need this information as a workflow parameter for the counting step. We'll need to reprocess existing projects after re-iding b/c the new workflow uses a different assembler.
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re-iding needs to re-process metaT data. File type enum for metaT isn't sorted out.
Adding support for metaT allowed in soft freeze.
TBD, specific to 1 data type, so impacts shouldn't be huge.
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Related Issues (20)
- `berkeley-schema-fy24`: Delete obsolete code, including code obsoleted by Berkeley schema changes
- write a notebook report class.slot paths that take a ControlledTermValue* range
- Remodel class that aggregates steps of `WorkflowExecution` for easier schema traversal HOT 1
- `has_input`, `has_output`, and `has_process_parts` slots on `ProtocolExecution` need pattern constraints
- `berkeley-schema-fy24`: Facilitate access to `nmdc_materialized_patterns` schema via PyPI package HOT 2
- Delete Class WorkflowChain in Berkeley schema HOT 2
- `berkeley-schema-fy24`: Implement super migrator that runs all partial migrators in correct order HOT 1
- Find a home for these comments taken from `src/scripts/report_biosamples_per_study.py`
- check if classes associated with `alternative_identifiers` can use ANY `alternative_identifiers` HOT 5
- Migrations: Make it easier to test migrators against a Mongo database
- `berkeley-schema-fy24`: Update migrators to account for `WorkflowChain` class being removed
- Publish schema to PyPI via GitHub Release `v10.5.4` HOT 1
- Migrations: Implement "no op" migrator from `v10.4.0` to `v10.5.4`
- `berkeley-schema-fy24`: Some migrators use incorrect collection name (instead of `mags_set`)
- Rename branches to eliminate Berkeley commits from `main` HOT 6
- 2024-06-18 `id` pattern validation summaries and SPARQL-based referential integrity checks on MongoDB contents with and without migration HOT 6
- Facilitate access to `nmdc_materialized_patterns` schema variant via PyPI package HOT 1
- produce a nmdc-schema YAML artifact with deprecated elements included
- Remove WorkflowExeuctionActivity as a range for Database slot activity_set
- tighter pattern constraint on was_generated_by
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